ChimeraX bug report submission

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-14.2.1-x86_64-i386-64bit
ChimeraX Version: 1.7 (2023-12-19 08:36:03 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault

Thread 0x0000000324fba000 (most recent call first):
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 579 in _handle_results
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000323fb7000 (most recent call first):
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 531 in _handle_tasks
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000322fb4000 (most recent call first):
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py", line 415 in select
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py", line 930 in wait
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 502 in _wait_for_updates
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 522 in _handle_workers
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000321fb1000 (most recent call first):
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000320fae000 (most recent call first):
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000031ffab000 (most recent call first):
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000031efa8000 (most recent call first):
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000031dfa5000 (most recent call first):
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000031cfa2000 (most recent call first):
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000031bf9f000 (most recent call first):
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000031af9c000 (most recent call first):
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000319f99000 (most recent call first):
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000318f96000 (most recent call first):
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000317f93000 (most recent call first):
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000316f90000 (most recent call first):
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Current thread 0x0000000204859240 (most recent call first):
  Garbage-collecting
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/serialize.py", line 81 in msgpack_deserialize
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py", line 721 in restore
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py", line 1017 in open
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core_formats/__init__.py", line 37 in open
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 484 in remember_data_format
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 514 in collated_open
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 213 in provider_open
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2908 in run
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 131 in cmd_open
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2908 in run
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/run.py", line 49 in run
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/dialog.py", line 334 in _qt_safe
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 275 in event_loop
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 918 in init
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1069 in 
  File "", line 88 in _run_code
  File "", line 198 in _run_module_as_main

Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtWebChannel, PyQt6.QtNetwork, PyQt6.QtWebEngineCore, PyQt6.QtPrintSupport, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.surface._surface, chimerax.pdb_lib._load_libs, openmm._openmm, openmm.app.internal.compiled, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, numpy.linalg.lapack_lite, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree (total: 61)


{"app_name":"ChimeraX","timestamp":"2024-01-15 22:10:58.00 +0000","app_version":"1.7.0","slice_uuid":"194a3167-3db5-3029-8d22-1d742b826bb9","build_version":"1.7.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":1,"is_first_party":0,"bug_type":"309","os_version":"macOS 14.2.1 (23C71)","roots_installed":0,"name":"ChimeraX","incident_id":"A9BB8999-FB07-4A6C-8459-4E85AC447408"}
{
  "uptime" : 700000,
  "procRole" : "Foreground",
  "version" : 2,
  "userID" : 501,
  "deployVersion" : 210,
  "modelCode" : "Mac14,5",
  "coalitionID" : 109067,
  "osVersion" : {
    "train" : "macOS 14.2.1",
    "build" : "23C71",
    "releaseType" : "User"
  },
  "captureTime" : "2024-01-15 22:10:57.7385 +0000",
  "codeSigningMonitor" : 1,
  "incident" : "A9BB8999-FB07-4A6C-8459-4E85AC447408",
  "pid" : 81614,
  "translated" : true,
  "cpuType" : "X86-64",
  "roots_installed" : 0,
  "bug_type" : "309",
  "procLaunch" : "2024-01-15 22:08:43.9115 +0000",
  "procStartAbsTime" : 16952727606138,
  "procExitAbsTime" : 16955938913629,
  "procName" : "ChimeraX",
  "procPath" : "\/Applications\/ChimeraX-1.7.app\/Contents\/MacOS\/ChimeraX",
  "bundleInfo" : {"CFBundleShortVersionString":"1.7.0","CFBundleVersion":"1.7.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
  "storeInfo" : {"deviceIdentifierForVendor":"13C36163-CC03-5074-9FDF-F7545CEC4403","thirdParty":true},
  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "F9070259-436C-FF97-23D6-B37F3ACB6C68",
  "codeSigningID" : "edu.ucsf.cgl.ChimeraX",
  "codeSigningTeamID" : "LWV8X224YF",
  "codeSigningFlags" : 570491649,
  "codeSigningValidationCategory" : 6,
  "codeSigningTrustLevel" : 4294967295,
  "wakeTime" : 1065,
  "sleepWakeUUID" : "95A5E5B2-79E0-4A11-B417-45D68E7E9BE4",
  "sip" : "enabled",
  "vmRegionInfo" : "0xa9 is not in any region.  Bytes before following region: 140723233128279\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      mapped file              7ffcae528000-7ffcd6f40000 [650.1M] r-x\/r-x SM=COW  ...t_id=bdf72025",
  "exception" : {"codes":"0x0000000000000001, 0x00000000000000a9","rawCodes":[1,169],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x00000000000000a9"},
  "termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":81614},
  "vmregioninfo" : "0xa9 is not in any region.  Bytes before following region: 140723233128279\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      mapped file              7ffcae528000-7ffcd6f40000 [650.1M] r-x\/r-x SM=COW  ...t_id=bdf72025",
  "extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
  "faultingThread" : 0,
  "threads" : 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    "path" : "\/Applications\/ChimeraX-1.7.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/_datetime.cpython-311-darwin.so",
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    "path" : "\/Applications\/ChimeraX-1.7.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/math.cpython-311-darwin.so",
    "name" : "math.cpython-311-darwin.so"
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    "CFBundleIdentifier" : "org.python.python",
    "size" : 4079616,
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    "path" : "\/Applications\/ChimeraX-1.7.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/Python",
    "name" : "Python",
    "CFBundleVersion" : "3.11.2"
  },
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    "source" : "P",
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    "path" : "\/usr\/libexec\/rosetta\/runtime",
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    "arch" : "arm64",
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    "uuid" : "7af8ba1e-5c4d-393d-99cd-92566f60c450",
    "path" : "\/Library\/Apple\/*\/libRosettaRuntime",
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    "arch" : "x86_64",
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    "path" : "\/usr\/lib\/system\/libsystem_pthread.dylib",
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    "source" : "P",
    "arch" : "x86_64",
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    "size" : 557056,
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    "path" : "\/usr\/lib\/system\/libsystem_c.dylib",
    "name" : "libsystem_c.dylib"
  },
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    "source" : "P",
    "arch" : "x86_64",
    "base" : 140703543762944,
    "size" : 40960,
    "uuid" : "0f4e02db-a99c-353a-a9ec-3fa83ce01236",
    "path" : "\/usr\/lib\/system\/libsystem_platform.dylib",
    "name" : "libsystem_platform.dylib"
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    "size" : 4825085,
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    "name" : "CoreFoundation",
    "CFBundleVersion" : "2202"
  },
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    "arch" : "x86_64",
    "base" : 140703726333952,
    "CFBundleShortVersionString" : "2.1.1",
    "CFBundleIdentifier" : "com.apple.HIToolbox",
    "size" : 2736117,
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    "path" : "\/System\/Library\/Frameworks\/Carbon.framework\/Versions\/A\/Frameworks\/HIToolbox.framework\/Versions\/A\/HIToolbox",
    "name" : "HIToolbox"
  },
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    "arch" : "x86_64",
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    "CFBundleShortVersionString" : "6.9",
    "CFBundleIdentifier" : "com.apple.AppKit",
    "size" : 21024764,
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    "name" : "AppKit",
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    "size" : 12812276,
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],
  "sharedCache" : {
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  "size" : 21474836480,
  "uuid" : "aa32606f-3f8a-36dc-89ab-9c1bd7bf3104"
},
  "vmSummary" : "ReadOnly portion of Libraries: Total=1.2G resident=0K(0%) swapped_out_or_unallocated=1.2G(100%)\nWritable regions: Total=3.2G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=3.2G(100%)\n\n                                VIRTUAL   REGION \nREGION TYPE                        SIZE    COUNT (non-coalesced) \n===========                     =======  ======= \nAccelerate framework               128K        1 \nActivity Tracing                   256K        1 \nCG image                           224K       20 \nColorSync                          240K       30 \nCoreAnimation                      520K       55 \nCoreGraphics                        20K        3 \nCoreUI image data                 4500K       33 \nFoundation                          16K        1 \nKernel Alloc Once                    8K        1 \nMALLOC                             2.1G      130 \nMALLOC guard page                  384K       24 \nMach message                        16K        4 \nOpenGL GLSL                        256K        2 \nRosetta Arena                     4096K        2 \nRosetta Generic                   1596K      396 \nRosetta JIT                      128.0M        1 \nRosetta Return Stack              1100K      110 \nRosetta Thread Context            1100K      110 \nSTACK GUARD                         40K       10 \nStack                            403.2M       56 \nStack Guard                       56.2M       46 \nVM_ALLOCATE                      216.6M      330 \nVM_ALLOCATE (reserved)           256.1M       16         reserved VM address space (unallocated)\n__CTF                               824        1 \n__DATA                            55.9M      822 \n__DATA_CONST                      44.7M      427 \n__DATA_DIRTY                      1711K      226 \n__FONT_DATA                        2352        1 \n__GLSLBUILTINS                    5174K        1 \n__LINKEDIT                       177.4M      184 \n__OBJC_RO                         71.1M        1 \n__OBJC_RW                         2166K        2 \n__TEXT                             1.0G      826 \ndyld private memory                516K        4 \nmapped file                        7.4G     1533 \nshared memory                     3532K       27 \nunshared pmap                     15.7M       10 \n===========                     =======  ======= \nTOTAL                             12.0G     5447 \nTOTAL, minus reserved VM space    11.8G     5447 \n",
  "legacyInfo" : {
  "threadTriggered" : {
    "name" : "CrBrowserMain",
    "queue" : "com.apple.main-thread"
  }
},
  "logWritingSignature" : "f06a03e30220641bd2e560ef258fb6240354f3f7",
  "trialInfo" : {
  "rollouts" : [
    {
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      "factorPackIds" : {

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    },
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  "experiments" : [
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      "experimentId" : "6553f184553f07431fda611f",
      "deploymentId" : 400000004
    }
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},
  "reportNotes" : [
  "PC register does not match crashing frame (0x0 vs 0x7FF8A913EA78)"
]
}
===== Log before crash start =====
UCSF ChimeraX version: 1.7 (2023-12-19)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Filament-240114-onepf.cxs"

Opened 188_b250.mrc as #2, grid size 250,250,250, pixel 0.826, shown at level
0.00373, step 1, values float32  
Log from Sun Jan 14 15:43:04 2024UCSF ChimeraX version: 1.7 (2023-12-19)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Filament-240114-individuals.cxs" format session

Opened 188_b250.mrc as #2, grid size 250,250,250, pixel 0.826, shown at level
0.00373, step 1, values float32  
Log from Sun Jan 14 14:55:25 2024UCSF ChimeraX version: 1.7 (2023-12-19)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Fit-240114.cxs" format session

Opened postprocess_masked330_onepf.mrc as #6, grid size 274,274,274, pixel
1.51, shown at level 0.0124, step 2, values float32  
Log from Sun Jan 14 14:18:05 2024UCSF ChimeraX version: 1.7 (2023-12-19)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Fit14-27.cxs" format session

Opened post266.mrc as #1, grid size 274,274,274, pixel 1.51, shown at level
0.0195, step 1, values float32  
Opened post266flipy.mrc as #3, grid size 274,274,274, pixel 1.51, shown at
level 0.0174, step 1, values float32  
Opened post266flipy.mrc as #4, grid size 274,274,274, pixel 1.51, shown at
level 0.0209, step 1, values float32  
Opened post266flipy.mrc copy as #6, grid size 274,274,274, pixel 1.51, shown
at level 0.0176, step 1, values float32  
Opened postprocess_masked330.mrc as #5, grid size 274,274,274, pixel 1.51,
shown at level 0.0104, step 2, values float32  
Opened postprocess_masked330.mrc y flip as #7, grid size 274,274,274, pixel
1.51, shown at level 0.00964, step 1, values float32  
Opened postprocess_masked330_onepf.mrc as #8, grid size 274,274,274, pixel
1.51, shown at level 0.0121, step 1, values float32  
Opened postprocess_masked330.mrc y flip copy as #2.1.1.1, grid size
274,274,274, pixel 1.51, shown at level 0.0202, step 1, values float32  
Log from Fri Jan 12 07:27:46 2024UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Fit14-20.cxs" format session

Opened post266.mrc as #1, grid size 274,274,274, pixel 1.51, shown at level
0.0195, step 1, values float32  
Opened post266flipy.mrc as #3, grid size 274,274,274, pixel 1.51, shown at
level 0.0174, step 1, values float32  
Opened post266flipy.mrc as #4, grid size 274,274,274, pixel 1.51, shown at
level 0.0209, step 1, values float32  
Opened post266flipy.mrc copy as #6, grid size 274,274,274, pixel 1.51, shown
at level 0.0176, step 1, values float32  
Opened postprocess_masked330.mrc as #5, grid size 274,274,274, pixel 1.51,
shown at level 0.0104, step 2, values float32  
Opened postprocess_masked330.mrc y flip as #7, grid size 274,274,274, pixel
1.51, shown at level 0.00964, step 1, values float32  
Opened postprocess_masked330_onepf.mrc as #8, grid size 274,274,274, pixel
1.51, shown at level 0.014, step 1, values float32  
Opened postprocess_masked330.mrc y flip copy as #2.1.1.1, grid size
274,274,274, pixel 1.51, shown at level 0.0202, step 1, values float32  
Log from Wed Jan 10 14:43:33 2024UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Fit14-10.cxs" format session

Opened post266.mrc as #1, grid size 274,274,274, pixel 1.51, shown at level
0.0195, step 1, values float32  
Opened post266flipy.mrc as #3, grid size 274,274,274, pixel 1.51, shown at
level 0.0174, step 1, values float32  
Opened post266flipy.mrc as #4, grid size 274,274,274, pixel 1.51, shown at
level 0.0209, step 1, values float32  
Opened post266flipy.mrc copy as #6, grid size 274,274,274, pixel 1.51, shown
at level 0.0176, step 1, values float32  
Opened postprocess_masked330.mrc as #5, grid size 274,274,274, pixel 1.51,
shown at level 0.0104, step 2, values float32  
Opened postprocess_masked330.mrc y flip as #7, grid size 274,274,274, pixel
1.51, shown at level 0.0185, step 1, values float32  
Opened postprocess_masked330_onepf.mrc as #8, grid size 274,274,274, pixel
1.51, shown at level 0.0135, step 1, values float32  
Opened postprocess_masked330.mrc y flip copy as #2.1.1.1, grid size
274,274,274, pixel 1.51, shown at level 0.0202, step 1, values float32  
Log from Tue Jan 9 11:58:46 2024UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Fit14-9.cxs" format session

Opened post266.mrc as #1, grid size 274,274,274, pixel 1.51, shown at level
0.0195, step 1, values float32  
Opened post266flipy.mrc as #3, grid size 274,274,274, pixel 1.51, shown at
level 0.0174, step 1, values float32  
Opened post266flipy.mrc as #4, grid size 274,274,274, pixel 1.51, shown at
level 0.0209, step 1, values float32  
Opened post266flipy.mrc copy as #6, grid size 274,274,274, pixel 1.51, shown
at level 0.0176, step 1, values float32  
Opened postprocess_masked330.mrc as #5, grid size 274,274,274, pixel 1.51,
shown at level 0.0104, step 2, values float32  
Opened postprocess_masked330.mrc y flip as #7, grid size 274,274,274, pixel
1.51, shown at level 0.0185, step 1, values float32  
Opened postprocess_masked330_onepf.mrc as #8, grid size 274,274,274, pixel
1.51, shown at level 0.0135, step 1, values float32  
Opened postprocess_masked330.mrc y flip copy as #2.1.1.1, grid size
274,274,274, pixel 1.51, shown at level 0.0202, step 1, values float32  
Log from Mon Jan 8 19:50:54 2024UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Fit14-3.cxs" format session

Opened post266.mrc as #1, grid size 274,274,274, pixel 1.51, shown at level
0.0195, step 1, values float32  
Opened post266flipy.mrc as #3, grid size 274,274,274, pixel 1.51, shown at
level 0.0174, step 1, values float32  
Opened post266flipy.mrc as #4, grid size 274,274,274, pixel 1.51, shown at
level 0.0209, step 1, values float32  
Opened post266flipy.mrc copy as #6, grid size 274,274,274, pixel 1.51, shown
at level 0.0227, step 1, values float32  
Opened postprocess_masked330.mrc as #5, grid size 274,274,274, pixel 1.51,
shown at level 0.0104, step 2, values float32  
Opened postprocess_masked330.mrc y flip as #7, grid size 274,274,274, pixel
1.51, shown at level 0.0185, step 1, values float32  
Opened postprocess_masked330.mrc y flip copy as #9, grid size 274,274,274,
pixel 1.51, shown at level 0.0185, step 1, values float32  
Opened postprocess_masked330_onepf.mrc as #8, grid size 274,274,274, pixel
1.51, shown at level 0.0183, step 1, values float32  
Log from Mon Jan 8 14:05:26 2024UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Fit14-2.cxs" format session

Opened post266.mrc as #1, grid size 274,274,274, pixel 1.51, shown at level
0.0195, step 1, values float32  
Opened post266flipy.mrc as #3, grid size 274,274,274, pixel 1.51, shown at
level 0.0174, step 1, values float32  
Opened post266flipy.mrc as #4, grid size 274,274,274, pixel 1.51, shown at
level 0.0209, step 1, values float32  
Opened post266flipy.mrc copy as #6, grid size 274,274,274, pixel 1.51, shown
at level 0.0227, step 1, values float32  
Opened postprocess_masked330.mrc as #5, grid size 274,274,274, pixel 1.51,
shown at level 0.0104, step 2, values float32  
Opened postprocess_masked330.mrc y flip as #7, grid size 274,274,274, pixel
1.51, shown at level 0.0185, step 1, values float32  
Opened postprocess_masked330.mrc y flip copy as #9, grid size 274,274,274,
pixel 1.51, shown at level 0.0185, step 1, values float32  
Log from Mon Jan 8 13:30:47 2024UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter Lab/Diorge/Newestfit.cxs"

Opened post266.mrc as #1, grid size 274,274,274, pixel 1.51, shown at level
0.0195, step 1, values float32  
Opened post266flipy.mrc as #3, grid size 274,274,274, pixel 1.51, shown at
level 0.0174, step 1, values float32  
Opened post266flipy.mrc as #4, grid size 274,274,274, pixel 1.51, shown at
level 0.0209, step 1, values float32  
Opened post266flipy.mrc copy as #6, grid size 274,274,274, pixel 1.51, shown
at level 0.0227, step 1, values float32  
Log from Fri Dec 8 07:24:24 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter Lab/Chimera
> Sessions/CC2folds/CC2/Fip3/fip3cc2-clip28HCnterm-moreCterm-
> withWD/fip3cc2clip28HCntermmoreCtermwithWD_2760c_unrelaxed_rank_1_model_4.pdb"

Chain information for
fip3cc2clip28HCntermmoreCtermwithWD_2760c_unrelaxed_rank_1_model_4.pdb #1  
---  
Chain | Description  
B | No description available  
C | No description available  
D E | No description available  
  

> preset custom pretty-chain

Using preset: Custom / Pretty-chain  
Preset expands to these ChimeraX commands:

    
    
    lighting soft
    set bgColor white
    cartoon style coil width 1.5 thickness 0.8
    cartoon style helix xsection round width 3 thickness 0.8
    cartoon style strand xsection round width 3 thickness 0.8
    cartoon style strand arrowscale 1
    cartoon style helix xsection oval sides 10
    graphics silhouettes true
    graphics silhouettes width 1.5
    graphics silhouettes depthJump 0.003
    lighting msDepthBias 0.004
    lighting shadows true intensity 0.06
    lighting depthCueColor #000000
    color bychain

  

> hide atoms

> show atoms

> coulombic

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for
fip3cc2clip28HCntermmoreCtermwithWD_2760c_unrelaxed_rank_1_model_4.pdb_B SES
surface #1.1: minimum, -16.62, mean 0.21, maximum 13.62  
Coulombic values for
fip3cc2clip28HCntermmoreCtermwithWD_2760c_unrelaxed_rank_1_model_4.pdb_C SES
surface #1.2: minimum, -15.85, mean -2.58, maximum 9.11  
Coulombic values for
fip3cc2clip28HCntermmoreCtermwithWD_2760c_unrelaxed_rank_1_model_4.pdb_D SES
surface #1.3: minimum, -23.74, mean -3.35, maximum 9.88  
Coulombic values for
fip3cc2clip28HCntermmoreCtermwithWD_2760c_unrelaxed_rank_1_model_4.pdb_E SES
surface #1.4: minimum, -21.78, mean -3.20, maximum 7.16  
To also show corresponding color key, enter the above coulombic command and
add key true  

> mlp

Map values for surface
"fip3cc2clip28HCntermmoreCtermwithWD_2760c_unrelaxed_rank_1_model_4.pdb_B SES
surface": minimum -25.75, mean -3.686, maximum 23.3  
Map values for surface
"fip3cc2clip28HCntermmoreCtermwithWD_2760c_unrelaxed_rank_1_model_4.pdb_C SES
surface": minimum -29.33, mean -5.431, maximum 22.76  
Map values for surface
"fip3cc2clip28HCntermmoreCtermwithWD_2760c_unrelaxed_rank_1_model_4.pdb_D SES
surface": minimum -24.59, mean -4.072, maximum 21.66  
Map values for surface
"fip3cc2clip28HCntermmoreCtermwithWD_2760c_unrelaxed_rank_1_model_4.pdb_E SES
surface": minimum -24.06, mean -4.05, maximum 21.47  
To also show corresponding color key, enter the above mlp command and add key
true  

> hide surfaces

> color byhetero

> select /B:224

12 atoms, 12 bonds, 1 residue, 1 model selected  

> select clear

> hide surfaces

> hide atoms

> show atoms

> hide cartoons

[Repeated 1 time(s)]

> select /E:37@OE1

1 atom, 1 residue, 1 model selected  

> select /E:37@NE2

1 atom, 1 residue, 1 model selected  

> select add /B:224@O

2 atoms, 2 residues, 2 models selected  

> ui tool show Distances

> distance /E:37@NE2 /B:224@O

Distance between /E GLN 37 NE2 and /B TYR 224 O: 4.207Å  

> select /D:38@CE1

1 atom, 1 residue, 1 model selected  

> select add /B:224@CA

2 atoms, 2 residues, 2 models selected  

> distance /D:38@CE1 /B:224@CA

Distance between /D HIS 38 CE1 and /B TYR 224 CA: 3.770Å  

> select /E:30@OD1

1 atom, 1 residue, 1 model selected  

> select add /B:225@NZ

2 atoms, 2 residues, 2 models selected  

> distance /E:30@OD1 /B:225@NZ

Distance between /E ASP 30 OD1 and /B LYS 225 NZ: 5.064Å  

> select /D:38@CE1

1 atom, 1 residue, 1 model selected  

> select add /B:224@CA

2 atoms, 2 residues, 2 models selected  

> cofr sel

> select /B:224@CB

1 atom, 1 residue, 1 model selected  

> select add /D:38@CE1

2 atoms, 2 residues, 2 models selected  

> distance /B:224@CB /D:38@CE1

Distance between /B TYR 224 CB and /D HIS 38 CE1: 3.613Å  

> select clear

> ui mousemode right zoom

> select clear

> show cartoons

[Repeated 1 time(s)]

> open "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter Lab/Kashish/DDJL.pdb"

Summary of feedback from opening /Users/chaaban/Library/CloudStorage/OneDrive-
MRCLaboratoryofMolecularBiology/Documents/Carter Lab/Kashish/DDJL.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 57 57 PRO V 4
ASP V 8 1 5  
Start residue of secondary structure not found: HELIX 58 58 PRO V 52 LYS V 58
1 7  
Start residue of secondary structure not found: HELIX 117 117 CYS T 742 PHE T
770 1 29  
Start residue of secondary structure not found: HELIX 120 120 PRO T 821 ILE T
852 1 32  
Start residue of secondary structure not found: HELIX 124 124 LEU T 1099 LYS T
1120 1 22  
5 messages similar to the above omitted  
End residue of secondary structure not found: HELIX 130 130 GLN T 1274 HIS T
1281 1 8  
Start residue of secondary structure not found: HELIX 131 131 ASP T 1282 LEU T
1284 1 3  
Start residue of secondary structure not found: HELIX 176 176 CYS S 742 PHE S
770 1 29  
Start residue of secondary structure not found: HELIX 178 178 PRO S 821 ILE S
852 1 32  
Start residue of secondary structure not found: HELIX 182 182 PRO S 1096 LYS S
1138 1 43  
Start residue of secondary structure not found: HELIX 183 183 SER S 1140 PRO S
1142 1 3  
20 messages similar to the above omitted  
End residue of secondary structure not found: SHEET 157 15715 TYR o 327 CYS o
331 0  
Start residue of secondary structure not found: SHEET 158 15815 VAL o 335 PHE
o 340 0  
Start residue of secondary structure not found: SHEET 159 15915 LEU o 347 THR
o 352 0  
Start residue of secondary structure not found: SHEET 160 16016 ILE o 357 ASP
o 361 0  
Start residue of secondary structure not found: SHEET 161 16116 VAL o 384 GLY
o 391 0  
Start residue of secondary structure not found: SHEET 162 16216 HIS o 396 SER
o 402 0  
14 messages similar to the above omitted  
End residue of secondary structure not found: SHEET 177 17717 GLU o 584 GLY o
588 0  
Start residue of secondary structure not found: SHEET 178 17817 ILE o 594 VAL
o 599 0  
Start residue of secondary structure not found: SHEET 253 25325 LEU h 265 PHE
h 271 0  
Start residue of secondary structure not found: SHEET 254 25425 LEU h 285 TRP
h 287 0  
Start residue of secondary structure not found: SHEET 255 25525 LEU h 294 TYR
h 299 0  
Start residue of secondary structure not found: SHEET 256 25625 GLY h 311 ASN
h 317 0  
End residue of secondary structure not found: SHEET 257 25725 TYR h 327 CYS h
331 0  
Start residue of secondary structure not found: SHEET 258 25825 VAL h 335 PHE
h 340 0  
Start residue of secondary structure not found: SHEET 259 25925 LEU h 347 THR
h 352 0  
Start residue of secondary structure not found: SHEET 260 26026 ILE h 357 ASP
h 361 0  
Start residue of secondary structure not found: SHEET 261 26126 VAL h 387 GLY
h 391 0  
Start residue of secondary structure not found: SHEET 262 26226 HIS h 396 ILE
h 401 0  
14 messages similar to the above omitted  
End residue of secondary structure not found: SHEET 277 27727 GLU h 584 ASP h
589 0  
Start residue of secondary structure not found: SHEET 278 27827 ILE h 594 VAL
h 599 0  
Start residue of secondary structure not found: SHEET 489 48948 LEU p 265 PHE
p 271 0  
Start residue of secondary structure not found: SHEET 490 49049 LEU p 285 TRP
p 287 0  
Start residue of secondary structure not found: SHEET 491 49149 LEU p 294 TYR
p 299 0  
Start residue of secondary structure not found: SHEET 492 49249 GLY p 311 ASN
p 317 0  
End residue of secondary structure not found: SHEET 493 49349 TYR p 327 CYS p
331 0  
Start residue of secondary structure not found: SHEET 494 49449 VAL p 335 PHE
p 340 0  
Start residue of secondary structure not found: SHEET 495 49549 LEU p 347 THR
p 352 0  
Start residue of secondary structure not found: SHEET 496 49649 ILE p 357 ASP
p 361 0  
Start residue of secondary structure not found: SHEET 497 49749 VAL p 384 GLY
p 391 0  
Start residue of secondary structure not found: SHEET 498 49849 HIS p 396 SER
p 402 0  
14 messages similar to the above omitted  
End residue of secondary structure not found: SHEET 513 51351 GLU p 584 ASP p
589 0  
Start residue of secondary structure not found: SHEET 514 51451 ILE p 594 VAL
p 599 0  
Start residue of secondary structure not found: SHEET 530 53053 LEU g 265 PHE
g 271 0  
Start residue of secondary structure not found: SHEET 531 53153 LEU g 285 TRP
g 287 0  
Start residue of secondary structure not found: SHEET 532 53253 LEU g 294 TYR
g 299 0  
Start residue of secondary structure not found: SHEET 533 53353 GLY g 311 ASN
g 317 0  
End residue of secondary structure not found: SHEET 534 53453 TYR g 327 CYS g
331 0  
Start residue of secondary structure not found: SHEET 535 53553 VAL g 335 PHE
g 340 0  
Start residue of secondary structure not found: SHEET 536 53653 LEU g 347 THR
g 352 0  
Start residue of secondary structure not found: SHEET 537 53753 ILE g 357 ASP
g 361 0  
Start residue of secondary structure not found: SHEET 538 53853 VAL g 384 GLY
g 391 0  
Start residue of secondary structure not found: SHEET 539 53953 HIS g 396 SER
g 402 0  
14 messages similar to the above omitted  
End residue of secondary structure not found: SHEET 554 55455 GLU g 584 ASP g
589 0  
Start residue of secondary structure not found: SHEET 555 55555 ILE g 594 VAL
g 599 0  
  
Chain information for DDJL.pdb #3  
---  
Chain | Description  
1 2 | No description available  
3 4 | No description available  
A B D E F G I | No description available  
C | No description available  
H | No description available  
J | No description available  
K | No description available  
L | No description available  
M | No description available  
N | No description available  
O | No description available  
P | No description available  
Q | No description available  
R | No description available  
S | No description available  
T | No description available  
U | No description available  
W | No description available  
X | No description available  
Y | No description available  
a b d i | No description available  
e | No description available  
f | No description available  
g | No description available  
h | No description available  
j | No description available  
k l v y | No description available  
m | No description available  
n | No description available  
o | No description available  
p | No description available  
q | No description available  
r | No description available  
s t w z | No description available  
u | No description available  
x | No description available  
  

> hide #!2 models

> hide #!1 models

> hide #2.1 models

Drag select of 313 atoms  

> cofr sel

> select clear

> hide #!3 atoms

> show #!3 cartoons

> preset custom pretty-chain

Using preset: Custom / Pretty-chain  
Preset expands to these ChimeraX commands:

    
    
    lighting soft
    set bgColor white
    cartoon style coil width 1.5 thickness 0.8
    cartoon style helix xsection round width 3 thickness 0.8
    cartoon style strand xsection round width 3 thickness 0.8
    cartoon style strand arrowscale 1
    cartoon style helix xsection oval sides 10
    graphics silhouettes true
    graphics silhouettes width 1.5
    graphics silhouettes depthJump 0.003
    lighting msDepthBias 0.004
    lighting shadows true intensity 0.06
    lighting depthCueColor #000000
    color bychain

  

> show #!3 atoms

> style #!3 stick

Changed 161768 atom styles  

> color #!3 byhetero

> open /Users/chaaban/Downloads/D_1292131736_model-annotate_P1.pdb

D_1292131736_model-annotate_P1.pdb title:  
Cytoplasmic dynein-1 heavy chain bound to JIP3-lzi [more info...]  
  
Chain information for D_1292131736_model-annotate_P1.pdb #4  
---  
Chain | Description | UniProt  
B C | C-jun-amino-terminal kinase-interacting protein 3 | JIP3_HUMAN 1-1336  
f m | cytoplasmic dynein 1 heavy chain 1 | DYHC1_HUMAN 1-4646  
h | cytoplasmic dynein 1 intermediate chain 2 | DC1I2_HUMAN 1-612  
j | cytoplasmic dynein 1 light intermediate chain 2 | DC1L2_HUMAN 1-492  
  

> hide #!3 models

> select add #4

14906 atoms, 15177 bonds, 5 pseudobonds, 1816 residues, 2 models selected  

> view sel

> show sel atoms

> style sel stick

Changed 14906 atom styles  

> show sel cartoons

> color sel byhetero

> select clear

> preset custom pretty-chain

Using preset: Custom / Pretty-chain  
Preset expands to these ChimeraX commands:

    
    
    lighting soft
    set bgColor white
    cartoon style coil width 1.5 thickness 0.8
    cartoon style helix xsection round width 3 thickness 0.8
    cartoon style strand xsection round width 3 thickness 0.8
    cartoon style strand arrowscale 1
    cartoon style helix xsection oval sides 10
    graphics silhouettes true
    graphics silhouettes width 1.5
    graphics silhouettes depthJump 0.003
    lighting msDepthBias 0.004
    lighting shadows true intensity 0.06
    lighting depthCueColor #000000
    color bychain

  

> color #!4 byhetero

> select add #4/C:86@OD2

1 atom, 1 residue, 1 model selected  

> select add #4/f:827@OH

2 atoms, 2 residues, 1 model selected  

> distance #4/C:86@OD2 #4/f:827@OH

Distance between D_1292131736_model-annotate_P1.pdb #4/C ASP 86 OD2 and /f TYR
827 OH: 2.708Å  

> select clear

> open "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter Lab/Chimera
> Sessions/CC2folds/CC2/Spindly/spindlycc2-withWD/spindlycc2withWD_5d354_unrelaxed_rank_1_model_3.pdb"

Chain information for spindlycc2withWD_5d354_unrelaxed_rank_1_model_3.pdb #5  
---  
Chain | Description  
B | No description available  
C | No description available  
D E | No description available  
  

> hide #!4 models

> select add #5

7033 atoms, 7162 bonds, 871 residues, 1 model selected  

> view sel

> show sel atoms

> color sel byhetero

> select clear

> select #5/E:77@NZ

1 atom, 1 residue, 1 model selected  

> select add #5/B:184@NH2

2 atoms, 2 residues, 1 model selected  

> distance #5/E:77@NZ #5/B:184@NH2

Distance between spindlycc2withWD_5d354_unrelaxed_rank_1_model_3.pdb #5/E LYS
77 NZ and /B ARG 184 NH2: 1.126Å  

> open "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter Lab/Chimera
> Sessions/CC2folds/CC2/Hook3/hook3cc2moreClessN-
> withWD/hook3cc2moreClessNwithWD_63115_unrelaxed_rank_1_model_3.pdb"

Chain information for
hook3cc2moreClessNwithWD_63115_unrelaxed_rank_1_model_3.pdb #6  
---  
Chain | Description  
B | No description available  
C | No description available  
D E | No description available  
  

> hide #5 models

> show #6 atoms

> open "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter Lab/Chimera
> Sessions/CC2folds/CC2/Hook3/hook3cc2shorter/hook3cc2shorter_7fa91_unrelaxed_rank_1_model_5.pdb"

Chain information for hook3cc2shorter_7fa91_unrelaxed_rank_1_model_5.pdb #7  
---  
Chain | Description  
B | No description available  
C D | No description available  
  

> hide #6 models

> close session

> open "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter Lab/Chimera
> Sessions/CC2folds/CC2/Hook3/hook3cc2moreClessN-
> withWD/hook3cc2moreClessNwithWD_63115_unrelaxed_rank_1_model_3.pdb"

Chain information for
hook3cc2moreClessNwithWD_63115_unrelaxed_rank_1_model_3.pdb #1  
---  
Chain | Description  
B | No description available  
C | No description available  
D E | No description available  
  

> show atoms

> color byhetero

> lighting soft

> preset custom pretty-chain

Using preset: Custom / Pretty-chain  
Preset expands to these ChimeraX commands:

    
    
    lighting soft
    set bgColor white
    cartoon style coil width 1.5 thickness 0.8
    cartoon style helix xsection round width 3 thickness 0.8
    cartoon style strand xsection round width 3 thickness 0.8
    cartoon style strand arrowscale 1
    cartoon style helix xsection oval sides 10
    graphics silhouettes true
    graphics silhouettes width 1.5
    graphics silhouettes depthJump 0.003
    lighting msDepthBias 0.004
    lighting shadows true intensity 0.06
    lighting depthCueColor #000000
    color bychain

  

> color byhetero

> open "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter Lab/Chimera
> Sessions/CC2folds/CC2/Hook3/hook3cc2-withWD/hook3cc2withWD_f909d_unrelaxed_rank_1_model_1.pdb"

Chain information for hook3cc2withWD_f909d_unrelaxed_rank_1_model_1.pdb #2  
---  
Chain | Description  
B | No description available  
C | No description available  
D E | No description available  
  

> hide #1 models

> show #2 atoms

> select clear

> select #2/D:29

10 atoms, 10 bonds, 1 residue, 1 model selected  

> select add #2/D:48

19 atoms, 18 bonds, 2 residues, 1 model selected  

> ui tool show "Show Sequence Viewer"

> open /Users/chaaban/Desktop/post266.mrc

Opened post266.mrc as #3, grid size 274,274,274, pixel 1.51, shown at level
0.0161, step 2, values float32  

> close session

> open /Users/chaaban/Desktop/post266.mrc

Opened post266.mrc as #1, grid size 274,274,274, pixel 1.51, shown at level
0.0161, step 2, values float32  

> preset custom pretty-chain

Using preset: Custom / Pretty-chain  
Preset expands to these ChimeraX commands:

    
    
    lighting soft
    set bgColor white
    cartoon style coil width 1.5 thickness 0.8
    cartoon style helix xsection round width 3 thickness 0.8
    cartoon style strand xsection round width 3 thickness 0.8
    cartoon style strand arrowscale 1
    cartoon style helix xsection oval sides 10
    graphics silhouettes true
    graphics silhouettes width 1.5
    graphics silhouettes depthJump 0.003
    lighting msDepthBias 0.004
    lighting shadows true intensity 0.06
    lighting depthCueColor #000000
    color bychain

  

> volume #1 step 1

> volume #1 level 0.02356

> ui tool show "Hide Dust"

> surface dust #1 size 9.04

> volume #1 level 0.02177

> volume #1 level 0.01946

> open "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter Lab/Diorge/pointy.pdb"

Chain information for pointy.pdb #2  
---  
Chain | Description  
0 1 2 3 4 5 6 7 E F G I J K L M N O Y Z a b c d e f g h i j n o p q r s t u v
w x y z | No description available  
A | No description available  
B | No description available  
C S T U | No description available  
D V W | No description available  
P | No description available  
Q | No description available  
R | No description available  
X | No description available  
k | No description available  
l | No description available  
m | No description available  
  

> hide #!1 models

> style stick

Changed 70704 atom styles  

> hide atoms

> show cartoons

> select clear

Drag select of 26 residues, 1 pseudobonds  
Drag select of 404 residues, 6 pseudobonds  

> delete atoms (#!2 & sel)

> delete bonds (#!2 & sel)

Drag select of 700 residues, 9 pseudobonds  

> delete atoms (#!2 & sel)

> delete bonds (#!2 & sel)

Drag select of 664 residues, 9 pseudobonds  

> select clear

Drag select of 388 residues, 5 pseudobonds  

> delete atoms (#!2 & sel)

> delete bonds (#!2 & sel)

Drag select of 390 residues, 8 pseudobonds  
Drag select of 448 residues, 8 pseudobonds  

> delete atoms (#!2 & sel)

> delete bonds (#!2 & sel)

Drag select of 495 residues, 11 pseudobonds  
Drag select of 561 residues, 10 pseudobonds  

> delete atoms (#!2 & sel)

> delete bonds (#!2 & sel)

Drag select of 455 residues, 6 pseudobonds  

> delete atoms (#!2 & sel)

> delete bonds (#!2 & sel)

Drag select of 278 residues, 10 pseudobonds  

> delete atoms (#!2 & sel)

> delete bonds (#!2 & sel)

> select clear

Drag select of 2 pseudobonds  
No visible atoms or bonds selected  
Drag select of 306 residues, 8 pseudobonds  

> delete atoms (#!2 & sel)

> delete bonds (#!2 & sel)

Drag select of 223 residues, 5 pseudobonds  

> delete atoms (#!2 & sel)

> delete bonds (#!2 & sel)

Drag select of 35 residues, 1 pseudobonds  
Drag select of 679 residues, 5 pseudobonds  

> delete atoms (#!2 & sel)

> delete bonds (#!2 & sel)

Drag select of 3 residues  

> delete atoms sel

> delete bonds sel

> select #2/h/z/w/t/q/n/e/b

10144 atoms, 10184 bonds, 8 pseudobonds, 1304 residues, 2 models selected  

> select #2/h/z/w/t/q/n/e/b/Y/V/S

13624 atoms, 13678 bonds, 11 pseudobonds, 1750 residues, 2 models selected  

> select #2/h/z/w/t/q/n/e/b/Y/V/S/P/k

15408 atoms, 15469 bonds, 13 pseudobonds, 1979 residues, 2 models selected  

> delete atoms (#!2 & sel)

> delete bonds (#!2 & sel)

> select #2/2

1268 atoms, 1273 bonds, 1 pseudobond, 163 residues, 2 models selected  

> select #2/2/5

2536 atoms, 2546 bonds, 2 pseudobonds, 326 residues, 2 models selected  

> delete atoms (#!2 & sel)

> delete bonds (#!2 & sel)

> show atoms

Drag select of 24 atoms, 1 pseudobonds, 19 bonds  

> delete atoms (#!2 & sel)

> delete bonds (#!2 & sel)

Drag select of 12 atoms, 9 bonds  
Drag select of 8 atoms, 7 bonds  

> delete atoms sel

> delete bonds sel

> select clear

Drag select of 1 pseudobonds  
No visible atoms or bonds selected  
Drag select of 2 pseudobonds  
Drag select of 3 pseudobonds  
No visible atoms or bonds selected  
Drag select of 23 atoms, 19 bonds  

> delete atoms sel

> delete bonds sel

> style sphere

Changed 18079 atom styles  

> style sphere

Changed 18079 atom styles  

> nucleotides atoms

> style nucleic stick

Changed 0 atom styles  

> style ball

Changed 18079 atom styles  

> nucleotides atoms

> style nucleic stick

Changed 0 atom styles  

> style sphere

Changed 18079 atom styles  

> style stick

Changed 18079 atom styles  

> style stick

Changed 18079 atom styles  

> select #2/7

7 atoms, 4 bonds, 1 pseudobond, 2 residues, 2 models selected  

> delete atoms (#!2 & sel)

> delete bonds (#!2 & sel)

> select #2/l

857 atoms, 860 bonds, 1 pseudobond, 110 residues, 2 models selected  

> select #2/I

6 atoms, 2 bonds, 1 pseudobond, 2 residues, 2 models selected  

> delete atoms (#!2 & sel)

> delete bonds (#!2 & sel)

> select #2/M

6 atoms, 2 bonds, 1 pseudobond, 2 residues, 2 models selected  

> delete atoms (#!2 & sel)

> delete bonds (#!2 & sel)

> save "/Users/chaaban/Documents/Carter Lab/Diorge/bigpf.pdb" format pdb
> models #2

> show #!1 models

> select add #2

18060 atoms, 18116 bonds, 15 pseudobonds, 2323 residues, 2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.79646,-0.27202,-0.54006,89.974,0.23831,0.96202,-0.13311,-48.806,0.55576,-0.022687,0.83104,-124.26

> view matrix models
> #2,0.82732,-0.43683,-0.35315,117.41,-0.36972,0.049847,-0.9278,251.58,0.4229,0.89816,-0.12027,-285.09

> view matrix models
> #2,0.96831,-0.12444,-0.21652,27.702,-0.23053,-0.11197,-0.9666,250.42,0.096045,0.98589,-0.13711,-228.04

> flip #1 y

Unknown command: flip #1 y  

> flip #1 axis y

Unknown command: flip #1 axis y  

> volume flip #1 axis y

Opened post266.mrc y flip as #3, grid size 274,274,274, pixel 1.51, shown at
step 1, values float32  

> view matrix models
> #2,0.96307,0.01645,0.26874,9.3488,0.26921,-0.044524,-0.96205,124.25,-0.0038602,0.99887,-0.047308,-206.5

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.96307,0.01645,0.26874,-0.54111,0.26921,-0.044524,-0.96205,145.91,-0.0038602,0.99887,-0.047308,-1.3606

> hide sel atoms

> view matrix models
> #2,0.96307,0.01645,0.26874,-0.31703,0.26921,-0.044524,-0.96205,145.26,-0.0038602,0.99887,-0.047308,-6.5909

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.99688,-0.015645,0.077366,-4.6229,0.076181,-0.0658,-0.99492,192.71,0.020656,0.99771,-0.064403,-12.185

> view matrix models
> #2,0.9955,-0.012753,0.093878,-4.6244,0.092876,-0.064237,-0.9936,188.64,0.018702,0.99785,-0.062764,-11.745

> ui mousemode right zoom

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.89925,-0.21692,-0.37987,49.328,0.38697,-0.010474,0.92203,138.85,-0.20399,-0.97613,0.074524,416.15

> view matrix models
> #2,0.93672,-0.23635,-0.25826,46.238,0.278,0.053806,0.95907,151.92,-0.21278,-0.97018,0.11611,417.61

> view matrix models
> #2,0.94081,-0.22647,-0.25216,43.514,0.25311,-0.025333,0.96711,172.74,-0.22541,-0.97369,0.033487,419.97

> surface dust #3 size 9.04

> select clear

> volume #3 level 0.01741

> select #3

2 models selected  

> select clear

> save /Users/chaaban/Desktop/post266flipy.mrc models #3 format mrc

> open /Users/chaaban/Desktop/post266flipy.mrc

Opened post266flipy.mrc as #4, grid size 274,274,274, pixel 1.51, shown at
level 0.0161, step 2, values float32  

> hide #!2 models

> ui mousemode right zoom

> volume #4 step 1

> volume #4 level 0.02484

> ui tool show "Map Eraser"

> volume #4 level 0.02088

> volume erase #4 center 185.99,276.92,19.931 radius 111.11

Opened post266flipy.mrc copy as #6, grid size 274,274,274, pixel 1.51, shown
at step 1, values float32  

> volume erase #6 center 202.3,235.06,18.872 radius 111.1

> volume erase #6 center 229.61,166.17,24.906 radius 111.1

> volume erase #6 center 239.21,170.97,336.56 radius 111.1

> volume erase #6 center 210.49,186.25,341.7 radius 111.1

> volume erase #6 center 203.58,246.55,348.96 radius 111.1

> volume erase #6 center 182.7,291.55,344.18 radius 111.1

[Repeated 1 time(s)]

> surface dust #4 size 9.04

> surface dust #6 size 9.04

> ui mousemode right zoom

> show #!2 models

Drag select of 601 residues, 6 pseudobonds  

> delete atoms (#!2 & sel)

> delete bonds (#!2 & sel)

Drag select of 584 residues, 2 pseudobonds  
Drag select of 541 residues, 3 pseudobonds  

> delete atoms (#!2 & sel)

> delete bonds (#!2 & sel)

Drag select of 203 residues, 3 pseudobonds  

> delete atoms (#!2 & sel)

> delete bonds (#!2 & sel)

> select add #2

7579 atoms, 7588 bonds, 7 pseudobonds, 978 residues, 2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.96631,-0.22368,-0.12729,34.707,0.1298,-0.0035502,0.99153,196.69,-0.22224,-0.97466,0.025602,419.57

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.96631,-0.22368,-0.12729,27.109,0.1298,-0.0035502,0.99153,171.75,-0.22224,-0.97466,0.025602,420.93

> view matrix models
> #2,0.96631,-0.22368,-0.12729,26.314,0.1298,-0.0035502,0.99153,167.05,-0.22224,-0.97466,0.025602,416.05

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.98916,-0.10142,-0.10617,-2.9946,0.1083,0.015712,0.99399,168.28,-0.099142,-0.99472,0.026525,391.34

> ui mousemode right "translate selected models"

> ui mousemode right zoom

> select clear

[Repeated 1 time(s)]

> select #6

2 models selected  

> transparency #6.1 50

> select clear

> lighting simple

> set bgColor black

> set bgColor transparent

> lighting full

> ui windowfill toggle

> select /r:155

9 atoms, 8 bonds, 1 residue, 1 model selected  

> cofr sel

> select clear

> ui windowfill toggle

> select add #2

7579 atoms, 7588 bonds, 7 pseudobonds, 978 residues, 2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.96018,0.24405,-0.13597,-62.42,0.11752,0.088692,0.9891,152.14,0.25345,-0.9657,0.056481,303.34

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.96018,0.24405,-0.13597,-60.236,0.11752,0.088692,0.9891,152.79,0.25345,-0.9657,0.056481,293.64

> view matrix models
> #2,0.96018,0.24405,-0.13597,-57.62,0.11752,0.088692,0.9891,158.05,0.25345,-0.9657,0.056481,302.03

> view matrix models
> #2,0.96018,0.24405,-0.13597,-57.611,0.11752,0.088692,0.9891,158.34,0.25345,-0.9657,0.056481,301.92

> view matrix models
> #2,0.96018,0.24405,-0.13597,-58.067,0.11752,0.088692,0.9891,155.98,0.25345,-0.9657,0.056481,301.41

> view matrix models
> #2,0.96018,0.24405,-0.13597,-56.66,0.11752,0.088692,0.9891,157.2,0.25345,-0.9657,0.056481,302.97

> view matrix models
> #2,0.96018,0.24405,-0.13597,-56.607,0.11752,0.088692,0.9891,155.22,0.25345,-0.9657,0.056481,302.94

> view matrix models
> #2,0.96018,0.24405,-0.13597,-56.656,0.11752,0.088692,0.9891,155.78,0.25345,-0.9657,0.056481,302.98

> ui tool show "Fit in Map"

> fitmap #2 inMap #6

Fit molecule pointy.pdb (#2) to map post266flipy.mrc copy (#6) using 7579
atoms  
average map value = 0.01089, steps = 288  
shifted from previous position = 7.45  
rotated from previous position = 10.9 degrees  
atoms outside contour = 6155, contour level = 0.020879  
  
Position of pointy.pdb (#2) relative to post266flipy.mrc copy (#6)
coordinates:  
Matrix rotation and translation  
0.91204510 0.28144888 -0.29826207 -55.85294011  
0.29367037 0.05940351 0.95405919 118.23622327  
0.28623671 -0.95773574 -0.02847452 292.79266571  
Axis -0.95628627 -0.29236826 0.00611323  
Axis point 0.00000000 216.37594714 83.07017167  
Rotation angle (degrees) 91.63389342  
Shift along axis 20.63278912  
  

> select clear

> ui mousemode right "map eraser"

> volume erase #6 center 180.5,272.44,302.16 radius 111.1

> volume erase #6 center 191.25,216.43,304.49 radius 111.1

> volume erase #6 center 187.66,174.96,305.32 radius 111.1

> lighting simple

> volume erase #6 center 210.34,287.31,41.367 radius 111.1

> volume erase #6 center 227.24,244.64,47.986 radius 111.1

> volume erase #6 center 245.53,224.54,53.284 radius 111.1

> volume erase #6 center 259.09,197.53,58.677 radius 111.1

> volume erase #6 center 251.16,166.75,55.722 radius 111.1

> volume erase #6 center 198.08,155.79,43.177 radius 111.1

> volume erase #6 center 180.26,179,45.621 radius 111.1

> volume erase #6 center 158.13,198.56,228.18 radius 48.734

> volume erase #6 center 158.64,174.47,220.21 radius 48.734

> volume erase #6 center 171.67,148.07,226.87 radius 48.734

> volume erase #6 center 165.72,245.88,231.6 radius 48.734

> ui mousemode right zoom

> ui mousemode right "map eraser"

> surface dust #6 size 9.04

> volume erase #6 center 191.55,250.57,216.26 radius 29.736

> volume erase #6 center 194.91,230.64,217.88 radius 29.736

> volume erase #6 center 201.97,210.07,219.8 radius 29.736

> volume erase #6 center 196.06,188.67,219.47 radius 29.736

> volume erase #6 center 198.25,167.19,219.73 radius 29.736

> volume erase #6 center 185.77,208.49,217.12 radius 29.736

> volume #6 level 0.01753

> volume #6 level 0.01882

> volume #6 level 0.02036

> volume #6 level 0.02268

> select #2/f

1130 atoms, 1135 bonds, 1 pseudobond, 145 residues, 2 models selected  

> fitmap sel inMap #6

Fit molecule pointy.pdb (#2) to map post266flipy.mrc copy (#6) using 1130
atoms  
average map value = 0.01523, steps = 152  
shifted from previous position = 0.462  
rotated from previous position = 6.91 degrees  
atoms outside contour = 836, contour level = 0.022682  
  
Position of pointy.pdb (#2) relative to post266flipy.mrc copy (#6)
coordinates:  
Matrix rotation and translation  
0.86338957 0.36172059 -0.35173381 -59.14971604  
0.32754725 0.12840370 0.93606906 98.05900442  
0.38375938 -0.92340171 -0.00761816 263.57205201  
Axis -0.92976449 -0.36775811 -0.01708721  
Axis point 0.00000000 201.48324078 77.18067106  
Rotation angle (degrees) 90.45335440  
Shift along axis 14.42960202  
  

> ui mousemode right zoom

> ui windowfill toggle

[Repeated 1 time(s)]

> hide #!6 models

Drag select of 175 residues, 1 pseudobonds  
Drag select of 233 residues, 1 pseudobonds  

> fitmap sel inMap #6

Fit molecule pointy.pdb (#2) to map post266flipy.mrc copy (#6) using 1825
atoms  
average map value = 0.01483, steps = 68  
shifted from previous position = 1.14  
rotated from previous position = 4.44 degrees  
atoms outside contour = 1265, contour level = 0.022682  
  
Position of pointy.pdb (#2) relative to post266flipy.mrc copy (#6)
coordinates:  
Matrix rotation and translation  
0.88239972 0.32780224 -0.33751509 -56.53248731  
0.33652271 0.06162494 0.93965676 107.95732111  
0.32882094 -0.94273435 -0.05593507 280.12090619  
Axis -0.94267246 -0.33369081 0.00436708  
Axis point 0.00000000 204.42840799 82.69303315  
Rotation angle (degrees) 93.20767258  
Shift along axis 18.49056239  
  

> show #!6 models

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.89024,0.32189,-0.32227,-57.498,0.33424,0.019026,0.9423,116.66,0.30945,-0.94658,-0.090651,286.01

> view matrix models
> #2,0.88388,0.34011,-0.32106,-59.562,0.33286,0.024817,0.94265,115.86,0.32857,-0.94006,-0.091275,280.33

> view matrix models
> #2,0.88227,0.33274,-0.333,-57.541,0.33617,0.049841,0.94048,110.3,0.32954,-0.9417,-0.067886,279.98

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.88227,0.33274,-0.333,-57.81,0.33617,0.049841,0.94048,110.15,0.32954,-0.9417,-0.067886,280.57

> view matrix models
> #2,0.88227,0.33274,-0.333,-57.673,0.33617,0.049841,0.94048,108.16,0.32954,-0.9417,-0.067886,280.78

> view matrix models
> #2,0.88227,0.33274,-0.333,-58.186,0.33617,0.049841,0.94048,109.57,0.32954,-0.9417,-0.067886,280.41

> open /Users/chaaban/Desktop/run_it025_class001.mrc

Opened run_it025_class001.mrc as #7, grid size 274,274,274, pixel 1.51, shown
at level 0.00426, step 2, values float32  

> open /Users/chaaban/Desktop/run_it025_class002.mrc

Opened run_it025_class002.mrc as #8, grid size 274,274,274, pixel 1.51, shown
at level 0.00273, step 2, values float32  

> open /Users/chaaban/Desktop/run_it025_class003.mrc

Opened run_it025_class003.mrc as #9, grid size 274,274,274, pixel 1.51, shown
at level 0.0037, step 2, values float32  

> open /Users/chaaban/Desktop/run_it025_class004.mrc

Opened run_it025_class004.mrc as #10, grid size 274,274,274, pixel 1.51, shown
at level 0.00439, step 2, values float32  

> close #7-10

> view matrix models
> #2,0.88227,0.33274,-0.333,-58.125,0.33617,0.049841,0.94048,108.72,0.32954,-0.9417,-0.067886,280.45

> open /Users/chaaban/Desktop/post271.mrc

Opened post271.mrc as #7, grid size 274,274,274, pixel 1.51, shown at level
0.0202, step 2, values float32  

> open /Users/chaaban/Desktop/270.mrc

Opened 270.mrc as #8, grid size 274,274,274, pixel 1.51, shown at level
0.0171, step 2, values float32  

> close #7-8

> save "/Users/chaaban/Documents/Carter Lab/Diorge/Newestfit.cxs"

——— End of log from Fri Dec 8 07:24:24 2023 ———

opened ChimeraX session  

> hide #!2 models

> show #!2 models

> open "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/postprocess330.mrc"

MRC file is truncated. Failed reading 1 values, type int32  

> open "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/postprocess_masked330.mrc"

Opened postprocess_masked330.mrc as #5, grid size 274,274,274, pixel 1.51,
shown at level 0.0036, step 2, values float32  

> select #5

2 models selected  

> ui mousemode right "translate selected models"

> view matrix models #5,1,0,0,4.5878,0,1,0,-3.2577,0,0,1,-29.467

> transparency #5.1 50

> select clear

> hide #!6 models

> volume #5 level 0.01082

> volume #5 flipNormals y

Invalid "flipNormals" argument: Expected true or false (or 1 or 0)  

> volume flip #5 y

Expected a keyword  

> volume #5 flipNormals y

Invalid "flipNormals" argument: Expected true or false (or 1 or 0)  

> volume flip #5 y

Expected a keyword  

> volume flip #5 axis y

Opened postprocess_masked330.mrc y flip as #7, grid size 274,274,274, pixel
1.51, shown at step 1, values float32  

> volume #7 level 0.01398

> ui tool show "Fit in Map"

> fitmap #2 inMap #5

Fit molecule pointy.pdb (#2) to map postprocess_masked330.mrc (#5) using 7579
atoms  
average map value = 0.004806, steps = 148  
shifted from previous position = 1.79  
rotated from previous position = 5.24 degrees  
atoms outside contour = 6141, contour level = 0.01082  
  
Position of pointy.pdb (#2) relative to postprocess_masked330.mrc (#5)
coordinates:  
Matrix rotation and translation  
0.89619748 0.25222062 -0.36498608 -49.11868084  
0.36883489 0.03362816 0.92888642 106.77784362  
0.24655812 -0.96708526 -0.06289030 332.46944243  
Axis -0.95009098 -0.30645111 0.05843661  
Axis point 0.00000000 224.03921459 107.11753698  
Rotation angle (degrees) 93.81483975  
Shift along axis 33.37341468  
  

> volume #5 level 0.01044

> volume #7 level 0.007464

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Fit14.cxs"

> ui tool show "Map Eraser"

> volume #7 level 0.01852

> volume erase #7 center 193.08,238.55,246.16 radius 60.16

Opened postprocess_masked330.mrc y flip copy as #9, grid size 274,274,274,
pixel 1.51, shown at step 1, values float32  

> volume erase #9 center 202.05,212.14,250.12 radius 60.092

> volume erase #9 center 192.25,211.19,250.37 radius 60.092

> volume erase #9 center 213.78,213.83,255.99 radius 60.092

[Repeated 1 time(s)]

> volume erase #9 center 221.35,182.24,257.96 radius 60.092

> volume erase #9 center 217.99,161.59,259.2 radius 60.092

> volume erase #9 center 194.99,170.39,247.89 radius 60.092

> volume erase #9 center 191.22,192.67,245.61 radius 60.092

> volume erase #9 center 171,199.76,239.91 radius 60.092

[Repeated 1 time(s)]

> volume erase #9 center 176.03,144.41,240.55 radius 60.092

> volume erase #9 center 240,145.27,95.797 radius 60.092

> volume erase #9 center 226.29,186.57,88.389 radius 60.092

> volume erase #9 center 207.63,234.89,85.391 radius 60.092

> volume erase #9 center 226.9,243,94.523 radius 60.092

[Repeated 1 time(s)]

> volume erase #9 center 216.18,248.87,98.24 radius 60.092

> volume erase #9 center 240.36,232.39,106.38 radius 60.092

> volume erase #9 center 237.4,205.62,105.57 radius 60.092

> volume erase #9 center 243.84,195.62,107.39 radius 60.092

> volume erase #9 center 202.84,211.72,95.613 radius 60.092

> volume erase #9 center 201.03,165.57,94.905 radius 60.092

> volume erase #9 center 240.01,157.07,106.57 radius 60.092

> volume erase #9 center 235.01,130.01,103.78 radius 60.092

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Fit14-2.cxs"

——— End of log from Mon Jan 8 13:30:47 2024 ———

opened ChimeraX session  

> open "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/postprocess_masked330_onepf.mrc"

Opened postprocess_masked330_onepf.mrc as #8, grid size 274,274,274, pixel
1.51, shown at level 9.42e-06, step 2, values float32  

> volume #8 level 0.006547

> volume #8 step 1

> volume #8 level 0.0183

> select add #9

2 models selected  

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.8962,0.25222,-0.36499,-52.482,0.36883,0.033628,0.92889,105.97,0.24656,-0.96709,-0.06289,331.48,#9,1,0,0,-3.3629,0,1,0,-0.80469,0,0,1,-0.99407

> view matrix models
> #2,0.8962,0.25222,-0.36499,-49.671,0.36883,0.033628,0.92889,106.64,0.24656,-0.96709,-0.06289,333.6,#9,1,0,0,-0.5521,0,1,0,-0.1342,0,0,1,1.1318

> view matrix models
> #2,0.8962,0.25222,-0.36499,-49.233,0.36883,0.033628,0.92889,106.76,0.24656,-0.96709,-0.06289,332.49,#9,1,0,0,-0.11413,0,1,0,-0.019629,0,0,1,0.022279

> ui tool show "Fit in Map"

> fitmap #8 inMap #9

Fit map postprocess_masked330_onepf.mrc in map postprocess_masked330.mrc y
flip copy using 8870 points  
correlation = 1, correlation about mean = 0.9999, overlap = 8.477  
steps = 44, shift = 0.125, angle = 0.0484 degrees  
  
Position of postprocess_masked330_onepf.mrc (#8) relative to
postprocess_masked330.mrc y flip copy (#9) coordinates:  
Matrix rotation and translation  
0.99999965 -0.00003328 0.00084123 -0.17403765  
0.00003334 1.00000000 -0.00006481 0.00820305  
-0.00084122 0.00006484 0.99999964 0.14894204  
Axis 0.07677317 0.99626790 0.03944797  
Axis point 176.93422695 0.00000000 207.02293470  
Rotation angle (degrees) 0.04837919  
Shift along axis 0.00068647  
  

> select clear

> transparency #8.1#9.1 50

> select clear

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Fit14-3.cxs"

——— End of log from Mon Jan 8 14:05:26 2024 ———

opened ChimeraX session  

> volume #8 level 0.01009

> select add #8

2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #8,0.99663,0.081595,0.0088551,-17.107,-0.081375,0.99642,-0.022922,21.198,-0.010694,0.022124,0.9997,-2.1295

> undo

> select add #2

7579 atoms, 7588 bonds, 7 pseudobonds, 978 residues, 4 models selected  

> view matrix models
> #2,0.95632,0.23783,-0.17,-63.966,0.16572,0.038013,0.98544,151.06,0.24083,-0.97056,-0.0030601,333.3,#8,0.97907,0.20278,0.01729,-43.176,-0.20148,0.97777,-0.05811,56.03,-0.028689,0.05341,0.99816,-5.481

> undo

> select clear

> select add #2

7579 atoms, 7588 bonds, 7 pseudobonds, 978 residues, 2 models selected  

> view matrix models
> #2,0.95472,0.23838,-0.17798,-63.663,0.174,0.03778,0.98402,150.13,0.2413,-0.97044,-0.0054104,333.28

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.95472,0.23838,-0.17798,-63.774,0.174,0.03778,0.98402,150.9,0.2413,-0.97044,-0.0054104,333.33

> cofr sel

> ui tool show "Hide Dust"

> surface dust #9 size 9.04

> surface dust #8 size 20.38

> surface dust #8 size 70.91

[Repeated 1 time(s)]

> surface dust #8 size 221.21

> surface dust #8 size 230.57

> surface dust #8 size 200.96

> surface dust #8 size 87.12

> view matrix models
> #2,0.95472,0.23838,-0.17798,-64.373,0.174,0.03778,0.98402,155.69,0.2413,-0.97044,-0.0054104,333.27

> view matrix models
> #2,0.95472,0.23838,-0.17798,-63.821,0.174,0.03778,0.98402,153.51,0.2413,-0.97044,-0.0054104,333.65

> view matrix models
> #2,0.95472,0.23838,-0.17798,-62.947,0.174,0.03778,0.98402,155.1,0.2413,-0.97044,-0.0054104,333.96

> view matrix models
> #2,0.95472,0.23838,-0.17798,-62.915,0.174,0.03778,0.98402,155.63,0.2413,-0.97044,-0.0054104,333.75

> view matrix models
> #2,0.95472,0.23838,-0.17798,-62.601,0.174,0.03778,0.98402,154.67,0.2413,-0.97044,-0.0054104,333.67

> view matrix models
> #2,0.95472,0.23838,-0.17798,-62.896,0.174,0.03778,0.98402,153.54,0.2413,-0.97044,-0.0054104,333.04

> select clear

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Fit14-4.cxs"

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 66 residues in model #2 to IUPAC-IUB
standards.  

> clipper associate #9 toModel #2

Opened postprocess_masked330.mrc y flip copy as #2.1.1.1, grid size
274,274,274, pixel 1.51, shown at step 1, values float32  

> isolde restrain distances "#2/0", "#2/6", "#2/B", "#2/C", "#2/D", "#2/E",
> "#2/K", "#2/O", "#2/W", "#2/Z", "#2/c", "#2/f", "#2/m", "#2/o", "#2/r",
> "#2/u", "#2/v", "#2/x", "#2/y" templateAtoms "#2/0", "#2/6", "#2/B", "#2/C",
> "#2/D", "#2/E", "#2/K", "#2/O", "#2/W", "#2/Z", "#2/c", "#2/f", "#2/m",
> "#2/o", "#2/r", "#2/u", "#2/v", "#2/x", "#2/y" distanceCutoff 10

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  

> isolde sim start /B-E,O,K,W-f,6,o-u,x,0,m,v,y

Sim termination reason: None  
ISOLDE: stopped sim  

> isolde sim start /B-E,O,K,W-f,6,o-u,x,0,m,v,y

Sim termination reason: None  
ISOLDE: stopped sim  

> addh #2

Summary of feedback from adding hydrogens to pointy.pdb #2.2  
---  
warnings | Not adding hydrogens to /B GLU 119 N because it is missing heavy-
atom bond partners  
Not adding hydrogens to /B GLU 119 C because it is missing heavy-atom bond
partners  
Not adding hydrogens to /C GLU 119 N because it is missing heavy-atom bond
partners  
Not adding hydrogens to /C GLU 119 C because it is missing heavy-atom bond
partners  
Not adding hydrogens to /D GLU 119 N because it is missing heavy-atom bond
partners  
11 messages similar to the above omitted  
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /B GLU 119 N; /D GLU 119 N; /C GLU 119 N; /E ASP 153 N; /O VAL
116 N; /K LEU 18 N; /v GLU 170 N; /y ARG 59 N  
notes | No usable SEQRES records for pointy.pdb (#2.2) chain 0; guessing
termini instead  
No usable SEQRES records for pointy.pdb (#2.2) chain 6; guessing termini
instead  
No usable SEQRES records for pointy.pdb (#2.2) chain B; guessing termini
instead  
No usable SEQRES records for pointy.pdb (#2.2) chain C; guessing termini
instead  
No usable SEQRES records for pointy.pdb (#2.2) chain D; guessing termini
instead  
14 messages similar to the above omitted  
Chain-initial residues that are actual N termini: /6 LYS 3, /Z LYS 3, /c LYS
3, /f LYS 3, /m TRP 5, /o LYS 3  
Chain-initial residues that are not actual N termini: /0 GLY 150, /6 GLY 53,
/B GLU 119, /C GLU 119, /D GLU 119, /E ASP 153, /K LEU 18, /O VAL 116, /W ASN
4, /W GLY 53, /Z GLY 53, /c GLY 53, /f GLY 53, /o GLY 53, /r THR 98, /u LEU
18, /u GLU 119, /v GLU 170, /x GLU 136, /y ARG 59  
Chain-final residues that are actual C termini: /v GLU 170  
Chain-final residues that are not actual C termini: /0 GLU 170, /6 GLU 170, /6
MET 49, /B GLU 119, /C GLU 119, /D GLU 119, /E ASP 153, /K LEU 18, /O VAL 116,
/W ILE 89, /W MET 49, /Z SER 117, /Z MET 49, /c GLN 134, /c MET 49, /f GLY
150, /f MET 49, /m TRP 5, /o GLU 170, /o MET 49, /r GLU 170, /u GLU 170, /u
LEU 18, /x GLU 170, /y ARG 59  
1018 hydrogen bonds  
Adding 'H' to /0 GLY 150  
Adding 'H' to /6 GLY 53  
Adding 'H' to /W ASN 4  
Adding 'H' to /W GLY 53  
Adding 'H' to /Z GLY 53  
7 messages similar to the above omitted  
/0 GLU 170 is not terminus, removing H atom from 'C'  
/6 GLU 170 is not terminus, removing H atom from 'C'  
/W ILE 89 is not terminus, removing H atom from 'C'  
/Z SER 117 is not terminus, removing H atom from 'C'  
/c GLN 134 is not terminus, removing H atom from 'C'  
7 messages similar to the above omitted  
7659 hydrogens added  
  

> isolde sim start /B-E,O,K,W-f,6,o-u,x,0,m,v,y

Sim termination reason: None  
ISOLDE: stopped sim  

> select clear

> isolde sim start /W-f,6,o-r,x,0/u:119-170

ISOLDE: started sim  

> hide sel atoms

> hide sel cartoons

> show sel cartoons

> ui mousemode right "isolde tug selection"

> select clear

> isolde sim stop discardTo start

Sim termination reason: None  
reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> hide sel atoms

> hide sel cartoons

> show sel cartoons

> isolde sim start /W-f,6,o-r,x,0/u:119-170

ISOLDE: started sim  

> show sel cartoons

> select clear

> isolde sim stop discardTo start

Sim termination reason: None  
reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> close #2.2.7

> isolde sim start /W-f,6,o-r,x,0/u:119-170

ISOLDE: started sim  

> show sel cartoons

> ui windowfill toggle

> isolde sim stop discardTo start

Sim termination reason: None  
reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> close #2.2.4

[Repeated 1 time(s)]

> isolde restrain distances "#2/0", "#2/6", "#2/B", "#2/C", "#2/D", "#2/E",
> "#2/K", "#2/O", "#2/Z", "#2/c", "#2/f", "#2/m", "#2/o", "#2/r", "#2/u",
> "#2/v", "#2/x", "#2/y" templateAtoms "#2/0", "#2/6", "#2/B", "#2/C", "#2/D",
> "#2/E", "#2/K", "#2/O", "#2/Z", "#2/c", "#2/f", "#2/m", "#2/o", "#2/r",
> "#2/u", "#2/v", "#2/x", "#2/y" distanceCutoff 2.5

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  

> close #2.2.4

[Repeated 1 time(s)]

> isolde restrain distances "#2/0", "#2/6", "#2/B", "#2/C", "#2/D", "#2/E",
> "#2/K", "#2/O", "#2/Z", "#2/W", "#2/c", "#2/f", "#2/m", "#2/o", "#2/r",
> "#2/u", "#2/v", "#2/x", "#2/y" templateAtoms "#2/0", "#2/6", "#2/B", "#2/C",
> "#2/D", "#2/E", "#2/K", "#2/O", "#2/Z", "#2/W", "#2/c", "#2/f", "#2/m",
> "#2/o", "#2/r", "#2/u", "#2/v", "#2/x", "#2/y" distanceCutoff 2.5

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  

> show sel atoms

> close #2.2.4

[Repeated 8 time(s)]

> close #2.2.7

> close #2.2.4

[Repeated 4 time(s)]

> isolde restrain distances "#2/0", "#2/6", "#2/B", "#2/C", "#2/D", "#2/E",
> "#2/K", "#2/O", "#2/Z", "#2/W", "#2/c", "#2/f", "#2/m", "#2/o", "#2/r",
> "#2/u", "#2/v", "#2/x", "#2/y" templateAtoms "#2/0", "#2/6", "#2/B", "#2/C",
> "#2/D", "#2/E", "#2/K", "#2/O", "#2/Z", "#2/W", "#2/c", "#2/f", "#2/m",
> "#2/o", "#2/r", "#2/u", "#2/v", "#2/x", "#2/y" distanceCutoff 2.5

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  

> isolde restrain distances "#2/0", "#2/6", "#2/B", "#2/C", "#2/D", "#2/E",
> "#2/K", "#2/O", "#2/Z", "#2/W", "#2/c", "#2/f", "#2/m", "#2/o", "#2/r",
> "#2/u", "#2/v", "#2/x", "#2/y" templateAtoms "#2/0", "#2/6", "#2/B", "#2/C",
> "#2/D", "#2/E", "#2/K", "#2/O", "#2/Z", "#2/W", "#2/c", "#2/f", "#2/m",
> "#2/o", "#2/r", "#2/u", "#2/v", "#2/x", "#2/y" distanceCutoff 10

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  

> close #2.2.4

> isolde restrain distances "#2/0", "#2/6", "#2/B", "#2/C", "#2/D", "#2/E",
> "#2/K", "#2/O", "#2/Z", "#2/W", "#2/c", "#2/f", "#2/m", "#2/o", "#2/r",
> "#2/u", "#2/v", "#2/x", "#2/y" templateAtoms "#2/0", "#2/6", "#2/B", "#2/C",
> "#2/D", "#2/E", "#2/K", "#2/O", "#2/Z", "#2/W", "#2/c", "#2/f", "#2/m",
> "#2/o", "#2/r", "#2/u", "#2/v", "#2/x", "#2/y" distanceCutoff 3

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  

> isolde restrain distances "#2/0", "#2/6", "#2/B", "#2/C", "#2/D", "#2/E",
> "#2/K", "#2/O", "#2/Z", "#2/W", "#2/c", "#2/f", "#2/m", "#2/o", "#2/r",
> "#2/u", "#2/v", "#2/x", "#2/y" templateAtoms "#2/0", "#2/6", "#2/B", "#2/C",
> "#2/D", "#2/E", "#2/K", "#2/O", "#2/Z", "#2/W", "#2/c", "#2/f", "#2/m",
> "#2/o", "#2/r", "#2/u", "#2/v", "#2/x", "#2/y" distanceCutoff 4

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  

> isolde restrain distances "#2/0", "#2/6", "#2/B", "#2/C", "#2/D", "#2/E",
> "#2/K", "#2/O", "#2/Z", "#2/W", "#2/c", "#2/f", "#2/m", "#2/o", "#2/r",
> "#2/u", "#2/v", "#2/x", "#2/y" templateAtoms "#2/0", "#2/6", "#2/B", "#2/C",
> "#2/D", "#2/E", "#2/K", "#2/O", "#2/Z", "#2/W", "#2/c", "#2/f", "#2/m",
> "#2/o", "#2/r", "#2/u", "#2/v", "#2/x", "#2/y" distanceCutoff 5

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  

> close #2.2.4

[Repeated 8 time(s)]

> close #2.2.7

> isolde restrain distances "#2/0", "#2/6", "#2/B", "#2/C", "#2/D", "#2/E",
> "#2/K", "#2/O", "#2/Z", "#2/W", "#2/c", "#2/f", "#2/m", "#2/o", "#2/r",
> "#2/u", "#2/v", "#2/x", "#2/y" templateAtoms "#2/0", "#2/6", "#2/B", "#2/C",
> "#2/D", "#2/E", "#2/K", "#2/O", "#2/Z", "#2/W", "#2/c", "#2/f", "#2/m",
> "#2/o", "#2/r", "#2/u", "#2/v", "#2/x", "#2/y" distanceCutoff 3

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  

> ui windowfill toggle

> hide #!8 models

> ui windowfill toggle

> isolde restrain distances "#2/0", "#2/6", "#2/B", "#2/C", "#2/D", "#2/E",
> "#2/K", "#2/O", "#2/Z", "#2/W", "#2/c", "#2/f", "#2/m", "#2/o", "#2/r",
> "#2/u", "#2/v", "#2/x", "#2/y" templateAtoms "#2/0", "#2/6", "#2/B", "#2/C",
> "#2/D", "#2/E", "#2/K", "#2/O", "#2/Z", "#2/W", "#2/c", "#2/f", "#2/m",
> "#2/o", "#2/r", "#2/u", "#2/v", "#2/x", "#2/y" distanceCutoff 4

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  

> ui windowfill toggle

> show #!8 models

> hide #!8 models

> show #!8 models

> ui windowfill toggle

> isolde sim start /W-f,6,o-r,x,0/u:119-170

ISOLDE: started sim  

> hide sel atoms

> show sel cartoons

> ui windowfill toggle

> hide #!8 models

> show #!8 models

> show #!6 models

> volume #6 level 0.01761

> hide #!6 models

> isolde sim stop discardTo start

Sim termination reason: None  
reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> close #2.2.7

> isolde sim start /W-f,6,o-r,x,0/u:119-170

ISOLDE: started sim  

> isolde sim stop discardTo start

Sim termination reason: None  
reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde restrain distances "#2/0", "#2/6", "#2/B", "#2/C", "#2/D", "#2/E",
> "#2/K", "#2/O", "#2/Z", "#2/W", "#2/c", "#2/f", "#2/m", "#2/o", "#2/r",
> "#2/u", "#2/v", "#2/x", "#2/y" templateAtoms "#2/0", "#2/6", "#2/B", "#2/C",
> "#2/D", "#2/E", "#2/K", "#2/O", "#2/Z", "#2/W", "#2/c", "#2/f", "#2/m",
> "#2/o", "#2/r", "#2/u", "#2/v", "#2/x", "#2/y" distanceCutoff 5

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  

> isolde sim start /W-f,6,o-r,x,0/u:119-170

ISOLDE: started sim  

> hide sel atoms

> show sel cartoons

> ui mousemode right "isolde tug selection"

> select clear

[Repeated 4 time(s)]

> transparency #8#2.1,3#2.2.1,4-10#!2#!2.2#!2.2.2-3 70

> select clear

> isolde sim stop discardTo start

Sim termination reason: None  
reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> save #2.2

No known data format for file suffix '.2'  

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/pointy-1pf.pdb" format pdb #2.2

Expected a keyword  

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/pointy-1pf.pdb" #2.2 format pdb

> open "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/pointy-1pf.pdb"

Chain information for pointy-1pf.pdb #9  
---  
Chain | Description  
0 6 o r x | No description available  
W | No description available  
Z | No description available  
c | No description available  
f | No description available  
u | No description available  
  

> hide atoms

> show cartoons

> hide #!9 models

> isolde sim start #2.2/W-f,6,o-r,x,0/u:119-170

ISOLDE: started sim  

> show sel cartoons

> ui mousemode right "isolde tug selection"

> isolde sim stop discardTo start

Sim termination reason: None  
reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> select clear

> select up

15188 atoms, 15212 bonds, 969 residues, 1 model selected  

> select down

15169 atoms, 968 residues, 1 model selected  

> isolde sim start #2.2/W-f,6,o-r,x,0/u:119-170

ISOLDE: started sim  

> show sel cartoons

> isolde sim stop discardTo start

Sim termination reason: None  
reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> volume #8 level 0.01298

> hide #!2 models

> volume #8 level 0.007352

> show #!7 models

> hide #!7 models

> show #!7 models

> ui tool show "Fit in Map"

> fitmap #7 inMap #8

Fit map postprocess_masked330.mrc y flip in map
postprocess_masked330_onepf.mrc using 41934 points  
correlation = 0.4437, correlation about mean = 0.1428, overlap = 7.772  
steps = 128, shift = 5.86, angle = 0.449 degrees  
  
Position of postprocess_masked330.mrc y flip (#7) relative to
postprocess_masked330_onepf.mrc (#8) coordinates:  
Matrix rotation and translation  
0.99997505 -0.00413594 0.00572689 -0.43621875  
0.00412998 0.99999092 0.00105340 -1.03785357  
-0.00573119 -0.00102972 0.99998305 -28.44182592  
Axis -0.14586425 0.80231980 0.57879751  
Axis point -3223.93334686 0.00000000 501.00132576  
Rotation angle (degrees) 0.40912956  
Shift along axis -17.23111975  
  

> hide #!8 models

> show #!9 models

> hide #!7 models

> select #9/6

2554 atoms, 2559 bonds, 1 pseudobond, 163 residues, 2 models selected  

> combine #9/6

> hide #!9 models

> hide #!10 models

> show #!10 models

> select add #9

15238 atoms, 15247 bonds, 7 pseudobonds, 978 residues, 2 models selected  

> select subtract #9

Nothing selected  

> show #!9 models

> hide #!10 models

> hide #!9 models

> show #!10 models

> delete "#10/0", "#10/B", "#10/C", "#10/D", "#10/E", "#10/K", "#10/O",
> "#10/Z", "#10/W", "#10/c", "#10/f", "#10/m", "#10/o", "#10/r", "#10/u",
> "#10/v", "#10/x", "#10/y"

> show #!9 models

> hide #!10 models

> hide #!9 models

> show #!10 models

> select "#10/0", "#10/B", "#10/C", "#10/D", "#10/E", "#10/K", "#10/O",
> "#10/Z", "#10/W", "#10/c", "#10/f", "#10/m", "#10/o", "#10/r", "#10/u",
> "#10/v", "#10/x", "#10/y"

Nothing selected  

> select #10/0, #10/6, #10/B, #10/C, #10/D, #10/E, #10/K, #10/O, #10/Z, #10/W,
> #10/c, #10/f, #10/m, #10/o, #10/r, #10/u, #10/v, #10/x, #10/y

Expected an objects specifier or a keyword  

> select #10/0 #10/6 #10/B #10/C #10/D #10/E #10/K #10/O #10/Z #10/W #10/c
> #10/f #10/m #10/o #10/r #10/u #10/v #10/x #10/y

15235 atoms, 15246 bonds, 7 pseudobonds, 977 residues, 2 models selected  

> select #10/0 #10/B #10/C #10/D #10/E #10/K #10/O #10/Z #10/W #10/c #10/f
> #10/m #10/o #10/r #10/u #10/v #10/x #10/y

12681 atoms, 12687 bonds, 6 pseudobonds, 814 residues, 2 models selected  

> delete #10/0 #10/B #10/C #10/D #10/E #10/K #10/O #10/Z #10/W #10/c #10/f
> #10/m #10/o #10/r #10/u #10/v #10/x #10/y

> show #!8 models

> show #!9 models

> hide #!9 models

> hide #!8 models

> show #!7 models

> show #!9 models

> hide #!9 models

> show #!8 models

> hide #!7 models

> volume #8 level 0.01279

> select add #10

2554 atoms, 2559 bonds, 1 pseudobond, 163 residues, 2 models selected  

> ui mousemode right "translate selected models"

> view matrix models #10,1,0,0,3.6368,0,1,0,30.496,0,0,1,1.8197

> view matrix models #10,1,0,0,3.1251,0,1,0,30.655,0,0,1,1.7231

> hide #!8 models

> ui mousemode right select

Drag select of 74 residues, 1 pseudobonds  

> show #!8 models

> fitmap sel inMap #8

Fit molecule copy of pointy-1pf.pdb (#10) to map
postprocess_masked330_onepf.mrc (#8) using 1173 atoms  
average map value = 0.01589, steps = 88  
shifted from previous position = 2.16  
rotated from previous position = 17.2 degrees  
atoms outside contour = 539, contour level = 0.012786  
  
Position of copy of pointy-1pf.pdb (#10) relative to
postprocess_masked330_onepf.mrc (#8) coordinates:  
Matrix rotation and translation  
0.95798862 -0.27607387 -0.07772406 73.97159160  
0.26965352 0.95930373 -0.08380535 -3.06895317  
0.09769745 0.05932600 0.99344634 -28.32096568  
Axis 0.24225556 -0.29690793 0.92366548  
Axis point 59.49163008 265.31842560 0.00000000  
Rotation angle (degrees) 17.18236274  
Shift along axis -7.32787283  
  

> show #!9 models

> hide #!10 models

> show #!10 models

> hide #!8 models

> hide #!9 models

> hide #!10 models

> show #!10 models

> show #!9 models

> show #!8 models

> hide #!8 models

> hide #!9 models

> show #!9 models

> hide #!10 models

> select #10/0 #10/B #10/C #10/D #10/E #10/K #10/O #10/Z #10/W #10/c #10/f
> #10/m #10/o #10/r #10/u #10/v #10/x #10/y

Nothing selected  

> close #10

> combine #9

> select #10/0 #10/B #10/C #10/D #10/E #10/K #10/O #10/Z #10/W #10/c #10/f
> #10/m #10/o #10/r #10/u #10/v #10/x #10/y

12684 atoms, 12688 bonds, 6 pseudobonds, 815 residues, 2 models selected  

> hide #!9 models

> select #10/x #10/B #10/C #10/D #10/E #10/K #10/O #10/Z #10/W #10/c #10/f
> #10/m #10/o #10/r #10/u #10/v #10/x #10/y

12419 atoms, 12424 bonds, 6 pseudobonds, 796 residues, 2 models selected  

> select #10/0 #10/B #10/C #10/D #10/E #10/K #10/O #10/Z #10/W #10/c #10/f
> #10/m #10/o #10/r #10/u #10/v #10/x #10/y

12684 atoms, 12688 bonds, 6 pseudobonds, 815 residues, 2 models selected  

> select #10/0 #10/B #10/C #10/D #10/E #10/K #10/O #10/Z #10/W #10/c #10/f
> #10/m #10/o #10/r #10/u #10/v #10/y

12219 atoms, 12223 bonds, 6 pseudobonds, 782 residues, 2 models selected  

> delete atoms (#!10 & sel)

> delete bonds (#!10 & sel)

Drag select of 11 residues  
Drag select of 15 residues  
Drag select of 14 residues  
Drag select of 15 residues  

> delete atoms sel

> delete bonds sel

> combine #10

> hide #!10 models

> show #!10 models

> hide #!11 models

> close #11

> show #!9 models

> hide #!10 models

> show #!9 atoms

> style #!9 stick

Changed 15238 atom styles  

> color #!9 byhetero

> select H

16724 atoms, 2121 residues, 3 models selected  

> hide (#!9 & sel) target a

> select clear

> hide #!9 atoms

> show #!10 models

> hide #!10 models

> hide #!9 models

> show #!9 models

> hide #!9 models

> show #!10 models

> show #!9 models

> hide #!10 models

> show #!10 models

> hide #!9 models

> show #!9 models

> combine #9

> select #10/0 #10/B #10/C #10/D #10/E #10/K #10/O #10/Z #10/W #10/c #10/f
> #10/m #10/r #10/u #10/v #10/x #10/y

258 atoms, 257 bonds, 18 residues, 1 model selected  

> select #11/0 #11/B #11/C #11/D #11/E #11/K #11/O #11/Z #11/W #11/c #11/f
> #11/m #11/r #11/u #11/v #11/x #11/y

10130 atoms, 10129 bonds, 5 pseudobonds, 652 residues, 2 models selected  

> delete atoms (#!11 & sel)

> delete bonds (#!11 & sel)

> hide #!9 models

> hide #!10 models

> hide #!11 models

> show #!10 models

> show #!11 models

> hide #!10 models

> show #!10 models

> select clear

[Repeated 2 time(s)]Drag select of 1 residues  
Drag select of 17 residues  
Drag select of 1 residues  
Drag select of 18 residues  

> delete atoms sel

> delete bonds sel

> select clear

Drag select of 36 residues  
[Repeated 1 time(s)]

> delete atoms sel

> delete bonds sel

> hide #!10 models

Drag select of 93 residues  

> delete atoms sel

> delete bonds sel

Drag select of 16 residues, 2 pseudobonds  

> delete atoms (#!11 & sel)

> delete bonds (#!11 & sel)

> select clear

Drag select of 70 residues, 2 pseudobonds  

> delete atoms (#!11 & sel)

> delete bonds (#!11 & sel)

Drag select of 38 residues, 1 pseudobonds  
Drag select of 11 residues, 1 pseudobonds  

> select clear

Drag select of 39 residues, 1 pseudobonds  

> delete atoms (#!11 & sel)

> delete bonds (#!11 & sel)

> show #!10 models

> select clear

[Repeated 1 time(s)]Drag select of 1 residues  

> hide #!11 models

> show #!11 models

> hide #!11 models

Drag select of 7 residues  

> delete atoms sel

> delete bonds sel

Drag select of 25 residues  
Drag select of 27 residues  

> delete atoms sel

> delete bonds sel

> show #!11 models

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Fit14-5.cxs"

> show #!8 models

> select add #10

2037 atoms, 2039 bonds, 1 pseudobond, 129 residues, 2 models selected  

> ui mousemode right "rotate selected models"

> show #!9 models

> hide #!9 models

> view matrix models
> #10,0.99998,-0.0017193,-0.0064913,1.6578,0.0016839,0.99998,-0.0054568,0.77778,0.0065006,0.0054457,0.99996,-2.3417

> ui mousemode right "translate selected models"

> view matrix models
> #10,0.99998,-0.0017193,-0.0064913,4.9937,0.0016839,0.99998,-0.0054568,32.861,0.0065006,0.0054457,0.99996,-0.56089

> ui tool show "Fit in Map"

> fitmap #10 inMap #8

Fit molecule copy of pointy-1pf.pdb (#10) to map
postprocess_masked330_onepf.mrc (#8) using 2037 atoms  
average map value = 0.01321, steps = 88  
shifted from previous position = 5.75  
rotated from previous position = 13.7 degrees  
atoms outside contour = 1178, contour level = 0.012786  
  
Position of copy of pointy-1pf.pdb (#10) relative to
postprocess_masked330_onepf.mrc (#8) coordinates:  
Matrix rotation and translation  
0.97062574 -0.22669817 -0.08058301 64.51398236  
0.22679610 0.97390894 -0.00805680 -13.33421311  
0.08030698 -0.01045578 0.99671534 -13.24222148  
Axis -0.00498547 -0.33435525 0.94243393  
Axis point 102.28672450 271.14374672 0.00000000  
Rotation angle (degrees) 13.92180079  
Shift along axis -8.34318700  
  

> select add #11

3132 atoms, 3134 bonds, 3 pseudobonds, 201 residues, 4 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #10,0.99615,-0.057833,-0.065911,22.716,0.054982,0.9975,-0.044282,24.659,0.068307,0.040488,0.99684,-20.876,#11,0.98532,0.17016,0.01409,-38.101,-0.16927,0.9843,-0.049945,48.006,-0.022368,0.046826,0.99865,-5.7061

> undo

> select subtract #10

1095 atoms, 1095 bonds, 2 pseudobonds, 72 residues, 2 models selected  

> view matrix models
> #11,0.9986,0.052796,0.001443,-12.494,-0.052798,0.99719,0.053213,0.7351,0.0013705,-0.053215,0.99858,12.593

> undo

> ui mousemode right "translate selected models"

> view matrix models #11,1,0,0,4.5444,0,1,0,-22.619,0,0,1,-1.1339

> ui mousemode right "rotate selected models"

> view matrix models
> #11,0.98418,0.17659,0.014456,-36.92,-0.17563,0.98309,-0.051887,25.356,-0.023374,0.048527,0.99855,-7.8023

> ui mousemode right "translate selected models"

> view matrix models
> #11,0.98418,0.17659,0.014456,-34.436,-0.17563,0.98309,-0.051887,10.304,-0.023374,0.048527,0.99855,-8.7109

> ui mousemode right "rotate selected models"

> view matrix models
> #11,0.96876,0.24739,0.017664,-48.806,-0.2455,0.9666,-0.073577,31.899,-0.035276,0.066942,0.99713,-10.488

> ui mousemode right "translate selected models"

> view matrix models
> #11,0.96876,0.24739,0.017664,-48.403,-0.2455,0.9666,-0.073577,33.323,-0.035276,0.066942,0.99713,-10.22

> view matrix models
> #11,0.96876,0.24739,0.017664,-49.108,-0.2455,0.9666,-0.073577,37.059,-0.035276,0.066942,0.99713,-10.324

> hide #!11 models

> show #!11 models

> combine #11

> hide #!11 models

> select subtract #11

Nothing selected  

> select add #12

1095 atoms, 1095 bonds, 2 pseudobonds, 72 residues, 2 models selected  

> delete #12/6

> ui mousemode right "rotate selected models"

> view matrix models
> #12,0.93263,0.33122,-0.14314,-29.786,-0.32763,0.94355,0.048652,34.872,0.15117,0.0015234,0.98851,-30.775

> undo

> view matrix models
> #12,0.93679,0.34915,0.022882,-66.366,-0.34379,0.93062,-0.12551,74.259,-0.065117,0.10971,0.99183,-12.922

> ui mousemode right "translate selected models"

> view matrix models
> #12,0.93679,0.34915,0.022882,-65.552,-0.34379,0.93062,-0.12551,76.921,-0.065117,0.10971,0.99183,-12.138

> ui mousemode right "rotate selected models"

> view matrix models
> #12,0.87243,0.47936,0.095312,-95.623,-0.47749,0.87758,-0.042965,99.092,-0.10424,-0.0080268,0.99452,21.092

> ui mousemode right "translate selected models"

> view matrix models
> #12,0.87243,0.47936,0.095312,-97.207,-0.47749,0.87758,-0.042965,100.19,-0.10424,-0.0080268,0.99452,22.801

> view matrix models
> #12,0.87243,0.47936,0.095312,-98.832,-0.47749,0.87758,-0.042965,100.5,-0.10424,-0.0080268,0.99452,23.468

> undo

[Repeated 2 time(s)]

> view matrix models
> #12,0.93679,0.34915,0.022882,-66.018,-0.34379,0.93062,-0.12551,77.066,-0.065117,0.10971,0.99183,-12.047

> combine #12

> hide #!10 models

> show #!10 models

> combine #12

> hide #!12 models

> hide #!10 models

> hide #!8 models

> hide #!13 models

> select clear

> show #!8 models

> hide #!8 models

> ui mousemode right select

Drag select of 7 residues  
[Repeated 1 time(s)]

> delete atoms sel

> delete bonds sel

> show #!13 models

> hide #!14 models

> select clear

Drag select of 28 residues  

> delete atoms sel

> delete bonds sel

> show #!14 models

> show #!8 models

> select add #14

451 atoms, 450 bonds, 1 pseudobond, 29 residues, 2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #14,0.88061,0.46512,0.090494,-92.966,-0.46951,0.88226,0.034248,81.396,-0.06391,-0.072648,0.99531,26.293

> ui mousemode right "translate selected models"

> view matrix models
> #14,0.88061,0.46512,0.090494,-93.826,-0.46951,0.88226,0.034248,82.406,-0.06391,-0.072648,0.99531,28.026

> ui mousemode right "rotate selected models"

> view matrix models
> #14,0.92575,0.31612,0.20748,-92.932,-0.36494,0.89059,0.27141,14.887,-0.098979,-0.32697,0.93984,100.19

> view matrix models
> #14,0.90043,0.36759,0.23259,-103.88,-0.41862,0.87759,0.23364,35.361,-0.11823,-0.30774,0.94409,98.989

> ui mousemode right "translate selected models"

> view matrix models
> #14,0.90043,0.36759,0.23259,-104.15,-0.41862,0.87759,0.23364,36.227,-0.11823,-0.30774,0.94409,100.78

> view matrix models
> #14,0.90043,0.36759,0.23259,-103.34,-0.41862,0.87759,0.23364,35.85,-0.11823,-0.30774,0.94409,101.42

> view matrix models
> #14,0.90043,0.36759,0.23259,-103.31,-0.41862,0.87759,0.23364,35.606,-0.11823,-0.30774,0.94409,101.97

> view matrix models
> #14,0.90043,0.36759,0.23259,-104.03,-0.41862,0.87759,0.23364,34.842,-0.11823,-0.30774,0.94409,101.97

> ui mousemode right "rotate selected models"

> view matrix models
> #14,0.89792,0.32638,0.29531,-106.67,-0.41573,0.84925,0.32548,22.811,-0.14456,-0.41502,0.89825,138.95

> ui mousemode right "translate selected models"

> view matrix models
> #14,0.89792,0.32638,0.29531,-106.98,-0.41573,0.84925,0.32548,23.456,-0.14456,-0.41502,0.89825,139.1

> ui mousemode right "translate selected models"

> view matrix models
> #14,0.89792,0.32638,0.29531,-106.41,-0.41573,0.84925,0.32548,22.589,-0.14456,-0.41502,0.89825,139.3

> view matrix models
> #14,0.89792,0.32638,0.29531,-106.29,-0.41573,0.84925,0.32548,22.829,-0.14456,-0.41502,0.89825,139.33

> view matrix models
> #14,0.89792,0.32638,0.29531,-106.57,-0.41573,0.84925,0.32548,22.449,-0.14456,-0.41502,0.89825,139.36

> ui mousemode right "translate selected models"

> view matrix models
> #14,0.89792,0.32638,0.29531,-105.23,-0.41573,0.84925,0.32548,22.767,-0.14456,-0.41502,0.89825,139.81

> view matrix models
> #14,0.89792,0.32638,0.29531,-106.08,-0.41573,0.84925,0.32548,24.179,-0.14456,-0.41502,0.89825,138.73

> ui mousemode right "rotate selected models"

> view matrix models
> #14,0.89263,0.44788,0.051088,-84.482,-0.42587,0.8007,0.42132,18.267,0.1478,-0.39784,0.90547,76.719

> ui mousemode right "translate selected models"

> view matrix models
> #14,0.89263,0.44788,0.051088,-84.764,-0.42587,0.8007,0.42132,17.578,0.1478,-0.39784,0.90547,76.711

> select add #13

547 atoms, 545 bonds, 2 pseudobonds, 37 residues, 4 models selected  

> select subtract #14

96 atoms, 95 bonds, 1 pseudobond, 8 residues, 2 models selected  

> view matrix models
> #13,0.93679,0.34915,0.022882,-64.922,-0.34379,0.93062,-0.12551,77.887,-0.065117,0.10971,0.99183,-11.734

> view matrix models
> #13,0.93679,0.34915,0.022882,-64.935,-0.34379,0.93062,-0.12551,77.641,-0.065117,0.10971,0.99183,-11.25

> show #!12 models

> hide #!13 models

> show #!13 models

> hide #!12 models

> show #!12 models

> hide #!12 models

> show #!11 models

> hide #!11 models

> show #!10 models

> hide #!8 models

> hide #!13 models

> hide #!14 models

> show #!8 models

> hide #!8 models

> ui mousemode right select

Drag select of 72 residues, 1 pseudobonds  

> fitmap sel inMap #8

Fit molecule copy of pointy-1pf.pdb (#10) to map
postprocess_masked330_onepf.mrc (#8) using 1140 atoms  
average map value = 0.0153, steps = 56  
shifted from previous position = 2.41  
rotated from previous position = 2.89 degrees  
atoms outside contour = 542, contour level = 0.012786  
  
Position of copy of pointy-1pf.pdb (#10) relative to
postprocess_masked330_onepf.mrc (#8) coordinates:  
Matrix rotation and translation  
0.97590189 -0.21591907 -0.03153500 49.29669495  
0.21583685 0.97641083 -0.00602921 -10.79027973  
0.03209294 -0.00092249 0.99948446 -5.77232566  
Axis 0.01170061 -0.14578548 0.98924703  
Axis point 76.43879761 219.97280243 0.00000000  
Rotation angle (degrees) 12.60477192  
Shift along axis -3.56038854  
  

> show #!8 models

> combine #8

No structures specified  

> select clear

> combine #10

[Repeated 1 time(s)]

> hide #!10 models

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Fit14-5.cxs"

> hide #!8 models

> show #!8 models

> select #15/6:89

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select #15/6:86

19 atoms, 18 bonds, 1 residue, 1 model selected  

> hide #!8 models

Drag select of 160 residues, 2 pseudobonds  

> select add #16

3308 atoms, 2039 bonds, 2 pseudobonds, 209 residues, 4 models selected  

> hide #!16 models

Drag select of 83 residues, 1 pseudobonds  

> delete atoms (#!15 & sel)

> delete bonds (#!15 & sel)

Drag select of 16 residues  

> delete atoms sel

> delete bonds sel

> show #!16 models

> hide #!16 models

> show #!16 models

> hide #!15 models

Drag select of 30 residues  

> show #!15 models

> hide #!15 models

> show #!15 models

> hide #!16 models

> show #!16 models

> hide #!15 models

> delete atoms sel

> delete bonds sel

> show #!15 models

> show #!8 models

> select add #16

1587 atoms, 1589 bonds, 1 pseudobond, 99 residues, 2 models selected  

> select subtract #16

Nothing selected  

> select add #15

450 atoms, 449 bonds, 30 residues, 1 model selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #15,0.97976,-0.19824,-0.027689,44.01,0.19866,0.97998,0.013189,-12.047,0.02452,-0.018423,0.99953,-0.67882

> ui mousemode right select

> select clear

> select #15/6:89

19 atoms, 18 bonds, 1 residue, 1 model selected  

> cofr sel

> ui mousemode right "rotate selected models"

> view matrix models
> #15,0.98557,-0.16785,-0.021724,35.43,0.1687,0.98459,0.046122,-13.757,0.013648,-0.049121,0.9987,7.9206

> ui mousemode right "translate selected models"

> view matrix models
> #15,0.98557,-0.16785,-0.021724,36.44,0.1687,0.98459,0.046122,-12.863,0.013648,-0.049121,0.9987,7.0215

> ui mousemode right "rotate selected models"

> view matrix models
> #15,0.99639,0.062188,0.057872,-28.936,-0.076331,0.95439,0.28864,-7.5126,-0.037282,-0.29202,0.95569,75.528

> view matrix models
> #15,0.99938,-0.01956,0.029443,-6.9827,0.0071557,0.92764,0.3734,-34.66,-0.034616,-0.37296,0.9272,97.387

> ui mousemode right "translate selected models"

> view matrix models
> #15,0.99938,-0.01956,0.029443,-2.322,0.0071557,0.92764,0.3734,-36.356,-0.034616,-0.37296,0.9272,92.289

> ui mousemode right "rotate selected models"

> view matrix models
> #15,0.99979,-0.0091114,0.018457,-2.399,0.0019438,0.93448,0.35601,-33.347,-0.020492,-0.3559,0.9343,84.658

> view matrix models
> #15,0.8654,0.03289,-0.5,116.81,0.030703,0.99249,0.11843,-4.0334,0.50014,-0.11784,0.85789,-49.212

> view matrix models
> #15,0.86729,0.020575,-0.49738,118.48,0.070878,0.98386,0.16429,-18.977,0.49273,-0.17774,0.85184,-34.201

> view matrix models
> #15,0.82256,0.063947,-0.56508,131.41,-0.034952,0.99746,0.061999,18.624,0.56761,-0.031247,0.8227,-73.116

> ui mousemode right "translate selected models"

> view matrix models
> #15,0.82256,0.063947,-0.56508,131.3,-0.034952,0.99746,0.061999,19.65,0.56761,-0.031247,0.8227,-71.575

> view matrix models
> #15,0.82256,0.063947,-0.56508,134.13,-0.034952,0.99746,0.061999,22.363,0.56761,-0.031247,0.8227,-71.673

> view matrix models
> #15,0.82256,0.063947,-0.56508,134.85,-0.034952,0.99746,0.061999,20.691,0.56761,-0.031247,0.8227,-71.319

> view matrix models
> #15,0.82256,0.063947,-0.56508,134.53,-0.034952,0.99746,0.061999,20.424,0.56761,-0.031247,0.8227,-71.287

> view matrix models
> #15,0.82256,0.063947,-0.56508,134.78,-0.034952,0.99746,0.061999,20.007,0.56761,-0.031247,0.8227,-71.26

> view matrix models
> #15,0.82256,0.063947,-0.56508,136.2,-0.034952,0.99746,0.061999,20.41,0.56761,-0.031247,0.8227,-70.442

> view matrix models
> #15,0.82256,0.063947,-0.56508,135.64,-0.034952,0.99746,0.061999,21.291,0.56761,-0.031247,0.8227,-70.497

> view matrix models
> #15,0.82256,0.063947,-0.56508,135.96,-0.034952,0.99746,0.061999,21.557,0.56761,-0.031247,0.8227,-70.372

> ui mousemode right "rotate selected models"

> view matrix models
> #15,0.83031,-0.0029369,-0.5573,146.79,0.040958,0.9976,0.055765,8.2273,0.5558,-0.069127,0.82844,-61.4

> ui mousemode right "translate selected models"

> view matrix models
> #15,0.83031,-0.0029369,-0.5573,146.12,0.040958,0.9976,0.055765,7.4138,0.5558,-0.069127,0.82844,-61.602

> show #!14 models

> show #!13 models

> select clear

> hide #!8 models

> hide #!16 models

> combine #16

[Repeated 1 time(s)]

> hide #!15 models

> hide #!14 models

> hide #!13 models

> show #!8 models

> hide #!8 models

> ui mousemode right select

> select #17/6:16

12 atoms, 11 bonds, 1 residue, 1 model selected  

> show #!8 models

> hide #!8 models

> select #17/6:17

10 atoms, 9 bonds, 1 residue, 1 model selected  

> select #17/6:18

19 atoms, 18 bonds, 1 residue, 1 model selected  

> hide #!18 models

Drag select of 84 residues, 1 pseudobonds  

> delete atoms (#!17 & sel)

> delete bonds (#!17 & sel)

> show #!18 models

> hide #!17 models

Drag select of 15 residues  

> delete atoms sel

> delete bonds sel

> show #!17 models

> show #!8 models

> select add #18

1330 atoms, 1329 bonds, 1 pseudobond, 84 residues, 2 models selected  

> select add #17

1587 atoms, 1588 bonds, 1 pseudobond, 99 residues, 3 models selected  

> select subtract #18

257 atoms, 259 bonds, 15 residues, 1 model selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #17,0.78377,-0.61464,0.088966,135.07,0.61128,0.7888,0.06432,-61.396,-0.10971,0.0039707,0.99396,20.211

> ui mousemode right "translate selected models"

> view matrix models
> #17,0.78377,-0.61464,0.088966,133.07,0.61128,0.7888,0.06432,-66,-0.10971,0.0039707,0.99396,21.314

> ui mousemode right "rotate selected models"

> view matrix models
> #17,0.66001,-0.74079,0.125,172.11,0.73369,0.67136,0.10476,-74.213,-0.16153,0.022564,0.98661,28.696

> ui mousemode right "translate selected models"

> view matrix models
> #17,0.66001,-0.74079,0.125,172.04,0.73369,0.67136,0.10476,-76.053,-0.16153,0.022564,0.98661,29.229

> view matrix models
> #17,0.66001,-0.74079,0.125,172.32,0.73369,0.67136,0.10476,-76.161,-0.16153,0.022564,0.98661,29.339

> view matrix models
> #17,0.66001,-0.74079,0.125,172.68,0.73369,0.67136,0.10476,-76.498,-0.16153,0.022564,0.98661,28.844

> view matrix models
> #17,0.66001,-0.74079,0.125,172.34,0.73369,0.67136,0.10476,-76.869,-0.16153,0.022564,0.98661,28.925

> select clear

> show #!15 models

> show #!14 models

> show #!13 models

> select add #13

96 atoms, 95 bonds, 1 pseudobond, 8 residues, 2 models selected  

> select add #14

547 atoms, 545 bonds, 2 pseudobonds, 37 residues, 4 models selected  

> select add #15

997 atoms, 994 bonds, 2 pseudobonds, 67 residues, 5 models selected  

> select add #17

1254 atoms, 1253 bonds, 2 pseudobonds, 82 residues, 6 models selected  

> select add #18

2584 atoms, 2582 bonds, 3 pseudobonds, 166 residues, 8 models selected  

> color (#!13-15,17-18 & sel) red

> select clear

> combine #13,14,15,17,18

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '8'  

> hide #!18 models

> hide #!17 models

> hide #!15 models

> hide #!14 models

> hide #!13 models

> color #19 #ff7e79ff

> combine 19

Expected a keyword  

> combine #19

> color #20 #008f00ff

> color #20 #9437ffff

> select add #20

2584 atoms, 2582 bonds, 3 pseudobonds, 166 residues, 2 models selected  

> ui mousemode right "translate selected models"

> view matrix models
> #20,0.93679,0.34915,0.022882,-70.141,-0.34379,0.93062,-0.12551,53.67,-0.065117,0.10971,0.99183,-14.077

> ui mousemode right "rotate selected models"

> view matrix models
> #20,0.8241,0.56635,0.0098521,-97.03,-0.55779,0.81442,-0.16,129.49,-0.09864,0.12636,0.98707,-10.564

> ui mousemode right "translate selected models"

> view matrix models
> #20,0.8241,0.56635,0.0098521,-88.629,-0.55779,0.81442,-0.16,126.94,-0.09864,0.12636,0.98707,-9.7441

> view matrix models
> #20,0.8241,0.56635,0.0098521,-89.664,-0.55779,0.81442,-0.16,125.88,-0.09864,0.12636,0.98707,-6.1392

> view matrix models
> #20,0.8241,0.56635,0.0098521,-88.33,-0.55779,0.81442,-0.16,128.35,-0.09864,0.12636,0.98707,-5.3443

> fitmap sel inMap #8

Fit molecule copy of combination (#20) to map postprocess_masked330_onepf.mrc
(#8) using 2584 atoms  
average map value = 0.01163, steps = 168  
shifted from previous position = 3.43  
rotated from previous position = 13.2 degrees  
atoms outside contour = 1568, contour level = 0.012786  
  
Position of copy of combination (#20) relative to
postprocess_masked330_onepf.mrc (#8) coordinates:  
Matrix rotation and translation  
0.92439362 0.37954996 -0.03792455 -57.45510482  
-0.37728563 0.89516156 -0.23736330 91.34262060  
-0.05614263 0.23372550 0.97068038 -36.87912351  
Axis 0.52832814 0.02043166 -0.84879440  
Axis point 188.37296334 192.81777858 0.00000000  
Rotation angle (degrees) 26.47643820  
Shift along axis 2.81392628  
  

> combine #19

> color #21 #0096ffff

> select add #21

5168 atoms, 5164 bonds, 6 pseudobonds, 332 residues, 4 models selected  

> view matrix models
> #20,0.92436,0.37972,-0.0371,-53.603,-0.37725,0.89516,-0.23743,106.41,-0.056945,0.23346,0.9707,-40.076,#21,0.93679,0.34915,0.022882,-60.761,-0.34379,0.93062,-0.12551,92.72,-0.065117,0.10971,0.99183,-14.673

> undo

> select subtract #20

2584 atoms, 2582 bonds, 3 pseudobonds, 166 residues, 2 models selected  

> view matrix models
> #21,0.93679,0.34915,0.022882,-59.462,-0.34379,0.93062,-0.12551,98.71,-0.065117,0.10971,0.99183,-16.055

> view matrix models
> #21,0.93679,0.34915,0.022882,-60.654,-0.34379,0.93062,-0.12551,101.57,-0.065117,0.10971,0.99183,-10.64

> fitmap sel inMap #8

Fit molecule copy of combination (#21) to map postprocess_masked330_onepf.mrc
(#8) using 2584 atoms  
average map value = 0.01219, steps = 92  
shifted from previous position = 4.27  
rotated from previous position = 5.6 degrees  
atoms outside contour = 1553, contour level = 0.012786  
  
Position of copy of combination (#21) relative to
postprocess_masked330_onepf.mrc (#8) coordinates:  
Matrix rotation and translation  
0.95025893 0.30332679 0.07071647 -66.28913387  
-0.30004401 0.95242850 -0.05341864 71.95351234  
-0.08355569 0.02954349 0.99606507 10.31568500  
Axis 0.13204590 0.24554584 -0.96034948  
Axis point 200.81968835 251.03991714 0.00000000  
Rotation angle (degrees) 18.30898039  
Shift along axis -0.99198576  
  

> view matrix models
> #21,0.9502,0.30332,0.071556,-65.022,-0.30001,0.95244,-0.053481,69.805,-0.084374,0.02935,0.996,11.042

> view matrix models
> #21,0.9502,0.30332,0.071556,-65.229,-0.30001,0.95244,-0.053481,71.317,-0.084374,0.02935,0.996,11.032

> view matrix models
> #21,0.9502,0.30332,0.071556,-64.727,-0.30001,0.95244,-0.053481,70.366,-0.084374,0.02935,0.996,9.1808

> view matrix models
> #21,0.9502,0.30332,0.071556,-64.814,-0.30001,0.95244,-0.053481,70.357,-0.084374,0.02935,0.996,8.9663

> ui mousemode right "rotate selected models"

> view matrix models
> #21,0.91717,0.39769,-0.02539,-61.308,-0.39738,0.90794,-0.13315,115.68,-0.029899,0.13221,0.99077,-24.846

> view matrix models
> #21,0.9324,0.36072,-0.022695,-56.062,-0.36067,0.92452,-0.12323,102.67,-0.023468,0.12308,0.99212,-24.205

> ui mousemode right "translate selected models"

> view matrix models
> #21,0.9324,0.36072,-0.022695,-55.654,-0.36067,0.92452,-0.12323,103.92,-0.023468,0.12308,0.99212,-24.145

> view matrix models
> #21,0.9324,0.36072,-0.022695,-56.145,-0.36067,0.92452,-0.12323,104.45,-0.023468,0.12308,0.99212,-24.335

> select add #20

5168 atoms, 5164 bonds, 6 pseudobonds, 332 residues, 4 models selected  

> select subtract #21

2584 atoms, 2582 bonds, 3 pseudobonds, 166 residues, 2 models selected  

> view matrix models
> #20,0.92436,0.37972,-0.0371,-59.693,-0.37725,0.89516,-0.23743,91.326,-0.056945,0.23346,0.9707,-37.055

> view matrix models
> #20,0.92436,0.37972,-0.0371,-59.886,-0.37725,0.89516,-0.23743,91.193,-0.056945,0.23346,0.9707,-36.774

> ui mousemode right "rotate selected models"

> view matrix models
> #20,0.91631,0.39867,-0.037817,-62.664,-0.39911,0.90136,-0.16812,80.087,-0.032939,0.16914,0.98504,-29.096

> ui mousemode right "translate selected models"

> view matrix models
> #20,0.91631,0.39867,-0.037817,-62.865,-0.39911,0.90136,-0.16812,80.311,-0.032939,0.16914,0.98504,-28.342

> ui mousemode right "rotate selected models"

> view matrix models
> #20,0.89167,0.45141,0.033907,-84.913,-0.43907,0.88066,-0.17792,94.907,-0.11018,0.14376,0.98346,-7.0638

> ui mousemode right "translate selected models"

> view matrix models
> #20,0.89167,0.45141,0.033907,-84.674,-0.43907,0.88066,-0.17792,92.673,-0.11018,0.14376,0.98346,-7.8767

> view matrix models
> #20,0.89167,0.45141,0.033907,-84.3,-0.43907,0.88066,-0.17792,93.071,-0.11018,0.14376,0.98346,-6.9835

> ui mousemode right "rotate selected models"

> view matrix models
> #20,0.88803,0.4578,0.042725,-86.868,-0.44339,0.87725,-0.18393,95.916,-0.12168,0.14439,0.98201,-4.6132

> view matrix models
> #20,0.89696,0.44148,0.023867,-80.965,-0.42435,0.87481,-0.23375,102.78,-0.12407,0.19953,0.972,-15.178

> ui mousemode right "translate selected models"

> view matrix models
> #20,0.89696,0.44148,0.023867,-81.69,-0.42435,0.87481,-0.23375,104.67,-0.12407,0.19953,0.972,-15.328

> hide #!8 models

> ui mousemode right "rotate selected models"

> ui mousemode right "translate selected models"

> view matrix models
> #20,0.89696,0.44148,0.023867,-81.667,-0.42435,0.87481,-0.23375,103.93,-0.12407,0.19953,0.972,-16.378

> ui mousemode right "rotate selected models"

> view matrix models
> #20,0.94,0.33107,0.082477,-75.648,-0.30443,0.923,-0.23534,69.629,-0.15404,0.19611,0.96841,-9.0431

> view matrix models
> #20,0.94123,0.33183,0.063079,-72.183,-0.30903,0.92138,-0.23572,70.98,-0.13634,0.20237,0.96977,-14.226

> view matrix models
> #20,0.94021,0.33467,0.063257,-72.693,-0.31597,0.92639,-0.20484,64.958,-0.12716,0.17261,0.97675,-10.368

> view matrix models
> #20,0.93962,0.3363,0.063349,-72.983,-0.31867,0.92732,-0.19626,63.543,-0.12475,0.16423,0.9785,-9.2045

> view matrix models
> #20,0.93822,0.34079,0.060026,-73.107,-0.32929,0.93259,-0.14783,54.66,-0.10636,0.11893,0.98719,-3.8028

> ui mousemode right "translate selected models"

> view matrix models
> #20,0.93822,0.34079,0.060026,-73.292,-0.32929,0.93259,-0.14783,55.421,-0.10636,0.11893,0.98719,-2.5117

> ui mousemode right "rotate selected models"

> view matrix models
> #20,0.9497,0.30448,0.073256,-69.582,-0.29258,0.94606,-0.13916,43.389,-0.11168,0.11073,0.98756,0.38395

> view matrix models
> #20,0.94849,0.30877,0.070897,-69.891,-0.29714,0.94467,-0.13892,44.556,-0.10987,0.1107,0.98776,-0.001063

> view matrix models
> #20,0.94567,0.31821,0.066757,-70.745,-0.30806,0.94258,-0.129,45.177,-0.10397,0.10142,0.9894,0.7219

> show #!8 models

> view matrix models
> #20,0.92936,0.36557,0.051514,-75.725,-0.35548,0.92378,-0.14234,61.477,-0.099621,0.11397,0.98848,-2.9019

> view matrix models
> #20,0.92327,0.38136,0.046197,-77.214,-0.37136,0.91683,-0.14667,67.064,-0.098291,0.11826,0.98811,-4.1

> view matrix models
> #20,0.92924,0.36912,0.016295,-69.492,-0.3579,0.91019,-0.20846,78.394,-0.091778,0.18788,0.9779,-19.767

> undo

> select add #21

5168 atoms, 5164 bonds, 6 pseudobonds, 332 residues, 4 models selected  

> ui mousemode right "translate selected models"

> view matrix models
> #20,0.92327,0.38136,0.046197,-77.837,-0.37136,0.91683,-0.14667,67.639,-0.098291,0.11826,0.98811,-2.3363,#21,0.9324,0.36072,-0.022695,-56.767,-0.36067,0.92452,-0.12323,105.03,-0.023468,0.12308,0.99212,-22.571

> view matrix models
> #20,0.92327,0.38136,0.046197,-77.765,-0.37136,0.91683,-0.14667,67.833,-0.098291,0.11826,0.98811,-2.3147,#21,0.9324,0.36072,-0.022695,-56.696,-0.36067,0.92452,-0.12323,105.22,-0.023468,0.12308,0.99212,-22.549

> hide #!8 models

> show #!8 models

> ui tool show "Side View"

> select subtract #21

2584 atoms, 2582 bonds, 3 pseudobonds, 166 residues, 2 models selected  

> select subtract #20

Nothing selected  

> select add #20

2584 atoms, 2582 bonds, 3 pseudobonds, 166 residues, 2 models selected  

> view matrix models
> #20,0.92327,0.38136,0.046197,-77.016,-0.37136,0.91683,-0.14667,65.814,-0.098291,0.11826,0.98811,-4.6096

> view matrix models
> #20,0.92327,0.38136,0.046197,-76.866,-0.37136,0.91683,-0.14667,68.048,-0.098291,0.11826,0.98811,-3.6456

> view matrix models
> #20,0.92327,0.38136,0.046197,-75.924,-0.37136,0.91683,-0.14667,66.252,-0.098291,0.11826,0.98811,-4.2803

> view matrix models
> #20,0.92327,0.38136,0.046197,-77.692,-0.37136,0.91683,-0.14667,66.173,-0.098291,0.11826,0.98811,-4.6729

> view matrix models
> #20,0.92327,0.38136,0.046197,-76.514,-0.37136,0.91683,-0.14667,66.488,-0.098291,0.11826,0.98811,-5.0861

> ui mousemode right "rotate selected models"

> view matrix models
> #20,0.90412,0.4268,0.020284,-78.355,-0.42049,0.89717,-0.13516,78.347,-0.075885,0.11367,0.99062,-8.8437

> ui mousemode right "translate selected models"

> view matrix models
> #20,0.90412,0.4268,0.020284,-77.96,-0.42049,0.89717,-0.13516,79.576,-0.075885,0.11367,0.99062,-9.3827

> ui mousemode right "rotate selected models"

> view matrix models
> #20,0.90851,0.41751,0.017302,-76.017,-0.40685,0.89324,-0.19129,89.099,-0.09532,0.16675,0.98138,-16.312

> ui mousemode right zoom

> ui mousemode right "translate selected models"

> view matrix models
> #20,0.90851,0.41751,0.017302,-76.618,-0.40685,0.89324,-0.19129,86.509,-0.09532,0.16675,0.98138,-15.331

> view matrix models
> #20,0.90851,0.41751,0.017302,-76.634,-0.40685,0.89324,-0.19129,86.359,-0.09532,0.16675,0.98138,-15.254

> view matrix models
> #20,0.90851,0.41751,0.017302,-75.857,-0.40685,0.89324,-0.19129,85.947,-0.09532,0.16675,0.98138,-14.345

> view matrix models
> #20,0.90851,0.41751,0.017302,-77.034,-0.40685,0.89324,-0.19129,86.999,-0.09532,0.16675,0.98138,-14.711

> view matrix models
> #20,0.90851,0.41751,0.017302,-76.114,-0.40685,0.89324,-0.19129,87.812,-0.09532,0.16675,0.98138,-15.451

> ui mousemode right "rotate selected models"

> view matrix models
> #20,0.89514,0.44564,-0.011272,-74.453,-0.44004,0.87928,-0.18229,95.739,-0.071324,0.16813,0.98318,-20.787

> ui mousemode right "translate selected models"

> view matrix models
> #20,0.89514,0.44564,-0.011272,-73.394,-0.44004,0.87928,-0.18229,96.666,-0.071324,0.16813,0.98318,-21.634

> select add #21

5168 atoms, 5164 bonds, 6 pseudobonds, 332 residues, 4 models selected  

> select subtract #20

2584 atoms, 2582 bonds, 3 pseudobonds, 166 residues, 2 models selected  

> view matrix models
> #21,0.9324,0.36072,-0.022695,-56.166,-0.36067,0.92452,-0.12323,102.96,-0.023468,0.12308,0.99212,-22.706

> view matrix models
> #21,0.9324,0.36072,-0.022695,-54.4,-0.36067,0.92452,-0.12323,102.66,-0.023468,0.12308,0.99212,-22.217

> view matrix models
> #21,0.9324,0.36072,-0.022695,-54.36,-0.36067,0.92452,-0.12323,103.05,-0.023468,0.12308,0.99212,-21.933

> view matrix models
> #21,0.9324,0.36072,-0.022695,-54.671,-0.36067,0.92452,-0.12323,101.58,-0.023468,0.12308,0.99212,-22.513

> view matrix models
> #21,0.9324,0.36072,-0.022695,-54.209,-0.36067,0.92452,-0.12323,104.19,-0.023468,0.12308,0.99212,-22.5

> view matrix models
> #21,0.9324,0.36072,-0.022695,-54.505,-0.36067,0.92452,-0.12323,105.16,-0.023468,0.12308,0.99212,-24.106

> view matrix models
> #21,0.9324,0.36072,-0.022695,-54.09,-0.36067,0.92452,-0.12323,104.56,-0.023468,0.12308,0.99212,-25.558

> view matrix models
> #21,0.9324,0.36072,-0.022695,-53.007,-0.36067,0.92452,-0.12323,104.54,-0.023468,0.12308,0.99212,-23.494

> view matrix models
> #21,0.9324,0.36072,-0.022695,-52.381,-0.36067,0.92452,-0.12323,105.62,-0.023468,0.12308,0.99212,-24.046

> view matrix models
> #21,0.9324,0.36072,-0.022695,-52.518,-0.36067,0.92452,-0.12323,105.62,-0.023468,0.12308,0.99212,-23.153

> view matrix models
> #21,0.9324,0.36072,-0.022695,-52.737,-0.36067,0.92452,-0.12323,105.66,-0.023468,0.12308,0.99212,-22.644

> select add #20

5168 atoms, 5164 bonds, 6 pseudobonds, 332 residues, 4 models selected  

> select subtract #21

2584 atoms, 2582 bonds, 3 pseudobonds, 166 residues, 2 models selected  

> view matrix models
> #20,0.89514,0.44564,-0.011272,-73.952,-0.44004,0.87928,-0.18229,96.641,-0.071324,0.16813,0.98318,-20.344

> view matrix models
> #20,0.89514,0.44564,-0.011272,-74.165,-0.44004,0.87928,-0.18229,95.628,-0.071324,0.16813,0.98318,-20.497

> view matrix models
> #20,0.89514,0.44564,-0.011272,-74.559,-0.44004,0.87928,-0.18229,96.11,-0.071324,0.16813,0.98318,-19.619

> select add #21

5168 atoms, 5164 bonds, 6 pseudobonds, 332 residues, 4 models selected  

> select subtract #20

2584 atoms, 2582 bonds, 3 pseudobonds, 166 residues, 2 models selected  

> view matrix models
> #21,0.9324,0.36072,-0.022695,-53.029,-0.36067,0.92452,-0.12323,103.82,-0.023468,0.12308,0.99212,-22.764

> select add #20

5168 atoms, 5164 bonds, 6 pseudobonds, 332 residues, 4 models selected  

> select subtract #21

2584 atoms, 2582 bonds, 3 pseudobonds, 166 residues, 2 models selected  

> view matrix models
> #20,0.89514,0.44564,-0.011272,-74.799,-0.44004,0.87928,-0.18229,94.578,-0.071324,0.16813,0.98318,-19.39

> view matrix models
> #20,0.89514,0.44564,-0.011272,-73.933,-0.44004,0.87928,-0.18229,96.249,-0.071324,0.16813,0.98318,-19.936

> combine #19

> select add #22

5168 atoms, 5164 bonds, 6 pseudobonds, 332 residues, 4 models selected  

> select subtract #20

2584 atoms, 2582 bonds, 3 pseudobonds, 166 residues, 2 models selected  

> color #22 #00fa92ff

> color #22 #d4fb79ff

> color #22 #ff8ad8ff

> color #22 #942193ff

> color #22 #8efa00ff

> color #22 #fffb00ff

> view matrix models
> #22,0.93679,0.34915,0.022882,-73.916,-0.34379,0.93062,-0.12551,34.366,-0.065117,0.10971,0.99183,-13.158

> ui mousemode right "rotate selected models"

> view matrix models
> #22,0.82098,0.57014,-0.030517,-93.013,-0.56185,0.79722,-0.22082,127.21,-0.10157,0.19844,0.97484,-23.661

> ui mousemode right "translate selected models"

> ui mousemode right "rotate selected models"

> view matrix models
> #22,0.80727,0.57753,-0.12153,-73.883,-0.59005,0.79414,-0.14557,118.34,0.012443,0.18922,0.98186,-44.976

> ui mousemode right "translate selected models"

> view matrix models
> #22,0.80727,0.57753,-0.12153,-71.721,-0.59005,0.79414,-0.14557,119.91,0.012443,0.18922,0.98186,-44.908

> view matrix models
> #22,0.80727,0.57753,-0.12153,-70.655,-0.59005,0.79414,-0.14557,120.59,0.012443,0.18922,0.98186,-46.665

> view matrix models
> #22,0.80727,0.57753,-0.12153,-70.883,-0.59005,0.79414,-0.14557,120.31,0.012443,0.18922,0.98186,-46.829

> ui mousemode right "rotate selected models"

> view matrix models
> #22,0.84348,0.45656,-0.283,-16.987,-0.52908,0.79717,-0.29084,136.86,0.092814,0.39505,0.91396,-97.445

> ui mousemode right "translate selected models"

> view matrix models
> #22,0.84348,0.45656,-0.283,-15.892,-0.52908,0.79717,-0.29084,136.57,0.092814,0.39505,0.91396,-97.767

> hide #!22 models

> show #!22 models

> ui mousemode right "rotate selected models"

> view matrix models
> #22,0.8479,0.43756,-0.29934,-8.9865,-0.52944,0.72819,-0.43524,181.85,0.027534,0.52752,0.8491,-103.44

> view matrix models
> #22,0.89706,0.36372,-0.25098,-10.741,-0.44016,0.78598,-0.43417,150.68,0.039351,0.49995,0.86516,-102.43

> ui mousemode right "translate selected models"

> view matrix models
> #22,0.89706,0.36372,-0.25098,-12.167,-0.44016,0.78598,-0.43417,148.86,0.039351,0.49995,0.86516,-99.259

> ui mousemode right "rotate selected models"

> ui mousemode right "translate selected models"

> view matrix models
> #22,0.89706,0.36372,-0.25098,-16.531,-0.44016,0.78598,-0.43417,129.11,0.039351,0.49995,0.86516,-97.114

> hide #!22 models

> hide #!21 models

> hide #!20 models

> hide #!19 models

> select subtract #22

Nothing selected  

> show #!19 models

> hide #!19 models

> show #!18 models

> show #!17 models

> show #!14 models

> show #!15 models

> show #!13 models

> hide #!13 models

> show #!13 models

> select clear

> ui mousemode right select

> select #15/6:114

22 atoms, 21 bonds, 1 residue, 1 model selected  

> show #!19 models

> hide #!19 models

> show #!20 models

> show #!22 models

> hide #!22 models

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Fit14-6.cxs"

> ui mousemode right "translate selected models"

> hide #!20 models

> hide #!17 models

> show #!17 models

> hide #!14 models

> show #!14 models

> hide #!13 models

> show #!13 models

> hide #!18 models

> show #!18 models

> hide #!18 models

> show #!18 models

> combine #18

> select add #23

1352 atoms, 1350 bonds, 1 pseudobond, 85 residues, 3 models selected  

> select add #15

1780 atoms, 1778 bonds, 1 pseudobond, 114 residues, 3 models selected  

> select subtract #15

1330 atoms, 1329 bonds, 1 pseudobond, 84 residues, 2 models selected  

> view matrix models
> #23,0.97592,-0.21595,-0.030694,43.672,0.21587,0.9764,-0.006095,-34.301,0.031286,-0.00067755,0.99951,-11.004

> ui mousemode right "rotate selected models"

> view matrix models
> #23,0.98307,-0.097449,-0.15514,48.287,0.10636,0.99306,0.050178,-25.527,0.14917,-0.065829,0.98662,-22.499

> view matrix models
> #23,0.93089,-0.15194,-0.3322,105.32,0.091232,0.97728,-0.19133,30.593,0.35372,0.1478,0.9236,-88.479

> ui mousemode right "translate selected models"

> view matrix models
> #23,0.93089,-0.15194,-0.3322,110.35,0.091232,0.97728,-0.19133,32.494,0.35372,0.1478,0.9236,-85.958

> view matrix models
> #23,0.93089,-0.15194,-0.3322,108.26,0.091232,0.97728,-0.19133,30.767,0.35372,0.1478,0.9236,-83.194

> fitmap sel inMap #8

Fit molecule copy of copy of copy of copy of pointy-1pf.pdb (#23) to map
postprocess_masked330_onepf.mrc (#8) using 1330 atoms  
average map value = 0.01238, steps = 88  
shifted from previous position = 2.35  
rotated from previous position = 12 degrees  
atoms outside contour = 789, contour level = 0.012786  
  
Position of copy of copy of copy of copy of pointy-1pf.pdb (#23) relative to
postprocess_masked330_onepf.mrc (#8) coordinates:  
Matrix rotation and translation  
0.97599922 -0.14979710 -0.15807075 63.88156566  
0.13592121 0.98612789 -0.09527444 -1.63928013  
0.17014981 0.07150261 0.98282064 -43.66215117  
Axis 0.35787230 -0.70429986 0.61309797  
Axis point 283.77226195 0.00000000 367.27919177  
Rotation angle (degrees) 13.47446276  
Shift along axis -2.75318841  
  

> ui mousemode right "rotate selected models"

> view matrix models
> #23,0.97014,-0.082217,-0.2282,68.333,0.06201,0.9936,-0.094363,12.61,0.2345,0.077394,0.96903,-55.443

> ui mousemode right select

> select #15/6:114

22 atoms, 21 bonds, 1 residue, 1 model selected  

> ui mousemode right "translate selected models"

> color #23 #ebebebff

> ui mousemode right "translate selected models"

> view matrix models
> #15,0.83031,-0.0029369,-0.5573,145.91,0.040958,0.9976,0.055765,5.9943,0.5558,-0.069127,0.82844,-61.491

> view matrix models
> #15,0.83031,-0.0029369,-0.5573,146.87,0.040958,0.9976,0.055765,-15.437,0.5558,-0.069127,0.82844,-62.735

> view matrix models
> #15,0.83031,-0.0029369,-0.5573,148.42,0.040958,0.9976,0.055765,-14.85,0.5558,-0.069127,0.82844,-61.942

> ui mousemode right "rotate selected models"

> view matrix models
> #15,0.73144,0.29806,-0.61332,116.08,-0.31797,0.94473,0.079904,60.037,0.60324,0.13658,0.78578,-105.2

> ui mousemode right "translate selected models"

> view matrix models
> #15,0.73144,0.29806,-0.61332,121.21,-0.31797,0.94473,0.079904,62.292,0.60324,0.13658,0.78578,-102.65

> view matrix models
> #15,0.73144,0.29806,-0.61332,121.58,-0.31797,0.94473,0.079904,61.701,0.60324,0.13658,0.78578,-103.18

> view matrix models
> #15,0.73144,0.29806,-0.61332,121.13,-0.31797,0.94473,0.079904,61.434,0.60324,0.13658,0.78578,-102.88

> view matrix models
> #15,0.73144,0.29806,-0.61332,119.37,-0.31797,0.94473,0.079904,60.222,0.60324,0.13658,0.78578,-101.65

> view matrix models
> #15,0.73144,0.29806,-0.61332,118.64,-0.31797,0.94473,0.079904,59.913,0.60324,0.13658,0.78578,-101.58

> view matrix models
> #15,0.73144,0.29806,-0.61332,118.04,-0.31797,0.94473,0.079904,60.398,0.60324,0.13658,0.78578,-101.5

> view matrix models
> #15,0.73144,0.29806,-0.61332,118.64,-0.31797,0.94473,0.079904,60.304,0.60324,0.13658,0.78578,-101.54

> ui mousemode right "rotate selected models"

> view matrix models
> #15,0.727,0.29816,-0.61852,120.49,-0.31395,0.94547,0.08676,58.029,0.61066,0.13111,0.78097,-100.88

> view matrix models
> #15,0.7445,0.31142,-0.59055,108.89,-0.34029,0.93803,0.065663,68.768,0.5744,0.15207,0.80433,-102.88

> view matrix models
> #15,0.92214,0.37875,-0.078793,-39.914,-0.36609,0.92018,0.13876,62.994,0.12506,-0.099113,0.98719,-0.92484

> view matrix models
> #15,0.92322,0.38112,-0.049193,-46.445,-0.3729,0.91942,0.12494,67.178,0.092847,-0.097003,0.99094,4.0633

> ui mousemode right "translate selected models"

> view matrix models
> #15,0.92322,0.38112,-0.049193,-48.792,-0.3729,0.91942,0.12494,69.153,0.092847,-0.097003,0.99094,4.2959

> view matrix models
> #15,0.92322,0.38112,-0.049193,-47.631,-0.3729,0.91942,0.12494,68.575,0.092847,-0.097003,0.99094,3.1727

> view matrix models
> #15,0.92322,0.38112,-0.049193,-49.836,-0.3729,0.91942,0.12494,68.413,0.092847,-0.097003,0.99094,2.6535

> view matrix models
> #15,0.92322,0.38112,-0.049193,-50.951,-0.3729,0.91942,0.12494,68.065,0.092847,-0.097003,0.99094,2.3746

> ui mousemode right "rotate selected models"

> view matrix models
> #15,0.94572,0.32393,-0.026027,-47.986,-0.32412,0.94601,-0.0031921,78.478,0.023587,0.011454,0.99966,-8.5377

> view matrix models
> #15,0.94676,0.31281,-0.076102,-36.013,-0.31255,0.94977,0.015547,71.792,0.077143,0.009067,0.99698,-17.766

> show #!22 models

> hide #!23 models

> show #!23 models

> hide #!22 models

> ui mousemode right "translate selected models"

> view matrix models
> #15,0.94676,0.31281,-0.076102,-33.609,-0.31255,0.94977,0.015547,71.943,0.077143,0.009067,0.99698,-18.368

> view matrix models
> #15,0.94676,0.31281,-0.076102,-32.871,-0.31255,0.94977,0.015547,72.728,0.077143,0.009067,0.99698,-17.727

> view matrix models
> #15,0.94676,0.31281,-0.076102,-32.895,-0.31255,0.94977,0.015547,72.134,0.077143,0.009067,0.99698,-17.858

> ui mousemode right "rotate selected models"

> view matrix models
> #15,0.92692,0.36812,-0.072876,-41.183,-0.36645,0.92976,0.035649,82.631,0.08088,-0.0063386,0.9967,-15.33

> ui mousemode right "translate selected models"

> view matrix models
> #15,0.92692,0.36812,-0.072876,-40.603,-0.36645,0.92976,0.035649,82.3,0.08088,-0.0063386,0.9967,-15.495

> view matrix models
> #15,0.92692,0.36812,-0.072876,-39.672,-0.36645,0.92976,0.035649,82.834,0.08088,-0.0063386,0.9967,-14.886

> view matrix models
> #15,0.92692,0.36812,-0.072876,-39.896,-0.36645,0.92976,0.035649,82.754,0.08088,-0.0063386,0.9967,-15.225

> ui mousemode right "rotate selected models"

> view matrix models
> #15,0.91041,0.29782,-0.28714,20.044,-0.28752,0.95456,0.078463,54.075,0.29746,0.011122,0.95467,-52.007

> view matrix models
> #15,0.87246,0.36951,-0.3198,18.907,-0.36664,0.92761,0.071549,76.16,0.32309,0.054829,0.94478,-64.011

> ui mousemode right "translate selected models"

> view matrix models
> #15,0.87246,0.36951,-0.3198,18.728,-0.36664,0.92761,0.071549,75.779,0.32309,0.054829,0.94478,-65.425

> ui mousemode right "translate selected models"

> view matrix models
> #15,0.87246,0.36951,-0.3198,19.482,-0.36664,0.92761,0.071549,75.725,0.32309,0.054829,0.94478,-64.103

> view matrix models
> #15,0.87246,0.36951,-0.3198,21.13,-0.36664,0.92761,0.071549,75.843,0.32309,0.054829,0.94478,-63.842

> view matrix models
> #15,0.87246,0.36951,-0.3198,21.154,-0.36664,0.92761,0.071549,75.867,0.32309,0.054829,0.94478,-63.845

> view matrix models
> #15,0.87246,0.36951,-0.3198,21.384,-0.36664,0.92761,0.071549,75.962,0.32309,0.054829,0.94478,-64.354

> view matrix models
> #15,0.87246,0.36951,-0.3198,21.636,-0.36664,0.92761,0.071549,76.019,0.32309,0.054829,0.94478,-64.243

> ui mousemode right "rotate selected models"

> view matrix models
> #15,0.83575,0.44847,-0.31685,11.734,-0.44617,0.89097,0.084228,96.327,0.32008,0.070976,0.94473,-66.999

> ui mousemode right "translate selected models"

> view matrix models
> #15,0.83575,0.44847,-0.31685,13.657,-0.44617,0.89097,0.084228,95.464,0.32008,0.070976,0.94473,-66.607

> view matrix models
> #15,0.83575,0.44847,-0.31685,14.224,-0.44617,0.89097,0.084228,95.701,0.32008,0.070976,0.94473,-66.508

> view matrix models
> #15,0.83575,0.44847,-0.31685,15.166,-0.44617,0.89097,0.084228,95.326,0.32008,0.070976,0.94473,-66.317

> ui mousemode right "translate selected models"

> view matrix models
> #15,0.83575,0.44847,-0.31685,13.341,-0.44617,0.89097,0.084228,93.254,0.32008,0.070976,0.94473,-64.581

> ui mousemode right "rotate selected models"

> view matrix models
> #15,0.75824,0.49292,-0.42674,40.635,-0.48563,0.86371,0.13478,96.486,0.43502,0.10504,0.89427,-83.688

> view matrix models
> #15,0.74535,0.5077,-0.43208,41.094,-0.53226,0.84344,0.072884,121.81,0.40144,0.17566,0.89889,-92.786

> ui mousemode right "translate selected models"

> view matrix models
> #15,0.74535,0.5077,-0.43208,41.859,-0.53226,0.84344,0.072884,121.98,0.40144,0.17566,0.89889,-92.691

> ui mousemode right "rotate selected models"

> view matrix models
> #15,0.80743,0.49528,-0.32056,10.57,-0.52328,0.85216,-0.0014085,133.1,0.27247,0.16888,0.94723,-76.133

> view matrix models
> #15,0.83024,0.50674,-0.2322,-13.585,-0.52181,0.85305,-0.0041415,133.18,0.19598,0.1246,0.97266,-57.339

> ui mousemode right "translate selected models"

> view matrix models
> #15,0.83024,0.50674,-0.2322,-13.752,-0.52181,0.85305,-0.0041415,130.68,0.19598,0.1246,0.97266,-57.427

> ui mousemode right "rotate selected models"

> view matrix models
> #15,0.85177,0.52002,-0.063764,-53.819,-0.52372,0.84842,-0.076742,146.31,0.014191,0.098762,0.99501,-21.689

> ui mousemode right "translate selected models"

> view matrix models
> #15,0.85177,0.52002,-0.063764,-54.107,-0.52372,0.84842,-0.076742,148.13,0.014191,0.098762,0.99501,-21.774

> ui mousemode right "rotate selected models"

> hide #!23 models

> select clear

> combine #13,14,15,17,18

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '8'  

> combine #24

> color #25 #73fcd6ff

> select add #25

2584 atoms, 2582 bonds, 3 pseudobonds, 166 residues, 2 models selected  

> ui mousemode right zoom

> ui mousemode right "translate selected models"

> view matrix models
> #25,0.93679,0.34915,0.022882,-76.849,-0.34379,0.93062,-0.12551,32.6,-0.065117,0.10971,0.99183,-11.564

> ui mousemode right "rotate selected models"

> view matrix models
> #25,0.85855,0.51254,-0.013726,-91.518,-0.50736,0.84539,-0.16705,92.322,-0.074017,0.15039,0.98585,-17.91

> view matrix models
> #25,0.91424,0.4032,-0.039856,-71.93,-0.40257,0.89283,-0.20199,68.366,-0.04586,0.20071,0.97858,-33.374

> view matrix models
> #25,0.86182,0.27294,-0.42751,47.783,-0.42784,0.8439,-0.3237,109.49,0.27243,0.46188,0.84407,-127.07

> view matrix models
> #25,0.87993,0.078272,-0.46861,97.24,-0.3567,0.76036,-0.54278,159.9,0.31383,0.64476,0.69699,-146.63

> view matrix models
> #25,0.93607,0.26732,-0.22874,-6.2182,-0.34229,0.84228,-0.41642,112.37,0.081349,0.46809,0.87993,-98.85

> view matrix models
> #25,0.89383,0.2711,-0.35718,27.531,-0.3975,0.84767,-0.35134,108.44,0.20753,0.45602,0.86543,-117.55

> ui mousemode right zoom

> ui mousemode right "translate selected models"

> view matrix models
> #25,0.89383,0.2711,-0.35718,32.428,-0.3975,0.84767,-0.35134,109.63,0.20753,0.45602,0.86543,-123.27

> view matrix models
> #25,0.89383,0.2711,-0.35718,33.009,-0.3975,0.84767,-0.35134,108.09,0.20753,0.45602,0.86543,-123.17

> ui mousemode right "rotate selected models"

> view matrix models
> #25,0.87233,0.35066,-0.34069,15.588,-0.44227,0.86301,-0.24416,91.202,0.2084,0.36367,0.90792,-110.96

> ui mousemode right "translate selected models"

> view matrix models
> #25,0.87233,0.35066,-0.34069,16.223,-0.44227,0.86301,-0.24416,92.543,0.2084,0.36367,0.90792,-110

> ui mousemode right "rotate selected models"

> view matrix models
> #25,0.82932,0.4503,-0.33085,-0.25157,-0.5409,0.79551,-0.27312,133.04,0.14021,0.40546,0.90329,-105.4

> ui mousemode right "translate selected models"

> view matrix models
> #25,0.82932,0.4503,-0.33085,-2.2197,-0.5409,0.79551,-0.27312,135.75,0.14021,0.40546,0.90329,-105.69

> view matrix models
> #25,0.82932,0.4503,-0.33085,-1.2505,-0.5409,0.79551,-0.27312,136.36,0.14021,0.40546,0.90329,-104.53

> ui mousemode right "rotate selected models"

> view matrix models
> #25,0.89526,0.12322,-0.42816,80.783,-0.38815,0.6875,-0.61375,201.55,0.21874,0.71565,0.66332,-141.28

> view matrix models
> #25,0.91407,0.068259,-0.39977,83.862,-0.31534,0.73946,-0.59477,171.66,0.25501,0.66973,0.69745,-144.83

> ui mousemode right "translate selected models"

> view matrix models
> #25,0.91407,0.068259,-0.39977,81.673,-0.31534,0.73946,-0.59477,168.73,0.25501,0.66973,0.69745,-147.8

> view matrix models
> #25,0.91407,0.068259,-0.39977,90.339,-0.31534,0.73946,-0.59477,192.04,0.25501,0.66973,0.69745,-145.36

> view matrix models
> #25,0.91407,0.068259,-0.39977,90.55,-0.31534,0.73946,-0.59477,192.21,0.25501,0.66973,0.69745,-145.46

> fitmap sel inMap #8

Fit molecule copy of combination (#25) to map postprocess_masked330_onepf.mrc
(#8) using 2584 atoms  
average map value = 0.01103, steps = 352  
shifted from previous position = 6.05  
rotated from previous position = 46.5 degrees  
atoms outside contour = 1607, contour level = 0.012786  
  
Position of copy of combination (#25) relative to
postprocess_masked330_onepf.mrc (#8) coordinates:  
Matrix rotation and translation  
0.92106112 0.38935043 0.00725557 -70.20348161  
-0.38925581 0.92105535 -0.01170278 40.80160565  
-0.01123926 0.00795470 0.99990520 -0.83552664  
Axis 0.02523186 0.02373951 -0.99939971  
Axis point 65.55329993 193.60194072 0.00000000  
Rotation angle (degrees) 22.92569035  
Shift along axis 0.03227088  
  

> hide #!8 models

> show #!9 models

> hide #!24 models

> hide #!25 models

> hide #!18 models

> hide #!17 models

> hide #!13 models

> hide #!14 models

> hide #!15 models

> show #!24 models

> hide #!24 models

> show #!8 models

> hide #!8 models

> hide #!9 models

> show #!8 models

> show #!24 models

> hide #!24 models

> show #!24 models

> show #!25 models

> view matrix models
> #25,0.92106,0.38933,0.0080971,-65.879,-0.38922,0.92107,-0.011767,87.789,-0.012039,0.0076869,0.9999,4.8159

> view matrix models
> #25,0.92106,0.38933,0.0080971,-64.868,-0.38922,0.92107,-0.011767,87.585,-0.012039,0.0076869,0.9999,-0.073185

> view matrix models
> #25,0.92106,0.38933,0.0080971,-67.556,-0.38922,0.92107,-0.011767,89.995,-0.012039,0.0076869,0.9999,-0.76675

> view matrix models
> #25,0.92106,0.38933,0.0080971,-67.266,-0.38922,0.92107,-0.011767,90.4,-0.012039,0.0076869,0.9999,-0.98862

> ui mousemode right "rotate selected models"

> view matrix models
> #25,0.90674,0.42109,-0.022408,-65.476,-0.42158,0.90642,-0.026066,102.96,0.0093346,0.033082,0.99941,-10.835

> view matrix models
> #25,0.97429,0.16465,-0.15381,7.1109,-0.20613,0.927,-0.31333,115.63,0.090991,0.33698,0.9371,-83.315

> view matrix models
> #25,0.95358,0.25215,-0.16462,-6.6583,-0.29271,0.90455,-0.31003,136.86,0.070735,0.34383,0.93636,-80.804

> view matrix models
> #25,0.95105,0.25342,-0.17686,-3.9386,-0.29739,0.90612,-0.30083,135.51,0.084025,0.3387,0.93713,-82.365

> view matrix models
> #25,0.92424,0.32559,-0.19945,-10.597,-0.37622,0.86569,-0.3302,166.07,0.065154,0.38022,0.9226,-85.211

> hide #!24 models

> show #!24 models

> show #!17 models

> select add #17

2841 atoms, 2841 bonds, 3 pseudobonds, 181 residues, 3 models selected  

> select subtract #17

2584 atoms, 2582 bonds, 3 pseudobonds, 166 residues, 2 models selected  

> hide #!17 models

> show #!15 models

> select add #15

3034 atoms, 3031 bonds, 3 pseudobonds, 196 residues, 3 models selected  

> view matrix models
> #15,0.83831,0.54205,-0.058464,-57.559,-0.54515,0.83475,-0.077483,155.17,0.0068032,0.096826,0.99528,-20.06,#25,0.91486,0.35016,-0.20105,-14.07,-0.39965,0.85626,-0.32725,172.16,0.05756,0.37974,0.9233,-83.774

> undo

> select subtract #25

450 atoms, 449 bonds, 30 residues, 1 model selected  

> view matrix models
> #15,0.87856,0.47168,-0.075163,-46.98,-0.47667,0.87582,-0.075611,133.23,0.030165,0.10226,0.9943,-25.415

> view matrix models
> #15,0.92314,0.37181,-0.097787,-30.381,-0.37939,0.92218,-0.075212,104.94,0.062212,0.10653,0.99236,-32.051

> view matrix models
> #15,0.92391,0.34978,-0.15509,-14.672,-0.35458,0.93502,-0.0035936,83.415,0.14375,0.058312,0.98789,-36.796

> ui mousemode right "translate selected models"

> view matrix models
> #15,0.92391,0.34978,-0.15509,-14.969,-0.35458,0.93502,-0.0035936,83.805,0.14375,0.058312,0.98789,-36.757

> hide #!24 models

> ui mousemode right "rotate selected models"

> view matrix models
> #15,0.93681,0.33579,-0.098118,-25.773,-0.34534,0.93246,-0.10606,102.76,0.055878,0.13324,0.98951,-35.766

> ui mousemode right "translate selected models"

> view matrix models
> #15,0.93681,0.33579,-0.098118,-26.486,-0.34534,0.93246,-0.10606,103.49,0.055878,0.13324,0.98951,-34.283

> view matrix models
> #15,0.93681,0.33579,-0.098118,-26.367,-0.34534,0.93246,-0.10606,103.51,0.055878,0.13324,0.98951,-34.238

> view matrix models
> #15,0.93681,0.33579,-0.098118,-26.295,-0.34534,0.93246,-0.10606,103.4,0.055878,0.13324,0.98951,-33.517

> ui mousemode right "rotate selected models"

> view matrix models
> #15,0.92968,0.32942,-0.16486,-10.456,-0.36004,0.90722,-0.21755,133.41,0.077896,0.26161,0.96203,-58.888

> view matrix models
> #15,0.93264,0.31281,-0.17982,-4.6355,-0.34456,0.92004,-0.18656,121.69,0.10708,0.23595,0.96585,-59.916

> ui mousemode right "translate selected models"

> view matrix models
> #15,0.93264,0.31281,-0.17982,-4.836,-0.34456,0.92004,-0.18656,121.92,0.10708,0.23595,0.96585,-59.425

> ui mousemode right "rotate selected models"

> ui mousemode right "translate selected models"

> view matrix models
> #15,0.93264,0.31281,-0.17982,-4.6402,-0.34456,0.92004,-0.18656,123.56,0.10708,0.23595,0.96585,-61.496

> view matrix models
> #15,0.93264,0.31281,-0.17982,-4.387,-0.34456,0.92004,-0.18656,124.13,0.10708,0.23595,0.96585,-60.318

> ui mousemode right "rotate selected models"

> view matrix models
> #15,0.9368,0.29303,-0.19114,1.141,-0.33364,0.91268,-0.23603,133.31,0.10528,0.28488,0.95276,-67.524

> select add #25

3034 atoms, 3031 bonds, 3 pseudobonds, 196 residues, 3 models selected  

> close #25

> combine #13,14,15,17,18

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '8'  

> combine #13,14,15,17,18

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '8'  

> color #26 #0096ffff

> hide #!15 models

> select add #26

3034 atoms, 3031 bonds, 3 pseudobonds, 196 residues, 3 models selected  

> ui mousemode right "rotate selected models"

> select subtract #15

2584 atoms, 2582 bonds, 3 pseudobonds, 166 residues, 2 models selected  

> view matrix models
> #26,0.93954,0.34227,0.0104,-61.316,-0.33217,0.91836,-0.21512,96.654,-0.08318,0.19866,0.97653,-25.086

> undo

> ui mousemode right "translate selected models"

> view matrix models
> #26,0.93679,0.34915,0.022882,-64.152,-0.34379,0.93062,-0.12551,101.07,-0.065117,0.10971,0.99183,-8.9586

> view matrix models
> #26,0.93679,0.34915,0.022882,-62.441,-0.34379,0.93062,-0.12551,100.52,-0.065117,0.10971,0.99183,-9.5512

> view matrix models
> #26,0.93679,0.34915,0.022882,-62.722,-0.34379,0.93062,-0.12551,100.63,-0.065117,0.10971,0.99183,-9.6938

> view matrix models
> #26,0.93679,0.34915,0.022882,-64.157,-0.34379,0.93062,-0.12551,100.73,-0.065117,0.10971,0.99183,-9.7287

> hide #!26 models

> hide #!8 models

> hide #!25 models

> show #!15 models

> show #!14 models

> show #!13 models

> show #!18 models

> show #!17 models

> select add #18

3914 atoms, 3911 bonds, 4 pseudobonds, 250 residues, 4 models selected  

> select subtract #18

2584 atoms, 2582 bonds, 3 pseudobonds, 166 residues, 2 models selected  

> select add #17

2841 atoms, 2841 bonds, 3 pseudobonds, 181 residues, 3 models selected  

> select subtract #17

2584 atoms, 2582 bonds, 3 pseudobonds, 166 residues, 2 models selected  

> select add #15

3034 atoms, 3031 bonds, 3 pseudobonds, 196 residues, 3 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #15,0.93076,0.30939,-0.19483,-0.36148,-0.34958,0.90916,-0.22633,135.18,0.10711,0.27877,0.95437,-66.923,#26,0.93048,0.36573,0.021143,-66.201,-0.36085,0.92495,-0.11939,104.14,-0.063221,0.10346,0.99262,-8.89

> view matrix models
> #15,0.91216,0.36507,-0.18624,-10.021,-0.3754,0.92659,-0.022282,96.295,0.16443,0.090239,0.98225,-44.365,#26,0.90755,0.41838,0.036087,-76.196,-0.41993,0.90426,0.077297,81.187,-0.00029226,-0.085306,0.99635,19.342

> ui mousemode right "translate selected models"

> view matrix models
> #15,0.91216,0.36507,-0.18624,-9.6712,-0.3754,0.92659,-0.022282,95.448,0.16443,0.090239,0.98225,-47.845,#26,0.90755,0.41838,0.036087,-75.846,-0.41993,0.90426,0.077297,80.34,-0.00029226,-0.085306,0.99635,15.862

> view matrix models
> #15,0.91216,0.36507,-0.18624,-10.908,-0.3754,0.92659,-0.022282,93.427,0.16443,0.090239,0.98225,-48.87,#26,0.90755,0.41838,0.036087,-77.083,-0.41993,0.90426,0.077297,78.319,-0.00029226,-0.085306,0.99635,14.837

> view matrix models
> #15,0.91216,0.36507,-0.18624,-10.09,-0.3754,0.92659,-0.022282,93.363,0.16443,0.090239,0.98225,-48.956,#26,0.90755,0.41838,0.036087,-76.265,-0.41993,0.90426,0.077297,78.255,-0.00029226,-0.085306,0.99635,14.751

> view matrix models
> #15,0.91216,0.36507,-0.18624,-9.2778,-0.3754,0.92659,-0.022282,93.215,0.16443,0.090239,0.98225,-49.001,#26,0.90755,0.41838,0.036087,-75.453,-0.41993,0.90426,0.077297,78.107,-0.00029226,-0.085306,0.99635,14.706

> ui mousemode right "rotate selected models"

> view matrix models
> #15,0.87626,0.44677,-0.18044,-20.462,-0.45461,0.89069,-0.0023263,111.88,0.15968,0.084069,0.98358,-47.076,#26,0.86653,0.49662,0.049964,-87.261,-0.49911,0.8631,0.0771,102.93,-0.0048347,-0.091746,0.99577,17.141

> show #!26 models

> hide #!26 models

> show #!25 models

> hide #!25 models

> show #!24 models

> hide #!24 models

> show #!23 models

> ui mousemode right "translate selected models"

> view matrix models
> #15,0.87626,0.44677,-0.18044,-21.476,-0.45461,0.89069,-0.0023263,112.2,0.15968,0.084069,0.98358,-46.835,#26,0.86653,0.49662,0.049964,-88.276,-0.49911,0.8631,0.0771,103.26,-0.0048347,-0.091746,0.99577,17.382

> hide #!23 models

> show #!12 models

> hide #!12 models

> show #!8 models

> show #!26 models

> hide #!26 models

> show #!26 models

> hide #!26 models

> volume #8 level 0.009899

> select subtract #26

450 atoms, 449 bonds, 30 residues, 1 model selected  

> hide #!18 models

> hide #!17 models

> hide #!15 models

> hide #!14 models

> hide #!13 models

> show #!15 models

> hide #!15 models

> select subtract #15

Nothing selected  

> show #!9 models

> hide #!8 models

> show #!18 models

> show #!17 models

> show #!15 models

> show #!13 models

> show #!14 models

> hide #!9 models

> select add #17

257 atoms, 259 bonds, 15 residues, 1 model selected  

> select subtract #17

Nothing selected  

> select add #18

1330 atoms, 1329 bonds, 1 pseudobond, 84 residues, 2 models selected  

> select subtract #18

Nothing selected  

> select add #15

450 atoms, 449 bonds, 30 residues, 1 model selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #15,0.87264,0.46232,-0.15737,-28.549,-0.45282,0.88665,0.093809,93.751,0.1829,-0.010603,0.98307,-31.581

> ui mousemode right "translate selected models"

> view matrix models
> #15,0.87264,0.46232,-0.15737,-28.868,-0.45282,0.88665,0.093809,91.621,0.1829,-0.010603,0.98307,-32.672

> view matrix models
> #15,0.87264,0.46232,-0.15737,-28.941,-0.45282,0.88665,0.093809,91.794,0.1829,-0.010603,0.98307,-32.227

> show #!23 models

> show #!26 models

> hide #!26 models

> hide #!23 models

> select clear

> combine #13,14,15,17,18

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '8'  

> combine #13,14,15,17,18

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '8'  

> color #28 #76d6ffff

> select add #28

2584 atoms, 2582 bonds, 3 pseudobonds, 166 residues, 2 models selected  

> color #8 #00fa92ff models

> show #!8 models

> select clear

> ui mousemode right select

> select #8

2 models selected  

> transparency #8.1 60

> select clear

[Repeated 1 time(s)]

> select #8

2 models selected  

> transparency #8.1 70

> select clear

> select add #28

2584 atoms, 2582 bonds, 3 pseudobonds, 166 residues, 2 models selected  

> ui mousemode right "translate selected models"

> view matrix models
> #28,0.93679,0.34915,0.022882,-62.226,-0.34379,0.93062,-0.12551,103,-0.065117,0.10971,0.99183,-12.766

> view matrix models
> #28,0.93679,0.34915,0.022882,-62.363,-0.34379,0.93062,-0.12551,104.22,-0.065117,0.10971,0.99183,-10.656

> view matrix models
> #28,0.93679,0.34915,0.022882,-64.684,-0.34379,0.93062,-0.12551,100.68,-0.065117,0.10971,0.99183,-10.867

> fitmap sel inMap #8

Fit molecule combination (#28) to map postprocess_masked330_onepf.mrc (#8)
using 2584 atoms  
average map value = 0.01221, steps = 88  
shifted from previous position = 0.746  
rotated from previous position = 4.21 degrees  
atoms outside contour = 1367, contour level = 0.0098989  
  
Position of combination (#28) relative to postprocess_masked330_onepf.mrc (#8)
coordinates:  
Matrix rotation and translation  
0.93369851 0.35276918 0.06132698 -71.97796238  
-0.34903052 0.93492501 -0.06397592 87.95628099  
-0.07990486 0.03832924 0.99606530 7.80270428  
Axis 0.14147296 0.19530282 -0.97048555  
Axis point 207.07011821 242.72346329 0.00000000  
Rotation angle (degrees) 21.19673416  
Shift along axis -0.57723728  
  

> select clear

> ui windowfill toggle

[Repeated 1 time(s)]

> hide #!28 models

> hide #!27 models

> select add #13

96 atoms, 95 bonds, 1 pseudobond, 8 residues, 2 models selected  

> select add #14

547 atoms, 545 bonds, 2 pseudobonds, 37 residues, 4 models selected  

> select subtract #13

451 atoms, 450 bonds, 1 pseudobond, 29 residues, 2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #14,0.98009,0.16656,-0.10803,-10.826,-0.11763,0.92555,0.35988,-57.56,0.15993,-0.34001,0.92672,57.839

> ui mousemode right "translate selected models"

> view matrix models
> #14,0.98009,0.16656,-0.10803,-6.8369,-0.11763,0.92555,0.35988,-59.985,0.15993,-0.34001,0.92672,56.164

> ui mousemode right "rotate selected models"

> view matrix models
> #14,0.98484,0.038714,-0.1691,31.432,0.012301,0.95674,0.29068,-78.76,0.17304,-0.28835,0.94176,39.618

> ui mousemode right "translate selected models"

> view matrix models
> #14,0.98484,0.038714,-0.1691,33.223,0.012301,0.95674,0.29068,-79.589,0.17304,-0.28835,0.94176,38.85

> ui mousemode right "rotate selected models"

> view matrix models
> #14,0.88943,0.16718,-0.4254,73.182,-0.043261,0.95732,0.28578,-67.956,0.45502,-0.23578,0.8587,-11.486

> view matrix models
> #14,0.89,0.22071,-0.39899,56.503,-0.10802,0.95219,0.28576,-54.238,0.44298,-0.21122,0.87129,-16.834

> hide #!8 models

> ui mousemode right "rotate selected models"

> view matrix models
> #14,0.90484,0.21443,-0.36781,48.999,-0.036949,0.9002,0.43391,-85.229,0.42414,-0.37903,0.82246,32.284

> ui mousemode right "translate selected models"

> view matrix models
> #14,0.90484,0.21443,-0.36781,49.126,-0.036949,0.9002,0.43391,-84.876,0.42414,-0.37903,0.82246,34.244

> ui mousemode right "rotate selected models"

> view matrix models
> #14,0.90717,0.18128,-0.37971,58.083,0.058233,0.83966,0.53999,-110.67,0.41672,-0.51197,0.75115,77.937

> ui mousemode right "translate selected models"

> view matrix models
> #14,0.90717,0.18128,-0.37971,58.831,0.058233,0.83966,0.53999,-109.87,0.41672,-0.51197,0.75115,79.964

> show #!8 models

> view matrix models
> #14,0.90717,0.18128,-0.37971,59.109,0.058233,0.83966,0.53999,-111.47,0.41672,-0.51197,0.75115,80.291

> ui mousemode right "rotate selected models"

> view matrix models
> #14,0.93444,0.19819,-0.29588,34.125,-0.096387,0.94058,0.32562,-62.075,0.34283,-0.27575,0.89801,15.757

> ui mousemode right "translate selected models"

> view matrix models
> #14,0.93444,0.19819,-0.29588,33.416,-0.096387,0.94058,0.32562,-62.214,0.34283,-0.27575,0.89801,11.72

> view matrix models
> #14,0.93444,0.19819,-0.29588,33.428,-0.096387,0.94058,0.32562,-62.14,0.34283,-0.27575,0.89801,11.728

> ui mousemode right "rotate selected models"

> view matrix models
> #14,0.94277,0.18985,-0.27412,29.437,-0.096174,0.94197,0.32162,-61.717,0.31927,-0.27685,0.90632,14.964

> view matrix models
> #14,0.94294,0.13505,-0.30435,46.978,-0.058897,0.96729,0.24675,-60.102,0.32772,-0.21474,0.92005,-2.67

> ui mousemode right "translate selected models"

> view matrix models
> #14,0.94294,0.13505,-0.30435,47.464,-0.058897,0.96729,0.24675,-60.328,0.32772,-0.21474,0.92005,-2.5666

> view matrix models
> #14,0.94294,0.13505,-0.30435,47.403,-0.058897,0.96729,0.24675,-60.07,0.32772,-0.21474,0.92005,-2.4292

> hide #!8 models

> select add #16

2038 atoms, 2039 bonds, 2 pseudobonds, 128 residues, 4 models selected  

> select subtract #14

1587 atoms, 1589 bonds, 1 pseudobond, 99 residues, 2 models selected  

> select add #17

1844 atoms, 1848 bonds, 1 pseudobond, 114 residues, 3 models selected  

> select subtract #16

257 atoms, 259 bonds, 15 residues, 1 model selected  

> select add #18

1587 atoms, 1588 bonds, 1 pseudobond, 99 residues, 3 models selected  

> select subtract #18

257 atoms, 259 bonds, 15 residues, 1 model selected  

> select subtract #17

Nothing selected  

> select add #15

450 atoms, 449 bonds, 30 residues, 1 model selected  

> show #!8 models

> ui mousemode right "rotate selected models"

> view matrix models
> #15,0.82799,0.53803,-0.15798,-35.946,-0.52482,0.84277,0.11958,109.58,0.19748,-0.016101,0.98017,-33.309

> show #!23 models

> view matrix models
> #15,0.84681,0.50834,-0.15655,-33.685,-0.49655,0.86102,0.10994,102.29,0.19068,-0.015364,0.98153,-32.427

> view matrix models
> #15,0.8478,0.50795,-0.15239,-34.614,-0.49462,0.86103,0.11825,100.28,0.19128,-0.02488,0.98122,-30.51

> ui mousemode right zoom

> ui mousemode right "translate selected models"

> view matrix models
> #15,0.8478,0.50795,-0.15239,-34.996,-0.49462,0.86103,0.11825,100.97,0.19128,-0.02488,0.98122,-30.69

> show #!26 models

> hide #!26 models

> view matrix models
> #15,0.8478,0.50795,-0.15239,-35.002,-0.49462,0.86103,0.11825,101.23,0.19128,-0.02488,0.98122,-30.049

> view matrix models
> #15,0.8478,0.50795,-0.15239,-35.368,-0.49462,0.86103,0.11825,100.77,0.19128,-0.02488,0.98122,-29.525

> view matrix models
> #15,0.8478,0.50795,-0.15239,-35.409,-0.49462,0.86103,0.11825,100.58,0.19128,-0.02488,0.98122,-29.695

> view matrix models
> #15,0.8478,0.50795,-0.15239,-34.446,-0.49462,0.86103,0.11825,100.28,0.19128,-0.02488,0.98122,-29.775

> view matrix models
> #15,0.8478,0.50795,-0.15239,-34.012,-0.49462,0.86103,0.11825,100.23,0.19128,-0.02488,0.98122,-29.454

> view matrix models
> #15,0.8478,0.50795,-0.15239,-33.525,-0.49462,0.86103,0.11825,100.65,0.19128,-0.02488,0.98122,-29.444

> select subtract #15

Nothing selected  

> select add #23

1330 atoms, 1329 bonds, 1 pseudobond, 84 residues, 2 models selected  

> view matrix models
> #23,0.97014,-0.082217,-0.2282,69.666,0.06201,0.9936,-0.094363,11.968,0.2345,0.077394,0.96903,-55.32

> view matrix models
> #23,0.97014,-0.082217,-0.2282,69.887,0.06201,0.9936,-0.094363,11.818,0.2345,0.077394,0.96903,-55.09

> view matrix models
> #23,0.97014,-0.082217,-0.2282,69.936,0.06201,0.9936,-0.094363,11.805,0.2345,0.077394,0.96903,-55.085

> view matrix models
> #23,0.97014,-0.082217,-0.2282,69.382,0.06201,0.9936,-0.094363,12.208,0.2345,0.077394,0.96903,-54.865

> select subtract #23

Nothing selected  

> combine #13,14,15,17,18

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '8'  

> combine #13,14,15,17,18

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '8'  

> hide #!23 models

> color #30 #942193ff

> select add #30

2584 atoms, 2582 bonds, 3 pseudobonds, 166 residues, 2 models selected  

> hide #!13 models

> hide #!14 models

> hide #!15 models

> hide #!17 models

> hide #!18 models

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Fit14-7.cxs"

> view matrix models
> #30,0.93679,0.34915,0.022882,-62.691,-0.34379,0.93062,-0.12551,100.42,-0.065117,0.10971,0.99183,-13.008

> view matrix models
> #30,0.93679,0.34915,0.022882,-64.628,-0.34379,0.93062,-0.12551,101.71,-0.065117,0.10971,0.99183,-13.237

> view matrix models
> #30,0.93679,0.34915,0.022882,-65.248,-0.34379,0.93062,-0.12551,102.9,-0.065117,0.10971,0.99183,-10.662

> view matrix models
> #30,0.93679,0.34915,0.022882,-66.264,-0.34379,0.93062,-0.12551,102.75,-0.065117,0.10971,0.99183,-10.056

> volume #8 level 0.01346

> fitmap sel inMap #8

Fit molecule combination (#30) to map postprocess_masked330_onepf.mrc (#8)
using 2584 atoms  
average map value = 0.01305, steps = 72  
shifted from previous position = 3.11  
rotated from previous position = 2.08 degrees  
atoms outside contour = 1512, contour level = 0.013465  
  
Position of combination (#30) relative to postprocess_masked330_onepf.mrc (#8)
coordinates:  
Matrix rotation and translation  
0.94719418 0.31878448 0.03463582 -61.71232335  
-0.31322383 0.94294139 -0.11292639 89.12280109  
-0.06865873 0.09611446 0.99299949 -7.59439916  
Axis 0.31031144 0.15333597 -0.93818702  
Axis point 240.90564884 235.08878975 0.00000000  
Rotation angle (degrees) 19.68350894  
Shift along axis 1.64065725  
  

> combine #13,14,15,17,18

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '8'  

> color #31 #4f8f00ff

> color #31 #73fdffff

> select add #31

5168 atoms, 5164 bonds, 6 pseudobonds, 332 residues, 4 models selected  

> select subtract #30

2584 atoms, 2582 bonds, 3 pseudobonds, 166 residues, 2 models selected  

> view matrix models
> #31,0.93679,0.34915,0.022882,-68.26,-0.34379,0.93062,-0.12551,55.973,-0.065117,0.10971,0.99183,-17.389

> view matrix models
> #31,0.93679,0.34915,0.022882,-67.381,-0.34379,0.93062,-0.12551,57.118,-0.065117,0.10971,0.99183,-15.003

> ui mousemode right "move picked models"

> ui mousemode right "rotate selected models"

> view matrix models
> #31,0.85416,0.51997,-0.0069128,-83.91,-0.51465,0.84337,-0.15447,115.84,-0.074489,0.1355,0.98797,-18.23

> view matrix models
> #31,0.82409,0.55849,-0.094657,-68.903,-0.56633,0.81585,-0.11689,124.41,0.011944,0.14993,0.98862,-38.37

> ui mousemode right "translate selected models"

> view matrix models
> #31,0.82409,0.55849,-0.094657,-67.649,-0.56633,0.81585,-0.11689,126.22,0.011944,0.14993,0.98862,-37.144

> ui mousemode right "rotate selected models"

> view matrix models
> #31,0.90597,0.42307,-0.01514,-69.115,-0.42311,0.90368,-0.065893,68.228,-0.014196,0.066103,0.99771,-14.984

> ui mousemode right "translate selected models"

> view matrix models
> #31,0.90597,0.42307,-0.01514,-70.663,-0.42311,0.90368,-0.065893,64.726,-0.014196,0.066103,0.99771,-16.257

> fitmap sel inMap #8

Fit molecule combination (#31) to map postprocess_masked330_onepf.mrc (#8)
using 2584 atoms  
average map value = 0.01087, steps = 108  
shifted from previous position = 3.84  
rotated from previous position = 6 degrees  
atoms outside contour = 1650, contour level = 0.013465  
  
Position of combination (#31) relative to postprocess_masked330_onepf.mrc (#8)
coordinates:  
Matrix rotation and translation  
0.93906111 0.34356277 0.01135146 -64.20384039  
-0.33989292 0.93295036 -0.11864409 50.39987774  
-0.05135204 0.10755577 0.99287196 -13.93066859  
Axis 0.31301836 0.08676994 -0.94577507  
Axis point 108.72154288 203.83897060 0.00000000  
Rotation angle (degrees) 21.18130965  
Shift along axis -2.54850775  
  

> hide #!8 models

> show #!8 models

> show #!14 models

> select add #14

3035 atoms, 3032 bonds, 4 pseudobonds, 195 residues, 4 models selected  

> show #!13 models

> hide #!14 models

> select add #13

3131 atoms, 3127 bonds, 5 pseudobonds, 203 residues, 6 models selected  

> select subtract #14

2680 atoms, 2677 bonds, 4 pseudobonds, 174 residues, 4 models selected  

> select subtract #13

2584 atoms, 2582 bonds, 3 pseudobonds, 166 residues, 2 models selected  

> show #!15 models

> hide #!13 models

> select add #15

3034 atoms, 3031 bonds, 3 pseudobonds, 196 residues, 3 models selected  

> ui mousemode right "rotate selected models"

> select subtract #31

450 atoms, 449 bonds, 30 residues, 1 model selected  

> view matrix models
> #15,0.84068,0.5199,-0.15156,-34.799,-0.50486,0.85366,0.12796,102.22,0.1959,-0.031057,0.98013,-28.836

> undo

> view matrix models
> #15,0.91536,0.36828,-0.16274,-15.504,-0.37548,0.92671,-0.014764,90.463,0.14537,0.074619,0.98656,-42.307

> ui mousemode right "translate selected models"

> view matrix models
> #15,0.91536,0.36828,-0.16274,-19.806,-0.37548,0.92671,-0.014764,90.908,0.14537,0.074619,0.98656,-39.266

> view matrix models
> #15,0.91536,0.36828,-0.16274,-19.431,-0.37548,0.92671,-0.014764,90.586,0.14537,0.074619,0.98656,-40.223

> hide #!29 models

> view matrix models
> #15,0.91536,0.36828,-0.16274,-19.196,-0.37548,0.92671,-0.014764,90.447,0.14537,0.074619,0.98656,-40.891

> ui mousemode right "rotate selected models"

> view matrix models
> #15,0.9019,0.40197,-0.15807,-24.514,-0.3997,0.91542,0.047351,85.179,0.16373,0.020474,0.98629,-33.145

> view matrix models
> #15,0.92278,0.35915,-0.1396,-23.285,-0.35651,0.93324,0.044357,73.813,0.14621,0.0088357,0.98921,-27.957

> view matrix models
> #15,0.94056,0.32376,-0.10254,-26.668,-0.3208,0.94609,0.044612,64.269,0.11146,-0.0090642,0.99373,-18.49

> ui mousemode right "translate selected models"

> view matrix models
> #15,0.94056,0.32376,-0.10254,-30.001,-0.3208,0.94609,0.044612,65.511,0.11146,-0.0090642,0.99373,-17.181

> view matrix models
> #15,0.94056,0.32376,-0.10254,-29.924,-0.3208,0.94609,0.044612,65.455,0.11146,-0.0090642,0.99373,-17.205

> view matrix models
> #15,0.94056,0.32376,-0.10254,-30.702,-0.3208,0.94609,0.044612,66.082,0.11146,-0.0090642,0.99373,-18.252

> show #!29 models

> view matrix models
> #15,0.94056,0.32376,-0.10254,-30.985,-0.3208,0.94609,0.044612,64.895,0.11146,-0.0090642,0.99373,-18.08

> view matrix models
> #15,0.94056,0.32376,-0.10254,-30.807,-0.3208,0.94609,0.044612,64.368,0.11146,-0.0090642,0.99373,-18.508

> view matrix models
> #15,0.94056,0.32376,-0.10254,-31.101,-0.3208,0.94609,0.044612,64.873,0.11146,-0.0090642,0.99373,-18.105

> view matrix models
> #15,0.94056,0.32376,-0.10254,-31.171,-0.3208,0.94609,0.044612,64.319,0.11146,-0.0090642,0.99373,-18.506

> close #30-31

> hide #!29 models

> show #!29 models

> hide #!29 models

> close #29

> combine #13,14,15,17,18

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '8'  

> combine #13,14,15,17,18

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '8'  

> combine #13,14,15,17,18

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '8'  

> color #30 #73fcd6ff

> color #31 #fffb00ff

> select subtract #15

Nothing selected  

> select add #31

2584 atoms, 2582 bonds, 3 pseudobonds, 166 residues, 2 models selected  

> view matrix models
> #31,0.93679,0.34915,0.022882,-63.688,-0.34379,0.93062,-0.12551,101.65,-0.065117,0.10971,0.99183,-8.4868

> view matrix models
> #31,0.93679,0.34915,0.022882,-65.189,-0.34379,0.93062,-0.12551,101.18,-0.065117,0.10971,0.99183,-7.6541

> fitmap sel inMap #8

Fit molecule combination (#31) to map postprocess_masked330_onepf.mrc (#8)
using 2584 atoms  
average map value = 0.0137, steps = 76  
shifted from previous position = 3.78  
rotated from previous position = 4.9 degrees  
atoms outside contour = 1463, contour level = 0.013465  
  
Position of combination (#31) relative to postprocess_masked330_onepf.mrc (#8)
coordinates:  
Matrix rotation and translation  
0.96242794 0.26898400 0.03714923 -53.88391592  
-0.26305694 0.95752790 -0.11807354 77.16350417  
-0.06733131 0.10386492 0.99230972 -9.64230344  
Axis 0.37882039 0.17833484 -0.90812543  
Axis point 253.37054412 238.67962122 0.00000000  
Rotation angle (degrees) 17.03366943  
Shift along axis 2.10503599  
  

> select add #30

5168 atoms, 5164 bonds, 6 pseudobonds, 332 residues, 4 models selected  

> select subtract #31

2584 atoms, 2582 bonds, 3 pseudobonds, 166 residues, 2 models selected  

> view matrix models
> #30,0.93679,0.34915,0.022882,-73.179,-0.34379,0.93062,-0.12551,53.002,-0.065117,0.10971,0.99183,-11.821

> view matrix models
> #30,0.93679,0.34915,0.022882,-71.417,-0.34379,0.93062,-0.12551,53.356,-0.065117,0.10971,0.99183,-13.368

> fitmap sel inMap #8

Fit molecule combination (#30) to map postprocess_masked330_onepf.mrc (#8)
using 2584 atoms  
average map value = 0.0105, steps = 104  
shifted from previous position = 6.82  
rotated from previous position = 7.16 degrees  
atoms outside contour = 1733, contour level = 0.013465  
  
Position of combination (#30) relative to postprocess_masked330_onepf.mrc (#8)
coordinates:  
Matrix rotation and translation  
0.90383259 0.42370816 -0.05964936 -58.51606967  
-0.42734719 0.90087496 -0.07614907 65.75524177  
0.02147163 0.09431700 0.99531064 -25.53239206  
Axis 0.19554643 -0.09305617 -0.97626950  
Axis point 116.51572139 167.94879785 0.00000000  
Rotation angle (degrees) 25.84073691  
Shift along axis 7.36495629  
  

> view matrix models
> #30,0.90386,0.42376,-0.05881,-56.66,-0.42732,0.90088,-0.076216,62.013,0.020684,0.094019,0.99536,-24.605

> view matrix models
> #30,0.90386,0.42376,-0.05881,-62.521,-0.42732,0.90088,-0.076216,67.035,0.020684,0.094019,0.99536,-24.977

> view matrix models
> #30,0.90386,0.42376,-0.05881,-62.566,-0.42732,0.90088,-0.076216,66.975,0.020684,0.094019,0.99536,-24.965

> fitmap sel inMap #8

Fit molecule combination (#30) to map postprocess_masked330_onepf.mrc (#8)
using 2584 atoms  
average map value = 0.0105, steps = 56  
shifted from previous position = 3.95  
rotated from previous position = 0.00463 degrees  
atoms outside contour = 1734, contour level = 0.013465  
  
Position of combination (#30) relative to postprocess_masked330_onepf.mrc (#8)
coordinates:  
Matrix rotation and translation  
0.90385203 0.42366592 -0.05965485 -58.50966574  
-0.42730425 0.90090065 -0.07608616 65.72732695  
0.02150798 0.09426140 0.99531512 -25.52860500  
Axis 0.19543344 -0.09311509 -0.97628651  
Axis point 116.47693942 167.93584813 0.00000000  
Rotation angle (degrees) 25.83747664  
Shift along axis 7.36828130  
  

> view matrix models
> #30,0.90388,0.42372,-0.058815,-62.833,-0.42728,0.90091,-0.076153,66.371,0.02072,0.093963,0.99536,-25.131

> view matrix models
> #30,0.90388,0.42372,-0.058815,-61.91,-0.42728,0.90091,-0.076153,66.948,0.02072,0.093963,0.99536,-25.257

> combine #13,14,15,17,18

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '8'  

> color #32 #ff40ffff

> select add #32

5168 atoms, 5164 bonds, 6 pseudobonds, 332 residues, 4 models selected  

> select subtract #30

2584 atoms, 2582 bonds, 3 pseudobonds, 166 residues, 2 models selected  

> view matrix models
> #32,0.93679,0.34915,0.022882,-71.233,-0.34379,0.93062,-0.12551,31.398,-0.065117,0.10971,0.99183,-18.788

> view matrix models
> #32,0.93679,0.34915,0.022882,-71.905,-0.34379,0.93062,-0.12551,32.723,-0.065117,0.10971,0.99183,-12.806

> fitmap sel inMap #8

Fit molecule combination (#32) to map postprocess_masked330_onepf.mrc (#8)
using 2584 atoms  
average map value = 0.007417, steps = 248  
shifted from previous position = 6.6  
rotated from previous position = 13.1 degrees  
atoms outside contour = 1972, contour level = 0.013465  
  
Position of combination (#32) relative to postprocess_masked330_onepf.mrc (#8)
coordinates:  
Matrix rotation and translation  
0.84793356 0.52248716 -0.08953125 -67.52617584  
-0.52912700 0.84445592 -0.08317945 75.17707792  
0.03214499 0.11790405 0.99250458 -32.02887516  
Axis 0.18661031 -0.11291847 -0.97592316  
Axis point 96.89786555 161.07285308 0.00000000  
Rotation angle (degrees) 32.60057113  
Shift along axis 10.16775997  
  

> view matrix models
> #32,0.84798,0.52256,-0.088694,-70.705,-0.5291,0.84447,-0.083247,78.208,0.031397,0.11752,0.99257,-31.208

> view matrix models
> #32,0.84798,0.52256,-0.088694,-70.468,-0.5291,0.84447,-0.083247,78.813,0.031397,0.11752,0.99257,-31.852

> view matrix models
> #32,0.84798,0.52256,-0.088694,-70.915,-0.5291,0.84447,-0.083247,79.238,0.031397,0.11752,0.99257,-31.502

> ui windowfill toggle

[Repeated 1 time(s)]

> hide #!32 models

> hide #!31 models

> hide #!30 models

> hide #!29 models

> show #!32 models

> show #!31 models

> show #!30 models

> show #!29 models

> hide #!32 models

> hide #!31 models

> hide #!30 models

> hide #!29 models

> select subtract #32

Nothing selected  

> select add #15

450 atoms, 449 bonds, 30 residues, 1 model selected  

> view matrix models
> #15,0.94056,0.32376,-0.10254,-30.711,-0.3208,0.94609,0.044612,68.566,0.11146,-0.0090642,0.99373,-19.008

> show #!30 models

> hide #!30 models

> show #!14 models

> select add #14

901 atoms, 899 bonds, 1 pseudobond, 59 residues, 3 models selected  

> select subtract #15

451 atoms, 450 bonds, 1 pseudobond, 29 residues, 2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #14,0.88001,0.42518,-0.21166,-20.504,-0.33244,0.86969,0.36486,-8.3943,0.33921,-0.25072,0.90668,5.6314

> ui mousemode right "translate selected models"

> view matrix models
> #14,0.88001,0.42518,-0.21166,-25.847,-0.33244,0.86969,0.36486,-4.5312,0.33921,-0.25072,0.90668,6.2681

> ui mousemode right "rotate selected models"

> view matrix models
> #14,0.84971,0.50639,-0.14684,-49.818,-0.40191,0.80234,0.44126,8.8752,0.34127,-0.31593,0.88528,23.991

> ui mousemode right "translate selected models"

> view matrix models
> #14,0.84971,0.50639,-0.14684,-51.173,-0.40191,0.80234,0.44126,8.5088,0.34127,-0.31593,0.88528,24.728

> ui mousemode right "rotate selected models"

> view matrix models
> #14,0.83927,0.53383,-0.10322,-63.389,-0.42543,0.76295,0.48673,12.867,0.33858,-0.36459,0.86743,39.137

> select add #15

901 atoms, 899 bonds, 1 pseudobond, 59 residues, 3 models selected  

> select subtract #14

450 atoms, 449 bonds, 30 residues, 1 model selected  

> view matrix models
> #15,0.94772,0.30064,-0.10698,-26.419,-0.3038,0.95263,-0.014209,75.553,0.097641,0.045967,0.99416,-27.84

> ui mousemode right "translate selected models"

> view matrix models
> #15,0.94772,0.30064,-0.10698,-25.978,-0.3038,0.95263,-0.014209,75.325,0.097641,0.045967,0.99416,-28.909

> view matrix models
> #15,0.94772,0.30064,-0.10698,-25.796,-0.3038,0.95263,-0.014209,75.202,0.097641,0.045967,0.99416,-29.677

> view matrix models
> #15,0.94772,0.30064,-0.10698,-25.22,-0.3038,0.95263,-0.014209,75.315,0.097641,0.045967,0.99416,-29.378

> select add #14

901 atoms, 899 bonds, 1 pseudobond, 59 residues, 3 models selected  

> select subtract #15

451 atoms, 450 bonds, 1 pseudobond, 29 residues, 2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #14,0.89542,0.43806,-0.079483,-58.257,-0.32999,0.77286,0.54203,-18.426,0.29887,-0.45912,0.83659,73.109

> view matrix models
> #14,0.89146,0.44459,-0.087441,-57.366,-0.33082,0.7705,0.54488,-18.302,0.30962,-0.45681,0.83394,71.027

> ui mousemode right "translate selected models"

> view matrix models
> #14,0.89146,0.44459,-0.087441,-57.2,-0.33082,0.7705,0.54488,-18.845,0.30962,-0.45681,0.83394,71.886

> view matrix models
> #14,0.89146,0.44459,-0.087441,-57.03,-0.33082,0.7705,0.54488,-18.859,0.30962,-0.45681,0.83394,72.14

> view matrix models
> #14,0.89146,0.44459,-0.087441,-57.585,-0.33082,0.7705,0.54488,-18.498,0.30962,-0.45681,0.83394,72.252

> combine #13,14,15,17,18

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '8'  

> hide #!14 models

> hide #!15 models

> select subtract #14

Nothing selected  

> combine #13,14,15,17,18

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '8'  

> combine #13,14,15,17,18

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '8'  

> color #34 #ff85ffff

> color #35 #fffc79ff

> select add #34

2584 atoms, 2582 bonds, 3 pseudobonds, 166 residues, 2 models selected  

> view matrix models
> #34,0.93679,0.34915,0.022882,-63.948,-0.34379,0.93062,-0.12551,101.07,-0.065117,0.10971,0.99183,-8.8311

> fitmap sel inMap #8

Fit molecule combination (#34) to map postprocess_masked330_onepf.mrc (#8)
using 2584 atoms  
average map value = 0.01309, steps = 68  
shifted from previous position = 2.75  
rotated from previous position = 4.67 degrees  
atoms outside contour = 1525, contour level = 0.013465  
  
Position of combination (#34) relative to postprocess_masked330_onepf.mrc (#8)
coordinates:  
Matrix rotation and translation  
0.95788371 0.28066574 0.06070867 -61.42695670  
-0.27233693 0.95495467 -0.11787358 80.07796963  
-0.09105710 0.09637597 0.99117116 -2.89821379  
Axis 0.34998581 0.24791589 -0.90335355  
Axis point 250.53589003 257.66891761 0.00000000  
Rotation angle (degrees) 17.82334309  
Shift along axis 0.97214953  
  

> view matrix models
> #34,0.95782,0.28071,0.061546,-60.32,-0.2723,0.95496,-0.11794,78.858,-0.091881,0.096202,0.99111,-4.3242

> view matrix models
> #34,0.95782,0.28071,0.061546,-59.97,-0.2723,0.95496,-0.11794,78.81,-0.091881,0.096202,0.99111,-4.2979

> view matrix models
> #34,0.95782,0.28071,0.061546,-59.123,-0.2723,0.95496,-0.11794,77.645,-0.091881,0.096202,0.99111,-5.7533

> view matrix models
> #34,0.95782,0.28071,0.061546,-58.98,-0.2723,0.95496,-0.11794,78.65,-0.091881,0.096202,0.99111,-2.2808

> hide #!34 models

> hide #!35 models

> show #!34 models

> hide #!34 models

> hide #!33 models

> select subtract #34

Nothing selected  

> show #!24 models

> hide #!24 models

> show #!13 models

> show #!14 models

> show #!15 models

> show #!17 models

> show #!18 models

> select add #15

450 atoms, 449 bonds, 30 residues, 1 model selected  

> view matrix models
> #15,0.94772,0.30064,-0.10698,-26.089,-0.3038,0.95263,-0.014209,75.894,0.097641,0.045967,0.99416,-25.22

> view matrix models
> #15,0.94772,0.30064,-0.10698,-26.362,-0.3038,0.95263,-0.014209,75.63,0.097641,0.045967,0.99416,-25.834

> view matrix models
> #15,0.94772,0.30064,-0.10698,-26.488,-0.3038,0.95263,-0.014209,75.411,0.097641,0.045967,0.99416,-26.476

> ui mousemode right "rotate selected models"

> view matrix models
> #15,0.94016,0.32447,-0.10402,-30.557,-0.32093,0.9458,0.049655,67.515,0.1145,-0.013299,0.99333,-17.271

> view matrix models
> #15,0.94158,0.32353,-0.093578,-32.692,-0.32003,0.94605,0.050611,67.103,0.1049,-0.017707,0.99432,-14.718

> ui mousemode right "translate selected models"

> view matrix models
> #15,0.94158,0.32353,-0.093578,-33.233,-0.32003,0.94605,0.050611,67.312,0.1049,-0.017707,0.99432,-14.081

> hide #!8 models

> show #!8 models

> ui mousemode right "rotate selected models"

> view matrix models
> #15,0.98106,0.18292,-0.06379,-17.553,-0.18852,0.97726,-0.097062,64.786,0.044585,0.10725,0.99323,-28.187

> view matrix models
> #15,0.96664,0.24357,-0.079264,-24.298,-0.24682,0.96846,-0.034087,65.354,0.068461,0.052513,0.99627,-22.026

> view matrix models
> #15,0.99457,0.051063,-0.090684,12.456,-0.036153,0.98661,0.15905,-16.789,0.097591,-0.1549,0.9831,17.932

> view matrix models
> #15,0.94647,-0.095298,-0.3084,94.87,0.03881,0.98209,-0.18437,37.482,0.32045,0.16253,0.93322,-80.602

> ui mousemode right "translate selected models"

> view matrix models
> #15,0.94647,-0.095298,-0.3084,95.112,0.03881,0.98209,-0.18437,36.746,0.32045,0.16253,0.93322,-82.273

> view matrix models
> #15,0.94647,-0.095298,-0.3084,94.558,0.03881,0.98209,-0.18437,36.1,0.32045,0.16253,0.93322,-81.104

> view matrix models
> #15,0.94647,-0.095298,-0.3084,94.731,0.03881,0.98209,-0.18437,36.381,0.32045,0.16253,0.93322,-81.004

> ui mousemode right "rotate selected models"

> view matrix models
> #15,0.945,-0.079199,-0.31732,93.438,0.02666,0.98566,-0.16661,34.467,0.32597,0.14899,0.93357,-79.326

> select clear

> combine #13,14,15,17,18

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '8'  

> combine #13,14,15,17,18

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '8'  

> combine #13,14,15,17,18

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '8'  

> color #37 #8efa00ff

> color #38 #fffc79ff

> select add #37

2584 atoms, 2582 bonds, 3 pseudobonds, 166 residues, 2 models selected  

> view matrix models
> #37,0.9385,0.34222,-0.045796,-49.568,-0.31704,0.80162,-0.50684,180.14,-0.13674,0.49019,0.86082,-56.619

> undo

> ui mousemode right "translate selected models"

> view matrix models
> #37,0.93679,0.34915,0.022882,-61.476,-0.34379,0.93062,-0.12551,98.453,-0.065117,0.10971,0.99183,-5.2765

> fitmap sel inMap #8

Fit molecule combination (#37) to map postprocess_masked330_onepf.mrc (#8)
using 2584 atoms  
average map value = 0.01285, steps = 92  
shifted from previous position = 6.68  
rotated from previous position = 4.42 degrees  
atoms outside contour = 1504, contour level = 0.013465  
  
Position of combination (#37) relative to postprocess_masked330_onepf.mrc (#8)
coordinates:  
Matrix rotation and translation  
0.93230159 0.35691343 0.05853671 -72.58255923  
-0.35368843 0.93351547 -0.05876528 88.20520272  
-0.07561905 0.03408321 0.99655411 7.55297659  
Axis 0.12734829 0.18400415 -0.97464090  
Axis point 204.10263520 241.94180690 0.00000000  
Rotation angle (degrees) 21.37961317  
Shift along axis -0.37458156  
  

> close #37-38

> hide #!36 models

> select add #18

1330 atoms, 1329 bonds, 1 pseudobond, 84 residues, 2 models selected  

> select subtract #18

Nothing selected  

> select add #15

450 atoms, 449 bonds, 30 residues, 1 model selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #15,0.92903,0.12514,-0.34819,60.28,-0.17284,0.97886,-0.10936,62.777,0.32714,0.16178,0.93102,-81.699

> ui mousemode right "translate selected models"

> view matrix models
> #15,0.92903,0.12514,-0.34819,60.883,-0.17284,0.97886,-0.10936,64.339,0.32714,0.16178,0.93102,-81.466

> view matrix models
> #15,0.92903,0.12514,-0.34819,60.725,-0.17284,0.97886,-0.10936,63.814,0.32714,0.16178,0.93102,-82.594

> view matrix models
> #15,0.92903,0.12514,-0.34819,61.472,-0.17284,0.97886,-0.10936,64.619,0.32714,0.16178,0.93102,-82.965

> combine #13,14,15,17,18

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '8'  

> combine #13,14,15,17,18

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '8'  

> select subtract #15

Nothing selected  

> color #37 #9437ffff

> color #38 #fffc79ff

> select add #37

2584 atoms, 2582 bonds, 3 pseudobonds, 166 residues, 2 models selected  

> view matrix models
> #37,0.93679,0.34915,0.022882,-64.653,-0.34379,0.93062,-0.12551,101.14,-0.065117,0.10971,0.99183,-10.958

> fitmap sel inMap #8

Fit molecule combination (#37) to map postprocess_masked330_onepf.mrc (#8)
using 2584 atoms  
average map value = 0.01317, steps = 76  
shifted from previous position = 0.612  
rotated from previous position = 5.31 degrees  
atoms outside contour = 1502, contour level = 0.013465  
  
Position of combination (#37) relative to postprocess_masked330_onepf.mrc (#8)
coordinates:  
Matrix rotation and translation  
0.94687968 0.31403786 0.06927543 -68.41121818  
-0.31085182 0.94897655 -0.05305337 75.22393710  
-0.08240153 0.02870076 0.99618585 10.01633362  
Axis 0.12612283 0.23399339 -0.96402289  
Axis point 201.20792111 251.60467556 0.00000000  
Rotation angle (degrees) 18.91137332  
Shift along axis -0.68228664  
  

> select subtract #37

Nothing selected  

> select add #38

2584 atoms, 2582 bonds, 3 pseudobonds, 166 residues, 2 models selected  

> view matrix models
> #38,0.93679,0.34915,0.022882,-68.724,-0.34379,0.93062,-0.12551,56.67,-0.065117,0.10971,0.99183,-20.653

> fitmap sel inMap #8

Fit molecule combination (#38) to map postprocess_masked330_onepf.mrc (#8)
using 2584 atoms  
average map value = 0.01151, steps = 120  
shifted from previous position = 10.1  
rotated from previous position = 5.61 degrees  
atoms outside contour = 1607, contour level = 0.013465  
  
Position of combination (#38) relative to postprocess_masked330_onepf.mrc (#8)
coordinates:  
Matrix rotation and translation  
0.92817645 0.37094196 -0.02984186 -58.64119919  
-0.36895607 0.90680286 -0.20391173 80.25033291  
-0.04857873 0.20027640 0.97853435 -32.58645977  
Axis 0.47928891 0.02221829 -0.87737591  
Axis point 168.45837917 193.63481182 0.00000000  
Rotation angle (degrees) 24.93905224  
Shift along axis 2.26752362  
  

> hide #!8 models

> show #!8 models

> hide #!13-20 target m

> hide #!8 models

> show #!9 models

> select subtract #38

Nothing selected  

> hide #!38 models

> hide #!37 models

> hide #!9 models

> show #!18 models

> show #!17 models

> show #!15 models

> show #!14 models

> show #!13 models

> hide #!13-20 target m

> show #!36 models

> show #!37 models

> show #!38 models

> combine #13,14,15,17,18

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '8'  

> color #39 #00fdffff

> select add #39

2584 atoms, 2582 bonds, 3 pseudobonds, 166 residues, 2 models selected  

> hide #!36 models

> show #!36 models

> hide #!36 models

> close #36-39

> combine #13,14,15,17,18

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '8'  

> combine #13,14,15,17,18

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '8'  

> combine #13,14,15,17,18

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '8'  

> combine #13,14,15,17,18

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '8'  

> color #37 #73fdffff

> color #38 #76d6ffff

> color #38 #73fa79ff

> color #39 #fffc79ff

> show #!8 models

> select add #36

2584 atoms, 2582 bonds, 3 pseudobonds, 166 residues, 2 models selected  

> select add #37

5168 atoms, 5164 bonds, 6 pseudobonds, 332 residues, 4 models selected  

> select subtract #36

2584 atoms, 2582 bonds, 3 pseudobonds, 166 residues, 2 models selected  

> view matrix models
> #37,0.93679,0.34915,0.022882,-64.395,-0.34379,0.93062,-0.12551,101.94,-0.065117,0.10971,0.99183,-10.433

> fitmap sel inMap #8

Fit molecule combination (#37) to map postprocess_masked330_onepf.mrc (#8)
using 2584 atoms  
average map value = 0.01317, steps = 92  
shifted from previous position = 1.57  
rotated from previous position = 5.3 degrees  
atoms outside contour = 1499, contour level = 0.013465  
  
Position of combination (#37) relative to postprocess_masked330_onepf.mrc (#8)
coordinates:  
Matrix rotation and translation  
0.94693797 0.31397208 0.06877509 -68.31894225  
-0.31080190 0.94899393 -0.05303487 75.17806955  
-0.08191861 0.02884531 0.99622151 9.84988127  
Axis 0.12638066 0.23259314 -0.96432793  
Axis point 201.12292272 251.32549683 0.00000000  
Rotation angle (degrees) 18.90153083  
Shift along axis -0.64680544  
  

> select add #38

5168 atoms, 5164 bonds, 6 pseudobonds, 332 residues, 4 models selected  

> select subtract #37

2584 atoms, 2582 bonds, 3 pseudobonds, 166 residues, 2 models selected  

> view matrix models
> #38,0.93679,0.34915,0.022882,-71.514,-0.34379,0.93062,-0.12551,52.621,-0.065117,0.10971,0.99183,-11.498

> fitmap sel inMap #8

Fit molecule combination (#38) to map postprocess_masked330_onepf.mrc (#8)
using 2584 atoms  
average map value = 0.01151, steps = 112  
shifted from previous position = 5.39  
rotated from previous position = 5.61 degrees  
atoms outside contour = 1611, contour level = 0.013465  
  
Position of combination (#38) relative to postprocess_masked330_onepf.mrc (#8)
coordinates:  
Matrix rotation and translation  
0.92816793 0.37096041 -0.02987753 -58.63312168  
-0.36898453 0.90680628 -0.20384502 80.22859145  
-0.04852530 0.20022676 0.97854716 -32.60412219  
Axis 0.47916037 0.02211308 -0.87744877  
Axis point 168.39146606 193.61982832 0.00000000  
Rotation angle (degrees) 24.93852873  
Shift along axis 2.28787963  
  

> select add #39

5168 atoms, 5164 bonds, 6 pseudobonds, 332 residues, 4 models selected  

> select subtract #38

2584 atoms, 2582 bonds, 3 pseudobonds, 166 residues, 2 models selected  

> view matrix models
> #39,0.93679,0.34915,0.022882,-76.412,-0.34379,0.93062,-0.12551,29.436,-0.065117,0.10971,0.99183,-11.845

> fitmap sel inMap #8

Fit molecule combination (#39) to map postprocess_masked330_onepf.mrc (#8)
using 2584 atoms  
average map value = 0.007829, steps = 124  
shifted from previous position = 8.29  
rotated from previous position = 9.76 degrees  
atoms outside contour = 1941, contour level = 0.013465  
  
Position of combination (#39) relative to postprocess_masked330_onepf.mrc (#8)
coordinates:  
Matrix rotation and translation  
0.92112012 0.37937149 -0.08726396 -49.48445736  
-0.38893321 0.88744273 -0.24733855 71.59344644  
-0.01639143 0.26176837 0.96499152 -50.10926578  
Axis 0.55074648 -0.07666915 -0.83114389  
Axis point 136.14922419 171.67506745 0.00000000  
Rotation angle (degrees) 27.52897768  
Shift along axis 8.90561058  
  

> combine #13,14,15,17,18

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '8'  

> color #40 #0096ffff

> color #40 #0433ffff

> select add #40

5168 atoms, 5164 bonds, 6 pseudobonds, 332 residues, 4 models selected  

> select subtract #39

2584 atoms, 2582 bonds, 3 pseudobonds, 166 residues, 2 models selected  

> view matrix models
> #40,0.93679,0.34915,0.022882,-63.113,-0.34379,0.93062,-0.12551,123.4,-0.065117,0.10971,0.99183,-9.1624

> fitmap sel inMap #8

Fit molecule combination (#40) to map postprocess_masked330_onepf.mrc (#8)
using 2584 atoms  
average map value = 0.01033, steps = 108  
shifted from previous position = 9.5  
rotated from previous position = 8.75 degrees  
atoms outside contour = 1773, contour level = 0.013465  
  
Position of combination (#40) relative to postprocess_masked330_onepf.mrc (#8)
coordinates:  
Matrix rotation and translation  
0.97293927 0.21693771 0.07954376 -60.18334966  
-0.21037641 0.97406339 -0.08332031 80.49147095  
-0.09555598 0.06433147 0.99334310 3.83664779  
Axis 0.30454457 0.36115837 -0.88137236  
Axis point 329.42907006 328.84754176 0.00000000  
Rotation angle (degrees) 14.02906448  
Shift along axis 7.36014107  
  

> view matrix models
> #40,0.97287,0.21696,0.080382,-52.002,-0.21034,0.97407,-0.083382,78.728,-0.096388,0.064212,0.99327,4.8304

> view matrix models
> #40,0.97287,0.21696,0.080382,-52.044,-0.21034,0.97407,-0.083382,78.716,-0.096388,0.064212,0.99327,5.4916

> view matrix models
> #40,0.97287,0.21696,0.080382,-51.753,-0.21034,0.97407,-0.083382,79.391,-0.096388,0.064212,0.99327,4.9224

> view matrix models
> #40,0.97287,0.21696,0.080382,-51.756,-0.21034,0.97407,-0.083382,79.236,-0.096388,0.064212,0.99327,4.9567

> view matrix models
> #40,0.97287,0.21696,0.080382,-51.796,-0.21034,0.97407,-0.083382,79.256,-0.096388,0.064212,0.99327,5.0225

> view matrix models
> #40,0.97287,0.21696,0.080382,-50.784,-0.21034,0.97407,-0.083382,78.956,-0.096388,0.064212,0.99327,4.0891

> view matrix models
> #40,0.97287,0.21696,0.080382,-50.014,-0.21034,0.97407,-0.083382,78.606,-0.096388,0.064212,0.99327,4.058

> view matrix models
> #40,0.97287,0.21696,0.080382,-50.709,-0.21034,0.97407,-0.083382,77.569,-0.096388,0.064212,0.99327,3.6748

> view matrix models
> #40,0.97287,0.21696,0.080382,-51.056,-0.21034,0.97407,-0.083382,77.401,-0.096388,0.064212,0.99327,5.4984

> hide #!36 models

> hide #!37 models

> hide #!38 models

> show #!38 models

> color #38 #ff2f92ff

> show #!37 models

> hide #!37 models

> show #!37 models

> hide #!40 models

> hide #!39 models

> hide #!38 models

> hide #!37 models

> show #!13 models

> show #!14 models

> show #!15 models

> show #!17 models

> show #!18 models

> select add #13

2680 atoms, 2677 bonds, 4 pseudobonds, 174 residues, 4 models selected  

> select subtract #13

2584 atoms, 2582 bonds, 3 pseudobonds, 166 residues, 2 models selected  

> select add #14

3035 atoms, 3032 bonds, 4 pseudobonds, 195 residues, 4 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #14,0.93636,0.14269,-0.32072,43.254,-0.01992,0.93378,0.35729,-78.293,0.35047,-0.32816,0.8772,28.341,#40,0.98399,-0.16665,0.063238,16.233,0.17553,0.96765,-0.1812,21.392,-0.030994,0.1894,0.98141,-26.686

> ui mousemode right "translate selected models"

> view matrix models
> #14,0.93636,0.14269,-0.32072,49.559,-0.01992,0.93378,0.35729,-82.704,0.35047,-0.32816,0.8772,25.475,#40,0.98399,-0.16665,0.063238,22.538,0.17553,0.96765,-0.1812,16.981,-0.030994,0.1894,0.98141,-29.551

> ui mousemode right "rotate selected models"

> view matrix models
> #14,0.93867,0.26555,-0.21998,3.4025,-0.15307,0.89251,0.42426,-60.704,0.30899,-0.36456,0.87842,41.152,#40,0.9965,-0.0094951,0.083093,-10.946,0.023032,0.98627,-0.1635,40.487,-0.0804,0.16484,0.98304,-15.853

> ui mousemode right "translate selected models"

> view matrix models
> #14,0.93867,0.26555,-0.21998,0.26406,-0.15307,0.89251,0.42426,-59.365,0.30899,-0.36456,0.87842,42.17,#40,0.9965,-0.0094951,0.083093,-14.085,0.023032,0.98627,-0.1635,41.827,-0.0804,0.16484,0.98304,-14.835

> show #!36 models

> hide #!36 models

> show #!37 models

> hide #!37 models

> show #!38 models

> hide #!38 models

> show #!38 models

> show #!39 models

> show #!40 models

> show #!37 models

> hide #!40 models

> hide #!39 models

> hide #!38 models

> hide #!37 models

> select subtract #40

451 atoms, 450 bonds, 1 pseudobond, 29 residues, 2 models selected  

> select add #40

3035 atoms, 3032 bonds, 4 pseudobonds, 195 residues, 4 models selected  

> select subtract #40

451 atoms, 450 bonds, 1 pseudobond, 29 residues, 2 models selected  

> hide #!11-19 target m

> hide #!8 models

> show #!9 models

> hide #!9 models

> show #!24 models

> show #!25 models

> hide #!25 models

> hide #!24 models

> show #!13 models

> show #!14 models

> show #!15 models

> show #!17 models

> show #!18 models

> combine #13,14,15,17,18

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '8'  

> combine #13,14,15,17,18

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '8'  

> combine #13,14,15,17,18

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '8'  

> combine #13,14,15,17,18

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '8'  

> close #44

> color #41 #00f900ff

> hide #!42 models

> show #!42 models

> color #42 #fffc79ff

> color #43 #ff8ad8ff

> select subtract #14

Nothing selected  

> show #!8 models

> select add #41

2584 atoms, 2582 bonds, 3 pseudobonds, 166 residues, 2 models selected  

> view matrix models
> #41,0.93679,0.34915,0.022882,-62.198,-0.34379,0.93062,-0.12551,100.29,-0.065117,0.10971,0.99183,-8.9707

> fitmap sel inMap #8

Fit molecule combination (#41) to map postprocess_masked330_onepf.mrc (#8)
using 2584 atoms  
average map value = 0.0132, steps = 92  
shifted from previous position = 3.42  
rotated from previous position = 8.25 degrees  
atoms outside contour = 1501, contour level = 0.013465  
  
Position of combination (#41) relative to postprocess_masked330_onepf.mrc (#8)
coordinates:  
Matrix rotation and translation  
0.97635364 0.21617287 0.00169326 -37.13601339  
-0.21327494 0.96448556 -0.15582492 73.25731020  
-0.03531825 0.15177909 0.98778324 -26.43547376  
Axis 0.58088610 0.06989334 -0.81097858  
Axis point 305.45192334 218.60154493 0.00000000  
Rotation angle (degrees) 15.35336768  
Shift along axis 4.98700712  
  

> select add #42

5168 atoms, 5164 bonds, 6 pseudobonds, 332 residues, 4 models selected  

> select subtract #41

2584 atoms, 2582 bonds, 3 pseudobonds, 166 residues, 2 models selected  

> view matrix models
> #42,0.93679,0.34915,0.022882,-71.442,-0.34379,0.93062,-0.12551,50.689,-0.065117,0.10971,0.99183,-14.086

> fitmap sel inMap #8

Fit molecule combination (#42) to map postprocess_masked330_onepf.mrc (#8)
using 2584 atoms  
average map value = 0.0108, steps = 108  
shifted from previous position = 7.03  
rotated from previous position = 7.88 degrees  
atoms outside contour = 1670, contour level = 0.013465  
  
Position of combination (#42) relative to postprocess_masked330_onepf.mrc (#8)
coordinates:  
Matrix rotation and translation  
0.94102440 0.33473095 -0.04927756 -48.54200188  
-0.33647530 0.91059776 -0.23999186 80.39429404  
-0.03546067 0.24241888 0.96952340 -42.85277972  
Axis 0.58353957 -0.01671335 -0.81191270  
Axis point 189.41356021 187.32114179 0.00000000  
Rotation angle (degrees) 24.41537437  
Shift along axis 5.12287935  
  

> select add #43

5168 atoms, 5164 bonds, 6 pseudobonds, 332 residues, 4 models selected  

> select subtract #42

2584 atoms, 2582 bonds, 3 pseudobonds, 166 residues, 2 models selected  

> view matrix models
> #43,0.93679,0.34915,0.022882,-75.923,-0.34379,0.93062,-0.12551,29.386,-0.065117,0.10971,0.99183,-16.303

> fitmap sel inMap #8

Fit molecule combination (#43) to map postprocess_masked330_onepf.mrc (#8)
using 2584 atoms  
average map value = 0.007662, steps = 132  
shifted from previous position = 9.08  
rotated from previous position = 8.87 degrees  
atoms outside contour = 1947, contour level = 0.013465  
  
Position of combination (#43) relative to postprocess_masked330_onepf.mrc (#8)
coordinates:  
Matrix rotation and translation  
0.91401014 0.39897511 -0.07351416 -55.80544839  
-0.40480024 0.88490039 -0.23040846 72.00192839  
-0.02687453 0.24035422 0.97031315 -43.99953293  
Axis 0.50475479 -0.05000731 -0.86181313  
Axis point 128.75632904 175.40386142 0.00000000  
Rotation angle (degrees) 27.79620799  
Shift along axis 6.15068475  
  

> close #41-43

> select add #14

451 atoms, 450 bonds, 1 pseudobond, 29 residues, 2 models selected  

> select subtract #14

Nothing selected  

> select add #15

450 atoms, 449 bonds, 30 residues, 1 model selected  

> ui mousemode right "translate selected models"

> view matrix models
> #15,0.92903,0.12514,-0.34819,60.8,-0.17284,0.97886,-0.10936,64.279,0.32714,0.16178,0.93102,-80.513

> view matrix models
> #15,0.92903,0.12514,-0.34819,60.594,-0.17284,0.97886,-0.10936,65.221,0.32714,0.16178,0.93102,-80.761

> view matrix models
> #15,0.92903,0.12514,-0.34819,60.478,-0.17284,0.97886,-0.10936,64.823,0.32714,0.16178,0.93102,-80.684

> select add #14

901 atoms, 899 bonds, 1 pseudobond, 59 residues, 3 models selected  

> select subtract #15

451 atoms, 450 bonds, 1 pseudobond, 29 residues, 2 models selected  

> view matrix models
> #14,0.93867,0.26555,-0.21998,1.3452,-0.15307,0.89251,0.42426,-59.615,0.30899,-0.36456,0.87842,42.024

> view matrix models
> #14,0.93867,0.26555,-0.21998,3.0244,-0.15307,0.89251,0.42426,-60.011,0.30899,-0.36456,0.87842,42.009

> view matrix models
> #14,0.93867,0.26555,-0.21998,2.1975,-0.15307,0.89251,0.42426,-59.284,0.30899,-0.36456,0.87842,42.688

> view matrix models
> #14,0.93867,0.26555,-0.21998,2.6663,-0.15307,0.89251,0.42426,-59,0.30899,-0.36456,0.87842,43.865

> view matrix models
> #14,0.93867,0.26555,-0.21998,1.3142,-0.15307,0.89251,0.42426,-59.117,0.30899,-0.36456,0.87842,43.944

> view matrix models
> #14,0.93867,0.26555,-0.21998,0.52128,-0.15307,0.89251,0.42426,-58.855,0.30899,-0.36456,0.87842,43.521

> ui mousemode right "rotate selected models"

> view matrix models
> #14,0.93759,0.19788,-0.28596,27.913,-0.13627,0.96561,0.22141,-39.057,0.31994,-0.16863,0.93231,-11.081

> ui mousemode right "rotate selected models"

> ui mousemode right "translate selected models"

> view matrix models
> #14,0.93759,0.19788,-0.28596,27.706,-0.13627,0.96561,0.22141,-45.169,0.31994,-0.16863,0.93231,-13.652

> view matrix models
> #14,0.93759,0.19788,-0.28596,28.722,-0.13627,0.96561,0.22141,-40.786,0.31994,-0.16863,0.93231,-12.696

> view matrix models
> #14,0.93759,0.19788,-0.28596,29.073,-0.13627,0.96561,0.22141,-41.349,0.31994,-0.16863,0.93231,-12.85

> view matrix models
> #14,0.93759,0.19788,-0.28596,28.038,-0.13627,0.96561,0.22141,-40.917,0.31994,-0.16863,0.93231,-13.236

> view matrix models
> #14,0.93759,0.19788,-0.28596,28.997,-0.13627,0.96561,0.22141,-41.359,0.31994,-0.16863,0.93231,-13.385

> view matrix models
> #14,0.93759,0.19788,-0.28596,30.25,-0.13627,0.96561,0.22141,-40.769,0.31994,-0.16863,0.93231,-13.408

> view matrix models
> #14,0.93759,0.19788,-0.28596,29.938,-0.13627,0.96561,0.22141,-40.65,0.31994,-0.16863,0.93231,-13.487

> view matrix models
> #14,0.93759,0.19788,-0.28596,29.46,-0.13627,0.96561,0.22141,-41.115,0.31994,-0.16863,0.93231,-13.567

> view matrix models
> #14,0.93759,0.19788,-0.28596,28.678,-0.13627,0.96561,0.22141,-42.709,0.31994,-0.16863,0.93231,-13.582

> view matrix models
> #14,0.93759,0.19788,-0.28596,28.866,-0.13627,0.96561,0.22141,-43.529,0.31994,-0.16863,0.93231,-13.784

> view matrix models
> #14,0.93759,0.19788,-0.28596,27.831,-0.13627,0.96561,0.22141,-42.587,0.31994,-0.16863,0.93231,-14.107

> select add #13

547 atoms, 545 bonds, 2 pseudobonds, 37 residues, 4 models selected  

> select subtract #14

96 atoms, 95 bonds, 1 pseudobond, 8 residues, 2 models selected  

> view matrix models
> #13,0.93679,0.34915,0.022882,-66.485,-0.34379,0.93062,-0.12551,77.151,-0.065117,0.10971,0.99183,-11.256

> view matrix models
> #13,0.93679,0.34915,0.022882,-66.793,-0.34379,0.93062,-0.12551,76.01,-0.065117,0.10971,0.99183,-11.236

> view matrix models
> #13,0.93679,0.34915,0.022882,-66.996,-0.34379,0.93062,-0.12551,76.439,-0.065117,0.10971,0.99183,-11.297

> select add #14

547 atoms, 545 bonds, 2 pseudobonds, 37 residues, 4 models selected  

> select subtract #13

451 atoms, 450 bonds, 1 pseudobond, 29 residues, 2 models selected  

> ui mousemode right "move picked models"

> ui mousemode right "rotate selected models"

> view matrix models
> #14,0.95778,0.18403,-0.22087,14.429,-0.14413,0.97212,0.18497,-35.485,0.24875,-0.14533,0.9576,-10.095

> view matrix models
> #14,0.96305,0.11146,-0.24516,33.665,-0.075377,0.98551,0.15194,-45.437,0.25854,-0.12784,0.9575,-15.745

> ui mousemode right "translate selected models"

> view matrix models
> #14,0.96305,0.11146,-0.24516,35.589,-0.075377,0.98551,0.15194,-43.952,0.25854,-0.12784,0.9575,-15.917

> view matrix models
> #14,0.96305,0.11146,-0.24516,35.461,-0.075377,0.98551,0.15194,-44.173,0.25854,-0.12784,0.9575,-15.949

> view matrix models
> #14,0.96305,0.11146,-0.24516,36.095,-0.075377,0.98551,0.15194,-44.379,0.25854,-0.12784,0.9575,-15.979

> select subtract #14

Nothing selected  

> combine #13,14,15,17,18

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '8'  

> combine #13,14,15,17,18

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '8'  

> combine #13,14,15,17,18

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '8'  

> color #42 #9437ffff

> color #43 #00fa92ff

> select add #42

2584 atoms, 2582 bonds, 3 pseudobonds, 166 residues, 2 models selected  

> hide #!41 models

> show #!41 models

> color #41 #fffc79ff

> select add #41

5168 atoms, 5164 bonds, 6 pseudobonds, 332 residues, 4 models selected  

> select subtract #42

2584 atoms, 2582 bonds, 3 pseudobonds, 166 residues, 2 models selected  

> ui mousemode right "rotate selected models"

> ui mousemode right "translate selected models"

> view matrix models
> #41,0.93679,0.34915,0.022882,-72.632,-0.34379,0.93062,-0.12551,56.409,-0.065117,0.10971,0.99183,-18.56

> fitmap sel inMap #8

Fit molecule combination (#41) to map postprocess_masked330_onepf.mrc (#8)
using 2584 atoms  
average map value = 0.01078, steps = 88  
shifted from previous position = 9.48  
rotated from previous position = 3.59 degrees  
atoms outside contour = 1690, contour level = 0.013465  
  
Position of combination (#41) relative to postprocess_masked330_onepf.mrc (#8)
coordinates:  
Matrix rotation and translation  
0.92303332 0.38374078 -0.02743178 -63.08528755  
-0.38379562 0.91353179 -0.13476122 66.08089993  
-0.02665357 0.13491730 0.99049831 -24.47307825  
Axis 0.33148975 -0.00095658 -0.94345834  
Axis point 128.90816303 192.07676309 0.00000000  
Rotation angle (degrees) 24.00193621  
Shift along axis 2.11399159  
  

> select add #42

5168 atoms, 5164 bonds, 6 pseudobonds, 332 residues, 4 models selected  

> select subtract #41

2584 atoms, 2582 bonds, 3 pseudobonds, 166 residues, 2 models selected  

> view matrix models
> #42,0.93679,0.34915,0.022882,-63.754,-0.34379,0.93062,-0.12551,98.568,-0.065117,0.10971,0.99183,-3.4276

> fitmap sel inMap #8

Fit molecule combination (#42) to map postprocess_masked330_onepf.mrc (#8)
using 2584 atoms  
average map value = 0.01414, steps = 96  
shifted from previous position = 8.38  
rotated from previous position = 5.54 degrees  
atoms outside contour = 1445, contour level = 0.013465  
  
Position of combination (#42) relative to postprocess_masked330_onepf.mrc (#8)
coordinates:  
Matrix rotation and translation  
0.95266112 0.30219187 0.03341952 -60.73601760  
-0.30075358 0.95277521 -0.04203195 68.40598395  
-0.04454301 0.02999116 0.99855718 1.50546276  
Axis 0.11764325 0.12734477 -0.98485703  
Axis point 191.14749839 230.96096083 0.00000000  
Rotation angle (degrees) 17.82484289  
Shift along axis 0.08329611  
  

> select add #43

5168 atoms, 5164 bonds, 6 pseudobonds, 332 residues, 4 models selected  

> select subtract #42

2584 atoms, 2582 bonds, 3 pseudobonds, 166 residues, 2 models selected  

> view matrix models
> #43,0.93679,0.34915,0.022882,-75.62,-0.34379,0.93062,-0.12551,32.493,-0.065117,0.10971,0.99183,-27.039

> fitmap sel inMap #8

Fit molecule combination (#43) to map postprocess_masked330_onepf.mrc (#8)
using 2584 atoms  
average map value = 0.007706, steps = 232  
shifted from previous position = 17.6  
rotated from previous position = 9.01 degrees  
atoms outside contour = 1932, contour level = 0.013465  
  
Position of combination (#43) relative to postprocess_masked330_onepf.mrc (#8)
coordinates:  
Matrix rotation and translation  
0.90367188 0.41801744 -0.09294380 -56.27241034  
-0.42822555 0.88216661 -0.19597183 69.11024602  
0.00007228 0.21689514 0.97619490 -45.72291437  
Axis 0.43635585 -0.09830797 -0.89438756  
Axis point 116.41312842 171.40753366 0.00000000  
Rotation angle (degrees) 28.23474883  
Shift along axis 9.54512234  
  

> hide #!41-43 target m

> select add #14

3035 atoms, 3032 bonds, 4 pseudobonds, 195 residues, 4 models selected  

> ui mousemode right "rotate selected models"

> select subtract #43

451 atoms, 450 bonds, 1 pseudobond, 29 residues, 2 models selected  

> view matrix models
> #14,0.96007,0.18841,-0.20679,12.779,-0.12457,0.9498,0.287,-52.948,0.25048,-0.24978,0.93534,16.067

> ui mousemode right "translate selected models"

> view matrix models
> #14,0.96007,0.18841,-0.20679,11.458,-0.12457,0.9498,0.287,-52.611,0.25048,-0.24978,0.93534,18.09

> view matrix models
> #14,0.96007,0.18841,-0.20679,11.328,-0.12457,0.9498,0.287,-53.157,0.25048,-0.24978,0.93534,18.06

> ui mousemode right "rotate selected models"

> view matrix models
> #14,0.96066,0.21122,-0.18035,1.2461,-0.1416,0.93107,0.33623,-55.23,0.23894,-0.29747,0.92435,32.673

> ui mousemode right "translate selected models"

[Repeated 1 time(s)]

> view matrix models
> #14,0.96066,0.21122,-0.18035,1.0403,-0.1416,0.93107,0.33623,-55.063,0.23894,-0.29747,0.92435,33.263

> combine #13,14,15,17,18

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '8'  

> combine #13,14,15,17,18

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '8'  

> combine #13,14,15,17,18

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '8'  

> color #44 #00fa92ff

> color #45 #73fcd6ff

> color #46 #ff85ffff

> select add #44

3035 atoms, 3032 bonds, 4 pseudobonds, 195 residues, 4 models selected  

> select subtract #14

2584 atoms, 2582 bonds, 3 pseudobonds, 166 residues, 2 models selected  

> view matrix models
> #44,0.93679,0.34915,0.022882,-62.806,-0.34379,0.93062,-0.12551,100.45,-0.065117,0.10971,0.99183,-9.2676

> fitmap sel inMap #8

Fit molecule combination (#44) to map postprocess_masked330_onepf.mrc (#8)
using 2584 atoms  
average map value = 0.01377, steps = 84  
shifted from previous position = 4.5  
rotated from previous position = 7.2 degrees  
atoms outside contour = 1465, contour level = 0.013465  
  
Position of combination (#44) relative to postprocess_masked330_onepf.mrc (#8)
coordinates:  
Matrix rotation and translation  
0.97204928 0.23451988 -0.01098294 -39.72571306  
-0.23366931 0.96186561 -0.14217314 73.69126171  
-0.02277832 0.14076568 0.98978087 -27.26626432  
Axis 0.51709523 0.02155709 -0.85565636  
Axis point 280.29055946 212.44867055 -0.00000000  
Rotation angle (degrees) 15.87769676  
Shift along axis 4.37714484  
  

> select add #45

5168 atoms, 5164 bonds, 6 pseudobonds, 332 residues, 4 models selected  

> view matrix models
> #44,0.97204,0.23461,-0.010146,-46.808,-0.23364,0.96186,-0.14224,47.633,-0.023611,0.14063,0.98978,-28.52,#45,0.93679,0.34915,0.022882,-73.764,-0.34379,0.93062,-0.12551,50.392,-0.065117,0.10971,0.99183,-12.761

> undo

> select subtract #44

2584 atoms, 2582 bonds, 3 pseudobonds, 166 residues, 2 models selected  

> view matrix models
> #45,0.93679,0.34915,0.022882,-73.717,-0.34379,0.93062,-0.12551,51.556,-0.065117,0.10971,0.99183,-12.611

> fitmap sel inMap #8

Fit molecule combination (#45) to map postprocess_masked330_onepf.mrc (#8)
using 2584 atoms  
average map value = 0.01112, steps = 92  
shifted from previous position = 6.11  
rotated from previous position = 7.15 degrees  
atoms outside contour = 1639, contour level = 0.013465  
  
Position of combination (#45) relative to postprocess_masked330_onepf.mrc (#8)
coordinates:  
Matrix rotation and translation  
0.93504097 0.34772683 -0.06916959 -48.12545350  
-0.35440914 0.91144207 -0.20896772 76.23900516  
-0.00961961 0.21990771 0.97547325 -44.74578176  
Axis 0.51990621 -0.07218973 -0.85116754  
Axis point 171.25422569 181.69828587 0.00000000  
Rotation angle (degrees) 24.35912373  
Shift along axis 7.56176192  
  

> select add #46

5168 atoms, 5164 bonds, 6 pseudobonds, 332 residues, 4 models selected  

> select subtract #45

2584 atoms, 2582 bonds, 3 pseudobonds, 166 residues, 2 models selected  

> view matrix models
> #46,0.93679,0.34915,0.022882,-78.879,-0.34379,0.93062,-0.12551,28.916,-0.065117,0.10971,0.99183,-14.122

> fitmap sel inMap #8

Fit molecule combination (#46) to map postprocess_masked330_onepf.mrc (#8)
using 2584 atoms  
average map value = 0.007906, steps = 136  
shifted from previous position = 9.01  
rotated from previous position = 8.8 degrees  
atoms outside contour = 1911, contour level = 0.013465  
  
Position of combination (#46) relative to postprocess_masked330_onepf.mrc (#8)
coordinates:  
Matrix rotation and translation  
0.90681352 0.41131768 -0.09223340 -55.32496436  
-0.42153165 0.88512519 -0.19714072 67.26696276  
0.00055064 0.21764917 0.97602691 -45.92741365  
Axis 0.44360715 -0.09923016 -0.89071099  
Axis point 115.24010580 171.06631423 -0.00000000  
Rotation angle (degrees) 27.87339513  
Shift along axis 9.69059100  
  

> hide #!44-46 target m

> select add #14

3035 atoms, 3032 bonds, 4 pseudobonds, 195 residues, 4 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #14,0.95352,0.27498,-0.12321,-22.22,-0.17441,0.8371,0.5185,-63.317,0.24571,-0.47292,0.84615,84.656,#46,0.86993,0.48738,-0.075381,-71.509,-0.48885,0.87237,-0.0011636,46.247,0.065193,0.037862,0.99715,-15.237

> view matrix models
> #14,0.95554,0.26025,-0.13864,-16.489,-0.16642,0.8641,0.47501,-62.363,0.24342,-0.43082,0.86899,71.674,#46,0.87948,0.46901,-0.080928,-67.474,-0.47356,0.87933,-0.05017,50.805,0.047632,0.082447,0.99546,-23.226

> ui mousemode right "translate selected models"

> view matrix models
> #14,0.95554,0.26025,-0.13864,-17.476,-0.16642,0.8641,0.47501,-61.263,0.24342,-0.43082,0.86899,74.285,#46,0.87948,0.46901,-0.080928,-68.461,-0.47356,0.87933,-0.05017,51.904,0.047632,0.082447,0.99546,-20.615

> ui mousemode right "rotate selected models"

> view matrix models
> #14,0.89918,0.34155,-0.27354,1.8076,-0.19749,0.87458,0.44283,-51.314,0.39048,-0.34416,0.85386,29.894,#46,0.8519,0.46244,-0.24579,-30.953,-0.49475,0.86455,-0.088161,66.682,0.17173,0.19671,0.96531,-67.143

> view matrix models
> #14,0.87016,0.44245,-0.21693,-25.083,-0.28023,0.80643,0.52072,-35.433,0.40533,-0.39232,0.82571,42.75,#46,0.78733,0.56253,-0.25233,-43.785,-0.58186,0.81328,-0.0024901,79.83,0.20382,0.14878,0.96764,-61.063

> ui mousemode right "translate selected models"

> view matrix models
> #14,0.87016,0.44245,-0.21693,-26.836,-0.28023,0.80643,0.52072,-34.315,0.40533,-0.39232,0.82571,43.587,#46,0.78733,0.56253,-0.25233,-45.538,-0.58186,0.81328,-0.0024901,80.948,0.20382,0.14878,0.96764,-60.225

> view matrix models
> #14,0.87016,0.44245,-0.21693,-26.765,-0.28023,0.80643,0.52072,-33.623,0.40533,-0.39232,0.82571,42.738,#46,0.78733,0.56253,-0.25233,-45.467,-0.58186,0.81328,-0.0024901,81.64,0.20382,0.14878,0.96764,-61.074

> view matrix models
> #14,0.87016,0.44245,-0.21693,-27,-0.28023,0.80643,0.52072,-33.997,0.40533,-0.39232,0.82571,42.778,#46,0.78733,0.56253,-0.25233,-45.701,-0.58186,0.81328,-0.0024901,81.266,0.20382,0.14878,0.96764,-61.035

> view matrix models
> #14,0.87016,0.44245,-0.21693,-26.29,-0.28023,0.80643,0.52072,-34.517,0.40533,-0.39232,0.82571,41.933,#46,0.78733,0.56253,-0.25233,-44.991,-0.58186,0.81328,-0.0024901,80.746,0.20382,0.14878,0.96764,-61.879

> view matrix models
> #14,0.87016,0.44245,-0.21693,-27.004,-0.28023,0.80643,0.52072,-34.864,0.40533,-0.39232,0.82571,42.41,#46,0.78733,0.56253,-0.25233,-45.706,-0.58186,0.81328,-0.0024901,80.399,0.20382,0.14878,0.96764,-61.402

> view matrix models
> #14,0.87016,0.44245,-0.21693,-27.593,-0.28023,0.80643,0.52072,-34.076,0.40533,-0.39232,0.82571,42.086,#46,0.78733,0.56253,-0.25233,-46.294,-0.58186,0.81328,-0.0024901,81.187,0.20382,0.14878,0.96764,-61.727

> select subtract #14

2584 atoms, 2582 bonds, 3 pseudobonds, 166 residues, 2 models selected  

> select add #15

3034 atoms, 3031 bonds, 3 pseudobonds, 196 residues, 3 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #15,0.93792,0.029309,-0.34562,78.109,-0.13901,0.94466,-0.29713,102.43,0.31779,0.32673,0.89009,-104.97,#46,0.83724,0.48064,-0.2608,-29.927,-0.53259,0.82487,-0.18959,105.4,0.124,0.29763,0.94659,-86.343

> view matrix models
> #15,0.95255,0.04479,-0.30106,63.321,-0.11879,0.96538,-0.23223,81.485,0.28024,0.25698,0.92489,-90.204,#46,0.84269,0.49421,-0.21363,-43.665,-0.52484,0.84253,-0.1212,86.076,0.12009,0.21425,0.96937,-66.532

> show #!23 models

> view matrix models
> #15,0.96935,0.046326,-0.24127,48.002,-0.10474,0.96627,-0.23527,79.209,0.22223,0.25333,0.94151,-81.62,#46,0.85587,0.49406,-0.15291,-57.414,-0.51253,0.84982,-0.12294,82.298,0.069209,0.18359,0.98056,-51.53

> view matrix models
> #15,0.94736,0.15889,-0.27796,36.141,-0.23023,0.94138,-0.24657,110.61,0.22249,0.29758,0.92841,-88.249,#46,0.78756,0.59021,-0.17722,-68.47,-0.61418,0.77525,-0.14752,124.98,0.050327,0.22503,0.97305,-58.625

> view matrix models
> #15,0.95537,0.13724,-0.26161,35.868,-0.21592,0.92877,-0.30126,121.26,0.20163,0.3443,0.91695,-91.67,#46,0.8039,0.57198,-0.16305,-68.766,-0.59466,0.7782,-0.20198,131.29,0.011355,0.25933,0.96572,-60.387

> ui mousemode right "translate selected models"

> view matrix models
> #15,0.95537,0.13724,-0.26161,37.478,-0.21592,0.92877,-0.30126,121.45,0.20163,0.3443,0.91695,-90.263,#46,0.8039,0.57198,-0.16305,-67.157,-0.59466,0.7782,-0.20198,131.47,0.011355,0.25933,0.96572,-58.981

> view matrix models
> #15,0.95537,0.13724,-0.26161,37.897,-0.21592,0.92877,-0.30126,121.34,0.20163,0.3443,0.91695,-88.978,#46,0.8039,0.57198,-0.16305,-66.737,-0.59466,0.7782,-0.20198,131.37,0.011355,0.25933,0.96572,-57.696

> view matrix models
> #15,0.95537,0.13724,-0.26161,37.857,-0.21592,0.92877,-0.30126,121.38,0.20163,0.3443,0.91695,-88.919,#46,0.8039,0.57198,-0.16305,-66.777,-0.59466,0.7782,-0.20198,131.41,0.011355,0.25933,0.96572,-57.637

> ui mousemode right "rotate selected models"

> view matrix models
> #15,0.97151,-0.16037,-0.17452,79.212,0.10079,0.94597,-0.30819,58.571,0.21452,0.28182,0.93518,-82.044,#46,0.94697,0.30115,-0.11205,-24.053,-0.31742,0.93093,-0.18057,37.981,0.049932,0.20656,0.97716,-51.387

> view matrix models
> #15,0.97608,-0.10344,-0.19123,69.843,0.040142,0.95019,-0.30907,69.478,0.21367,0.294,0.93162,-83.701,#46,0.92649,0.35627,-0.12122,-34.421,-0.37376,0.9087,-0.18593,54.678,0.043911,0.21757,0.97506,-53.082

> ui mousemode right "translate selected models"

> view matrix models
> #15,0.97608,-0.10344,-0.19123,65.495,0.040142,0.95019,-0.30907,67.735,0.21367,0.294,0.93162,-84.673,#46,0.92649,0.35627,-0.12122,-38.769,-0.37376,0.9087,-0.18593,52.936,0.043911,0.21757,0.97506,-54.055

> view matrix models
> #15,0.97608,-0.10344,-0.19123,65.14,0.040142,0.95019,-0.30907,66.653,0.21367,0.294,0.93162,-84.817,#46,0.92649,0.35627,-0.12122,-39.124,-0.37376,0.9087,-0.18593,51.853,0.043911,0.21757,0.97506,-54.199

> ui mousemode right "rotate selected models"

> view matrix models
> #15,0.97412,0.0047884,-0.22597,49.959,-0.050981,0.97867,-0.19903,56.513,0.22019,0.2054,0.95358,-72.056,#46,0.87804,0.45689,-0.14248,-55.341,-0.47041,0.87871,-0.081138,56.444,0.088126,0.13827,0.98647,-41.404

> ui mousemode right "translate selected models"

[Repeated 1 time(s)]

> view matrix models
> #15,0.97412,0.0047884,-0.22597,52.335,-0.050981,0.97867,-0.19903,56.93,0.22019,0.2054,0.95358,-71.724,#46,0.87804,0.45689,-0.14248,-52.965,-0.47041,0.87871,-0.081138,56.86,0.088126,0.13827,0.98647,-41.072

> view matrix models
> #15,0.97412,0.0047884,-0.22597,52.629,-0.050981,0.97867,-0.19903,57.531,0.22019,0.2054,0.95358,-72.128,#46,0.87804,0.45689,-0.14248,-52.671,-0.47041,0.87871,-0.081138,57.461,0.088126,0.13827,0.98647,-41.476

> ui mousemode right "rotate selected models"

> view matrix models
> #15,0.96754,0.025808,-0.2514,54.55,-0.054053,0.99289,-0.1061,36.858,0.24688,0.11624,0.96205,-60.446,#46,0.86344,0.47649,-0.1656,-51.347,-0.48132,0.87646,0.012266,42.094,0.15099,0.069117,0.98612,-32.413

> ui mousemode right "translate selected models"

> view matrix models
> #15,0.96754,0.025808,-0.2514,54.402,-0.054053,0.99289,-0.1061,36.344,0.24688,0.11624,0.96205,-62.77,#46,0.86344,0.47649,-0.1656,-51.496,-0.48132,0.87646,0.012266,41.579,0.15099,0.069117,0.98612,-34.737

> view matrix models
> #15,0.96754,0.025808,-0.2514,55.05,-0.054053,0.99289,-0.1061,36.188,0.24688,0.11624,0.96205,-63.63,#46,0.86344,0.47649,-0.1656,-50.848,-0.48132,0.87646,0.012266,41.423,0.15099,0.069117,0.98612,-35.597

> view matrix models
> #15,0.96754,0.025808,-0.2514,55.295,-0.054053,0.99289,-0.1061,36.489,0.24688,0.11624,0.96205,-63.543,#46,0.86344,0.47649,-0.1656,-50.602,-0.48132,0.87646,0.012266,41.725,0.15099,0.069117,0.98612,-35.51

> select clear

> combine #13,14,15,17,18

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '8'  

> hide #!23 models

> combine #13,14,15,17,18

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '8'  

> combine #13,14,15,17,18

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '8'  

> color #47 #73fa79ff

> color #48 #ff8ad8ff

> color #49 #fffc79ff

> select add #47

2584 atoms, 2582 bonds, 3 pseudobonds, 166 residues, 2 models selected  

> view matrix models
> #47,0.93679,0.34915,0.022882,-62.232,-0.34379,0.93062,-0.12551,99.48,-0.065117,0.10971,0.99183,-11.275

> fitmap sel inMap #8

Fit molecule combination (#47) to map postprocess_masked330_onepf.mrc (#8)
using 2584 atoms  
average map value = 0.01299, steps = 80  
shifted from previous position = 5.13  
rotated from previous position = 3.34 degrees  
atoms outside contour = 1527, contour level = 0.013465  
  
Position of combination (#47) relative to postprocess_masked330_onepf.mrc (#8)
coordinates:  
Matrix rotation and translation  
0.93429364 0.35193488 0.05689661 -74.33525106  
-0.34718149 0.93445833 -0.07907366 90.26911374  
-0.08099629 0.05412457 0.99524376 3.97768223  
Axis 0.18374007 0.19021611 -0.96439485  
Axis point 212.83886941 250.78680791 0.00000000  
Rotation angle (degrees) 21.25158154  
Shift along axis -0.32378132  
  

> select add #48

5168 atoms, 5164 bonds, 6 pseudobonds, 332 residues, 4 models selected  

> select subtract #47

2584 atoms, 2582 bonds, 3 pseudobonds, 166 residues, 2 models selected  

> view matrix models
> #48,0.93679,0.34915,0.022882,-73.546,-0.34379,0.93062,-0.12551,53.044,-0.065117,0.10971,0.99183,-11.833

> fitmap sel inMap #8

Fit molecule combination (#48) to map postprocess_masked330_onepf.mrc (#8)
using 2584 atoms  
average map value = 0.01135, steps = 112  
shifted from previous position = 5.04  
rotated from previous position = 7.08 degrees  
atoms outside contour = 1631, contour level = 0.013465  
  
Position of combination (#48) relative to postprocess_masked330_onepf.mrc (#8)
coordinates:  
Matrix rotation and translation  
0.90905774 0.41457059 -0.04177629 -64.68519892  
-0.41405563 0.88758732 -0.20185809 92.72612520  
-0.04660432 0.20079837 0.97852340 -33.63506908  
Axis 0.43705680 0.00524050 -0.89941864  
Axis point 170.68293528 196.07188799 0.00000000  
Rotation angle (degrees) 27.42876541  
Shift along axis 2.46683336  
  

> select add #49

5168 atoms, 5164 bonds, 6 pseudobonds, 332 residues, 4 models selected  

> select subtract #48

2584 atoms, 2582 bonds, 3 pseudobonds, 166 residues, 2 models selected  

> view matrix models
> #49,0.93679,0.34915,0.022882,-76.73,-0.34379,0.93062,-0.12551,30.365,-0.065117,0.10971,0.99183,-11.403

> fitmap sel inMap #8

Fit molecule combination (#49) to map postprocess_masked330_onepf.mrc (#8)
using 2584 atoms  
average map value = 0.007607, steps = 132  
shifted from previous position = 7.08  
rotated from previous position = 12.5 degrees  
atoms outside contour = 1950, contour level = 0.013465  
  
Position of combination (#49) relative to postprocess_masked330_onepf.mrc (#8)
coordinates:  
Matrix rotation and translation  
0.90179327 0.41568133 -0.11822829 -49.66296417  
-0.43207472 0.86153159 -0.26659850 89.70157466  
-0.00896261 0.29150019 0.95652878 -57.37770885  
Axis 0.54670820 -0.10703562 -0.83045380  
Axis point 155.64087773 170.57656295 -0.00000000  
Rotation angle (degrees) 30.69163275  
Shift along axis 10.89712291  
  

> hide #!8 models

> hide #!13-25 target m

> hide #!47-49 target m

> select subtract #49

Nothing selected  

> show #!9 models

> hide #!9 models

> show #!47-49 target m

> show #!13-15,17-18 target m

> show #!9 models

> hide #!9 models

> show #!9 models

> hide #!9 models

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Fit14-8.cxs"

> select add #14

451 atoms, 450 bonds, 1 pseudobond, 29 residues, 2 models selected  

> select subtract #14

Nothing selected  

> select add #15

450 atoms, 449 bonds, 30 residues, 1 model selected  

> ui mousemode right "translate selected models"

> view matrix models
> #15,0.96754,0.025808,-0.2514,54.666,-0.054053,0.99289,-0.1061,36.811,0.24688,0.11624,0.96205,-61.046

> view matrix models
> #15,0.96754,0.025808,-0.2514,52.8,-0.054053,0.99289,-0.1061,36.606,0.24688,0.11624,0.96205,-61.355

> view matrix models
> #15,0.96754,0.025808,-0.2514,52.585,-0.054053,0.99289,-0.1061,36.772,0.24688,0.11624,0.96205,-60.603

> view matrix models
> #15,0.96754,0.025808,-0.2514,52.732,-0.054053,0.99289,-0.1061,36.453,0.24688,0.11624,0.96205,-61.518

> select add #14

901 atoms, 899 bonds, 1 pseudobond, 59 residues, 3 models selected  

> select subtract #15

451 atoms, 450 bonds, 1 pseudobond, 29 residues, 2 models selected  

> view matrix models
> #14,0.87016,0.44245,-0.21693,-27.109,-0.28023,0.80643,0.52072,-34.047,0.40533,-0.39232,0.82571,40.659

> ui mousemode right "rotate selected models"

> view matrix models
> #14,0.87715,0.42217,-0.22889,-21.817,-0.28741,0.84334,0.45405,-27.84,0.38472,-0.33249,0.86107,25.034

> close #47-49

> combine #13,14,15,17,18

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '8'  

> combine #13,14,15,17,18

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '8'  

> combine #13,14,15,17,18

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '8'  

> combine #13,14,15,17,18

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '8'  

> close #50

> color #47 #fffb00ff

> color #48 #ff85ffff

> color #49 #00fdffff

> select add #47

3035 atoms, 3032 bonds, 4 pseudobonds, 195 residues, 4 models selected  

> select subtract #14

2584 atoms, 2582 bonds, 3 pseudobonds, 166 residues, 2 models selected  

> show #!8 models

> view matrix models
> #47,0.93779,0.336,-0.08745,-41.443,-0.34718,0.90937,-0.22914,103.3,0.002535,0.24524,0.96946,-50.638

> ui mousemode right "translate selected models"

> view matrix models
> #47,0.93779,0.336,-0.08745,-45.604,-0.34718,0.90937,-0.22914,79.157,0.002535,0.24524,0.96946,-50.728

> fitmap sel inMap #8

Fit molecule combination (#47) to map postprocess_masked330_onepf.mrc (#8)
using 2584 atoms  
average map value = 0.01094, steps = 188  
shifted from previous position = 3.41  
rotated from previous position = 9.56 degrees  
atoms outside contour = 1669, contour level = 0.013465  
  
Position of combination (#47) relative to postprocess_masked330_onepf.mrc (#8)
coordinates:  
Matrix rotation and translation  
0.88558376 0.46388801 -0.02343760 -74.32406141  
-0.46152820 0.87315587 -0.15681378 95.76963429  
-0.05227935 0.14968886 0.98735005 -22.04259493  
Axis 0.31427146 0.02957279 -0.94887243  
Axis point 153.00231682 198.22140267 0.00000000  
Rotation angle (degrees) 29.18557954  
Shift along axis 0.38985440  
  

> select add #48

5168 atoms, 5164 bonds, 6 pseudobonds, 332 residues, 4 models selected  

> select subtract #47

2584 atoms, 2582 bonds, 3 pseudobonds, 166 residues, 2 models selected  

> view matrix models
> #48,0.93679,0.34915,0.022882,-62.894,-0.34379,0.93062,-0.12551,99.225,-0.065117,0.10971,0.99183,-11.121

> fitmap sel inMap #8

Fit molecule combination (#48) to map postprocess_masked330_onepf.mrc (#8)
using 2584 atoms  
average map value = 0.01288, steps = 112  
shifted from previous position = 1.6  
rotated from previous position = 9.65 degrees  
atoms outside contour = 1519, contour level = 0.013465  
  
Position of combination (#48) relative to postprocess_masked330_onepf.mrc (#8)
coordinates:  
Matrix rotation and translation  
0.97350640 0.22192238 -0.05509758 -26.18543385  
-0.22848136 0.95360173 -0.19606125 85.40629253  
0.00903077 0.20345566 0.97904251 -45.57734822  
Axis 0.65984968 -0.10591560 -0.74389534  
Axis point 340.52016479 181.18500652 0.00000000  
Rotation angle (degrees) 17.62184404  
Shift along axis 7.58046849  
  

> select add #49

5168 atoms, 5164 bonds, 6 pseudobonds, 332 residues, 4 models selected  

> select subtract #48

2584 atoms, 2582 bonds, 3 pseudobonds, 166 residues, 2 models selected  

> view matrix models
> #49,0.93679,0.34915,0.022882,-78.241,-0.34379,0.93062,-0.12551,28.94,-0.065117,0.10971,0.99183,-13.066

> fitmap sel inMap #8

Fit molecule combination (#49) to map postprocess_masked330_onepf.mrc (#8)
using 2584 atoms  
average map value = 0.007533, steps = 120  
shifted from previous position = 8.66  
rotated from previous position = 13.4 degrees  
atoms outside contour = 1947, contour level = 0.013465  
  
Position of combination (#49) relative to postprocess_masked330_onepf.mrc (#8)
coordinates:  
Matrix rotation and translation  
0.86831758 0.47972422 -0.12605259 -55.72759743  
-0.49600725 0.84041315 -0.21836334 97.28367521  
0.00118207 0.25213173 0.96769220 -52.28168252  
Axis 0.43137351 -0.11665513 -0.89459962  
Axis point 145.30863294 166.28838985 0.00000000  
Rotation angle (degrees) 33.04826621  
Shift along axis 11.38312395  
  

> select clear

> select add #49

2584 atoms, 2582 bonds, 3 pseudobonds, 166 residues, 2 models selected  

> view matrix models
> #49,0.86833,0.47991,-0.12523,-56.101,-0.49598,0.84041,-0.21843,97.336,0.00041946,0.25178,0.96778,-52.06

> view matrix models
> #49,0.86833,0.47991,-0.12523,-59.256,-0.49598,0.84041,-0.21843,99.897,0.00041946,0.25178,0.96778,-52.36

> view matrix models
> #49,0.86833,0.47991,-0.12523,-58.925,-0.49598,0.84041,-0.21843,100.73,0.00041946,0.25178,0.96778,-53.066

> view matrix models
> #49,0.86833,0.47991,-0.12523,-59.047,-0.49598,0.84041,-0.21843,100.56,0.00041946,0.25178,0.96778,-52.776

> view matrix models
> #49,0.86833,0.47991,-0.12523,-59.513,-0.49598,0.84041,-0.21843,101.06,0.00041946,0.25178,0.96778,-51.406

> view matrix models
> #49,0.86833,0.47991,-0.12523,-59.494,-0.49598,0.84041,-0.21843,101.58,0.00041946,0.25178,0.96778,-51.911

> select clear

> hide #!8 models

> show #!8 models

> select add #47

2584 atoms, 2582 bonds, 3 pseudobonds, 166 residues, 2 models selected  

> view matrix models
> #47,0.88555,0.46398,-0.022602,-77.436,-0.4615,0.87316,-0.15688,96.772,-0.053054,0.14936,0.98736,-22.057

> view matrix models
> #47,0.88555,0.46398,-0.022602,-77.446,-0.4615,0.87316,-0.15688,96.851,-0.053054,0.14936,0.98736,-22.008

> view matrix models
> #47,0.88555,0.46398,-0.022602,-77.225,-0.4615,0.87316,-0.15688,97.194,-0.053054,0.14936,0.98736,-22.742

> view matrix models
> #47,0.88555,0.46398,-0.022602,-77.528,-0.4615,0.87316,-0.15688,97.181,-0.053054,0.14936,0.98736,-22.806

> view matrix models
> #47,0.88555,0.46398,-0.022602,-77.954,-0.4615,0.87316,-0.15688,97.077,-0.053054,0.14936,0.98736,-21.441

> view matrix models
> #47,0.88555,0.46398,-0.022602,-77.743,-0.4615,0.87316,-0.15688,97.635,-0.053054,0.14936,0.98736,-21.852

> ui mousemode right "rotate selected models"

> view matrix models
> #47,0.88917,0.45745,-0.01099,-79.362,-0.42857,0.82414,-0.3703,146.37,-0.16034,0.33397,0.92885,-30.716

> view matrix models
> #47,0.88807,0.45967,-0.0057502,-80.732,-0.44306,0.85251,-0.27736,123.58,-0.12259,0.24887,0.96075,-25.36

> ui mousemode right "translate selected models"

> view matrix models
> #47,0.88807,0.45967,-0.0057502,-80.501,-0.44306,0.85251,-0.27736,123.97,-0.12259,0.24887,0.96075,-25.29

> ui mousemode right "rotate selected models"

> view matrix models
> #47,0.91062,0.40805,-0.065346,-60.895,-0.39014,0.79676,-0.46148,164.28,-0.13624,0.44572,0.88474,-51.603

> ui mousemode right "translate selected models"

> view matrix models
> #47,0.91062,0.40805,-0.065346,-60.341,-0.39014,0.79676,-0.46148,165.29,-0.13624,0.44572,0.88474,-51.428

> view matrix models
> #47,0.91062,0.40805,-0.065346,-61.21,-0.39014,0.79676,-0.46148,162.14,-0.13624,0.44572,0.88474,-54.396

> fitmap sel inMap #8

Fit molecule combination (#47) to map postprocess_masked330_onepf.mrc (#8)
using 2584 atoms  
average map value = 0.01094, steps = 220  
shifted from previous position = 3.81  
rotated from previous position = 18.9 degrees  
atoms outside contour = 1669, contour level = 0.013465  
  
Position of combination (#47) relative to postprocess_masked330_onepf.mrc (#8)
coordinates:  
Matrix rotation and translation  
0.88556722 0.46392202 -0.02338930 -74.33974357  
-0.46155263 0.87313659 -0.15684918 95.78687556  
-0.05234374 0.14969589 0.98734557 -22.02592470  
Axis 0.31429173 0.02968614 -0.94886218  
Axis point 153.01810848 198.24251363 0.00000000  
Rotation angle (degrees) 29.18794662  
Shift along axis 0.37874345  
  

> view matrix models
> #47,0.88554,0.46402,-0.022553,-77.838,-0.46152,0.87314,-0.15691,96.295,-0.053119,0.14936,0.98735,-22.173

> select subtract #47

Nothing selected  

> select add #48

2584 atoms, 2582 bonds, 3 pseudobonds, 166 residues, 2 models selected  

> view matrix models
> #48,0.97352,0.22206,-0.054267,-28.587,-0.22845,0.9536,-0.19613,85.746,0.008197,0.20333,0.97908,-45.801

> view matrix models
> #48,0.97352,0.22206,-0.054267,-28.534,-0.22845,0.9536,-0.19613,85.732,0.008197,0.20333,0.97908,-45.973

> view matrix models
> #48,0.97352,0.22206,-0.054267,-29.127,-0.22845,0.9536,-0.19613,85.907,0.008197,0.20333,0.97908,-45.974

> ui mousemode right "rotate selected models"

> view matrix models
> #48,0.96405,0.25823,-0.062708,-33.741,-0.26558,0.94443,-0.1937,94.735,0.0092032,0.20339,0.97905,-46.18

> ui mousemode right "translate selected models"

> view matrix models
> #48,0.96405,0.25823,-0.062708,-33.956,-0.26558,0.94443,-0.1937,94.761,0.0092032,0.20339,0.97905,-46.18

> select add #49

5168 atoms, 5164 bonds, 6 pseudobonds, 332 residues, 4 models selected  

> select subtract #48

2584 atoms, 2582 bonds, 3 pseudobonds, 166 residues, 2 models selected  

> view matrix models
> #49,0.86833,0.47991,-0.12523,-59.565,-0.49598,0.84041,-0.21843,101.55,0.00041946,0.25178,0.96778,-51.878

> ui mousemode right "rotate selected models"

> view matrix models
> #49,0.90343,0.41209,-0.11832,-52.456,-0.42868,0.86357,-0.26549,92.871,-0.0072273,0.29058,0.95682,-56.925

> view matrix models
> #49,0.89983,0.39701,-0.18082,-35.435,-0.43247,0.86621,-0.2503,89.876,0.05726,0.30343,0.95113,-71.256

> view matrix models
> #49,0.91256,0.28883,-0.28952,9.0499,-0.37643,0.86991,-0.31868,92.206,0.15981,0.3998,0.90256,-103.12

> ui mousemode right "translate selected models"

> view matrix models
> #49,0.91256,0.28883,-0.28952,8.6431,-0.37643,0.86991,-0.31868,89.691,0.15981,0.3998,0.90256,-105.34

> view matrix models
> #49,0.91256,0.28883,-0.28952,8.7922,-0.37643,0.86991,-0.31868,90.013,0.15981,0.3998,0.90256,-105.69

> select clear

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Fit14-4.cxs"

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Fit14-8.cxs"

> hide #!8 models

> select add #49

2584 atoms, 2582 bonds, 3 pseudobonds, 166 residues, 2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #49,0.93905,0.3336,0.083055,-83.414,-0.29513,0.90616,-0.30294,62.665,-0.17632,0.25996,0.94938,-18.001

> view matrix models
> #49,0.91985,0.38197,0.089313,-91.93,-0.36171,0.91401,-0.18369,49.278,-0.1518,0.13666,0.97892,-0.90961

> view matrix models
> #49,0.90687,0.2613,0.33062,-111.81,-0.23122,0.96444,-0.12801,0.87301,-0.35232,0.039642,0.93504,69.303

> view matrix models
> #49,0.87272,0.40678,0.26999,-125.64,-0.35497,0.90834,-0.22116,56.98,-0.33521,0.097173,0.93712,52.483

> view matrix models
> #49,0.81377,0.53575,0.22527,-134.16,-0.48247,0.83885,-0.25211,104.03,-0.32403,0.096475,0.94111,49.634

> view matrix models
> #49,0.83444,0.49862,0.23472,-131.72,-0.44333,0.86033,-0.25159,91.402,-0.32738,0.10588,0.93894,48.602

> ui mousemode right "rotate selected models"

> ui mousemode right "translate selected models"

> view matrix models
> #49,0.83444,0.49862,0.23472,-130.18,-0.44333,0.86033,-0.25159,90.871,-0.32738,0.10588,0.93894,48.224

> view matrix models
> #49,0.83444,0.49862,0.23472,-130.03,-0.44333,0.86033,-0.25159,91.243,-0.32738,0.10588,0.93894,48.204

> ui mousemode right "rotate selected models"

> view matrix models
> #49,0.8384,0.48078,0.25679,-131.31,-0.4528,0.87661,-0.16288,71.097,-0.30342,0.020285,0.95264,60.117

> ui mousemode right "translate selected models"

> view matrix models
> #49,0.8384,0.48078,0.25679,-132.02,-0.4528,0.87661,-0.16288,70.715,-0.30342,0.020285,0.95264,63.839

> ui mousemode right "rotate selected models"

> view matrix models
> #49,0.8678,0.4717,0.15626,-114.95,-0.45661,0.88102,-0.12371,62.373,-0.19602,0.036002,0.97994,33.675

> view matrix models
> #49,0.8293,0.55556,0.060078,-106.62,-0.54815,0.82967,-0.10576,88.19,-0.1086,0.054772,0.99258,9.7399

> ui mousemode right "translate selected models"

> view matrix models
> #49,0.8293,0.55556,0.060078,-110.01,-0.54815,0.82967,-0.10576,87.985,-0.1086,0.054772,0.99258,8.7683

> view matrix models
> #49,0.8293,0.55556,0.060078,-110.15,-0.54815,0.82967,-0.10576,89.72,-0.1086,0.054772,0.99258,8.7854

> view matrix models
> #49,0.8293,0.55556,0.060078,-108.73,-0.54815,0.82967,-0.10576,88.677,-0.1086,0.054772,0.99258,9.4745

> view matrix models
> #49,0.8293,0.55556,0.060078,-110.09,-0.54815,0.82967,-0.10576,88.973,-0.1086,0.054772,0.99258,9.5253

> view matrix models
> #49,0.8293,0.55556,0.060078,-110.83,-0.54815,0.82967,-0.10576,88.291,-0.1086,0.054772,0.99258,9.4879

> ui mousemode right "rotate selected models"

> select add #47

5168 atoms, 5164 bonds, 6 pseudobonds, 332 residues, 4 models selected  

> view matrix models
> #47,0.90117,0.42666,-0.076528,-61.711,-0.42904,0.90312,-0.017117,54.38,0.061811,0.048259,0.99692,-25.259,#49,0.85109,0.52501,0.0039991,-96.271,-0.52477,0.85042,0.037492,49.614,0.016283,-0.034008,0.99929,5.3699

> undo

> ui mousemode right "translate selected models"

> view matrix models
> #47,0.88554,0.46402,-0.022553,-77.526,-0.46152,0.87314,-0.15691,96.274,-0.053119,0.14936,0.98735,-20.569,#49,0.8293,0.55556,0.060078,-110.52,-0.54815,0.82967,-0.10576,88.269,-0.1086,0.054772,0.99258,11.092

> select add #48

7752 atoms, 7746 bonds, 9 pseudobonds, 498 residues, 6 models selected  

> select subtract #49

5168 atoms, 5164 bonds, 6 pseudobonds, 332 residues, 4 models selected  

> select subtract #47

2584 atoms, 2582 bonds, 3 pseudobonds, 166 residues, 2 models selected  

> view matrix models
> #48,0.96405,0.25823,-0.062708,-34.438,-0.26558,0.94443,-0.1937,93.346,0.0092032,0.20339,0.97905,-45.768

> select add #49

5168 atoms, 5164 bonds, 6 pseudobonds, 332 residues, 4 models selected  

> select subtract #48

2584 atoms, 2582 bonds, 3 pseudobonds, 166 residues, 2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #49,0.83272,0.5506,0.058447,-109.73,-0.54074,0.8314,-0.128,91.021,-0.11907,0.074984,0.99005,9.0717

> undo

> view matrix models
> #49,0.90632,0.42258,-0.0030504,-82.363,-0.42163,0.90375,-0.073933,40.196,-0.028486,0.068293,0.99726,-8.5828

> ui mousemode right "translate selected models"

> view matrix models
> #49,0.90632,0.42258,-0.0030504,-82.551,-0.42163,0.90375,-0.073933,41.183,-0.028486,0.068293,0.99726,-7.4474

> view matrix models
> #49,0.90632,0.42258,-0.0030504,-80.199,-0.42163,0.90375,-0.073933,41.321,-0.028486,0.068293,0.99726,-6.7089

> view matrix models
> #49,0.90632,0.42258,-0.0030504,-82.058,-0.42163,0.90375,-0.073933,40.855,-0.028486,0.068293,0.99726,-6.8326

> view matrix models
> #49,0.90632,0.42258,-0.0030504,-80.883,-0.42163,0.90375,-0.073933,41.378,-0.028486,0.068293,0.99726,-6.8149

> view matrix models
> #49,0.90632,0.42258,-0.0030504,-80.447,-0.42163,0.90375,-0.073933,40.603,-0.028486,0.068293,0.99726,-6.7478

> select add #48

5168 atoms, 5164 bonds, 6 pseudobonds, 332 residues, 4 models selected  

> select subtract #49

2584 atoms, 2582 bonds, 3 pseudobonds, 166 residues, 2 models selected  

> view matrix models
> #48,0.96405,0.25823,-0.062708,-34.47,-0.26558,0.94443,-0.1937,94.448,0.0092032,0.20339,0.97905,-45.838

> view matrix models
> #48,0.96405,0.25823,-0.062708,-34.383,-0.26558,0.94443,-0.1937,94.841,0.0092032,0.20339,0.97905,-45.661

> view matrix models
> #48,0.96405,0.25823,-0.062708,-34.615,-0.26558,0.94443,-0.1937,94.766,0.0092032,0.20339,0.97905,-45.64

> show #!16 models

> hide #!16 models

> show #!8 models

> select add #49

5168 atoms, 5164 bonds, 6 pseudobonds, 332 residues, 4 models selected  

> select subtract #48

2584 atoms, 2582 bonds, 3 pseudobonds, 166 residues, 2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #49,0.87356,0.48653,-0.013541,-86.395,-0.48609,0.87067,-0.075156,60.945,-0.024777,0.072235,0.99708,-8.3294

> ui mousemode right "translate selected models"

> view matrix models
> #49,0.87356,0.48653,-0.013541,-86.864,-0.48609,0.87067,-0.075156,61.695,-0.024777,0.072235,0.99708,-8.394

> view matrix models
> #49,0.87356,0.48653,-0.013541,-86.212,-0.48609,0.87067,-0.075156,62.137,-0.024777,0.072235,0.99708,-9.6149

> view matrix models
> #49,0.87356,0.48653,-0.013541,-86.119,-0.48609,0.87067,-0.075156,61.978,-0.024777,0.072235,0.99708,-10.553

> view matrix models
> #49,0.87356,0.48653,-0.013541,-86.24,-0.48609,0.87067,-0.075156,62.04,-0.024777,0.072235,0.99708,-10.305

> combine #13,14,15,17,18

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '8'  

> select add #50

5168 atoms, 5164 bonds, 6 pseudobonds, 332 residues, 4 models selected  

> select subtract #49

2584 atoms, 2582 bonds, 3 pseudobonds, 166 residues, 2 models selected  

> view matrix models
> #50,0.93679,0.34915,0.022882,-67.087,-0.34379,0.93062,-0.12551,119.74,-0.065117,0.10971,0.99183,-11.544

> color #50 #ff2f92ff

> color #50 #73fa79ff

> select clear

> select add #50

2584 atoms, 2582 bonds, 3 pseudobonds, 166 residues, 2 models selected  

> view matrix models
> #50,0.93679,0.34915,0.022882,-65.243,-0.34379,0.93062,-0.12551,121.05,-0.065117,0.10971,0.99183,-10.833

> view matrix models
> #50,0.93679,0.34915,0.022882,-66.888,-0.34379,0.93062,-0.12551,121.26,-0.065117,0.10971,0.99183,-11.333

> ui mousemode right "move picked models"

> view matrix models
> #8,1,-3.3282e-05,0.00084123,-1.2857,3.3336e-05,1,-6.4811e-05,1.5181,-0.00084122,6.4839e-05,1,0.0042275

> undo

> ui mousemode right "translate selected models"

> view matrix models
> #50,0.93679,0.34915,0.022882,-66.94,-0.34379,0.93062,-0.12551,121.35,-0.065117,0.10971,0.99183,-11.341

> view matrix models
> #50,0.93679,0.34915,0.022882,-66.497,-0.34379,0.93062,-0.12551,121.23,-0.065117,0.10971,0.99183,-11.212

> ui mousemode right "rotate selected models"

> view matrix models
> #50,0.95137,0.30714,0.023853,-60.012,-0.30283,0.94661,-0.11059,106.53,-0.056545,0.097987,0.99358,-10.588

> view matrix models
> #50,0.95512,0.29529,0.02345,-57.974,-0.28815,0.94452,-0.15763,113.84,-0.068695,0.1438,0.98722,-17.296

> ui mousemode right "translate selected models"

> view matrix models
> #50,0.95512,0.29529,0.02345,-57.715,-0.28815,0.94452,-0.15763,111.84,-0.068695,0.1438,0.98722,-18.643

> view matrix models
> #50,0.95512,0.29529,0.02345,-57.982,-0.28815,0.94452,-0.15763,111.98,-0.068695,0.1438,0.98722,-18.67

> view matrix models
> #50,0.95512,0.29529,0.02345,-56.42,-0.28815,0.94452,-0.15763,113.81,-0.068695,0.1438,0.98722,-18.27

> view matrix models
> #50,0.95512,0.29529,0.02345,-56.182,-0.28815,0.94452,-0.15763,113.75,-0.068695,0.1438,0.98722,-18.266

> view matrix models
> #50,0.95512,0.29529,0.02345,-56.208,-0.28815,0.94452,-0.15763,113.75,-0.068695,0.1438,0.98722,-18.269

> view matrix models
> #50,0.95512,0.29529,0.02345,-56.467,-0.28815,0.94452,-0.15763,114.2,-0.068695,0.1438,0.98722,-16.87

> select clear

> hide #!8 models

> show #!8 models

> select add #49

2584 atoms, 2582 bonds, 3 pseudobonds, 166 residues, 2 models selected  

> select add #47

5168 atoms, 5164 bonds, 6 pseudobonds, 332 residues, 4 models selected  

> view matrix models
> #47,0.88554,0.46402,-0.022553,-77.29,-0.46152,0.87314,-0.15691,96.253,-0.053119,0.14936,0.98735,-21.57,#49,0.87356,0.48653,-0.013541,-86.004,-0.48609,0.87067,-0.075156,62.019,-0.024777,0.072235,0.99708,-11.306

> view matrix models
> #47,0.88554,0.46402,-0.022553,-77.01,-0.46152,0.87314,-0.15691,96.184,-0.053119,0.14936,0.98735,-22.419,#49,0.87356,0.48653,-0.013541,-85.724,-0.48609,0.87067,-0.075156,61.951,-0.024777,0.072235,0.99708,-12.156

> view matrix models
> #47,0.88554,0.46402,-0.022553,-76.013,-0.46152,0.87314,-0.15691,97.483,-0.053119,0.14936,0.98735,-22.223,#49,0.87356,0.48653,-0.013541,-84.726,-0.48609,0.87067,-0.075156,63.25,-0.024777,0.072235,0.99708,-11.96

> view matrix models
> #47,0.88554,0.46402,-0.022553,-76.72,-0.46152,0.87314,-0.15691,96.509,-0.053119,0.14936,0.98735,-22.657,#49,0.87356,0.48653,-0.013541,-85.434,-0.48609,0.87067,-0.075156,62.275,-0.024777,0.072235,0.99708,-12.393

> select subtract #47

2584 atoms, 2582 bonds, 3 pseudobonds, 166 residues, 2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #49,0.88645,0.46222,-0.023456,-80.391,-0.4592,0.87207,-0.16922,76.117,-0.057764,0.16078,0.9853,-23.61

> view matrix models
> #49,0.88929,0.45424,-0.053118,-73.014,-0.45014,0.84887,-0.2771,101.87,-0.08078,0.27034,0.95937,-38.622

> view matrix models
> #49,0.89355,0.44482,-0.060903,-70.1,-0.44185,0.8472,-0.29498,104.32,-0.079614,0.29049,0.95356,-42.222

> view matrix models
> #49,0.89623,0.4397,-0.058538,-69.952,-0.43647,0.85063,-0.29311,102.11,-0.079088,0.28825,0.95428,-41.966

> select add #47

5168 atoms, 5164 bonds, 6 pseudobonds, 332 residues, 4 models selected  

> select subtract #49

2584 atoms, 2582 bonds, 3 pseudobonds, 166 residues, 2 models selected  

> view matrix models
> #47,0.91636,0.38618,-0.10559,-47.944,-0.39878,0.85712,-0.32607,122.8,-0.035413,0.3409,0.93943,-59.68

> ui mousemode right "translate selected models"

> view matrix models
> #47,0.91636,0.38618,-0.10559,-47.055,-0.39878,0.85712,-0.32607,123.3,-0.035413,0.3409,0.93943,-59.319

> view matrix models
> #47,0.91636,0.38618,-0.10559,-46.667,-0.39878,0.85712,-0.32607,123.46,-0.035413,0.3409,0.93943,-59.136

> ui mousemode right "move picked models"

> ui mousemode right "rotate selected models"

> view matrix models
> #47,0.95494,0.28553,-0.081015,-36.437,-0.29655,0.90687,-0.2994,86.707,-0.012016,0.30993,0.95068,-59

> ui mousemode right "translate selected models"

> view matrix models
> #47,0.95494,0.28553,-0.081015,-36.868,-0.29655,0.90687,-0.2994,85.166,-0.012016,0.30993,0.95068,-59.299

> view matrix models
> #47,0.95494,0.28553,-0.081015,-36.831,-0.29655,0.90687,-0.2994,85.221,-0.012016,0.30993,0.95068,-59.38

> select add #49

5168 atoms, 5164 bonds, 6 pseudobonds, 332 residues, 4 models selected  

> view matrix models
> #47,0.95494,0.28553,-0.081015,-35.298,-0.29655,0.90687,-0.2994,83.98,-0.012016,0.30993,0.95068,-58.439,#49,0.89623,0.4397,-0.058538,-68.419,-0.43647,0.85063,-0.29311,100.87,-0.079088,0.28825,0.95428,-41.026

> undo

> select subtract #47

2584 atoms, 2582 bonds, 3 pseudobonds, 166 residues, 2 models selected  

> view matrix models
> #49,0.89623,0.4397,-0.058538,-68.62,-0.43647,0.85063,-0.29311,101.02,-0.079088,0.28825,0.95428,-41.011

> view matrix models
> #49,0.89623,0.4397,-0.058538,-68.543,-0.43647,0.85063,-0.29311,99.427,-0.079088,0.28825,0.95428,-41.428

> view matrix models
> #49,0.89623,0.4397,-0.058538,-68.572,-0.43647,0.85063,-0.29311,99.613,-0.079088,0.28825,0.95428,-41.438

> ui mousemode right "rotate selected models"

> view matrix models
> #49,0.92766,0.3704,-0.047461,-61.27,-0.36857,0.88774,-0.27582,74.369,-0.060029,0.27336,0.96004,-42.968

> view matrix models
> #49,0.93591,0.34986,-0.040852,-59.585,-0.34738,0.89761,-0.27133,67.066,-0.058256,0.26813,0.96162,-42.454

> select add #48

5168 atoms, 5164 bonds, 6 pseudobonds, 332 residues, 4 models selected  

> select subtract #49

2584 atoms, 2582 bonds, 3 pseudobonds, 166 residues, 2 models selected  

> view matrix models
> #48,0.96782,0.24343,-0.063765,-31.775,-0.25163,0.93912,-0.23396,101.55,0.0029319,0.24247,0.97015,-51.445

> undo

> ui mousemode right "translate selected models"

> view matrix models
> #48,0.96405,0.25823,-0.062708,-34.381,-0.26558,0.94443,-0.1937,94.755,0.0092032,0.20339,0.97905,-46.182

> view matrix models
> #48,0.96405,0.25823,-0.062708,-34.063,-0.26558,0.94443,-0.1937,95.182,0.0092032,0.20339,0.97905,-46.574

> view matrix models
> #48,0.96405,0.25823,-0.062708,-33.832,-0.26558,0.94443,-0.1937,94.894,0.0092032,0.20339,0.97905,-46.632

> select add #50

5168 atoms, 5164 bonds, 6 pseudobonds, 332 residues, 4 models selected  

> select subtract #48

2584 atoms, 2582 bonds, 3 pseudobonds, 166 residues, 2 models selected  

> ui mousemode right "translate selected models"

> view matrix models
> #50,0.95512,0.29529,0.02345,-58.955,-0.28815,0.94452,-0.15763,116.06,-0.068695,0.1438,0.98722,-17.498

> view matrix models
> #50,0.95512,0.29529,0.02345,-58.964,-0.28815,0.94452,-0.15763,116.07,-0.068695,0.1438,0.98722,-17.709

> ui mousemode right "rotate selected models"

> view matrix models
> #50,0.98767,0.15442,0.025863,-33.857,-0.14009,0.94531,-0.29457,115.24,-0.069936,0.28731,0.95528,-43.436

> ui mousemode right "translate selected models"

> view matrix models
> #50,0.98767,0.15442,0.025863,-35.401,-0.14009,0.94531,-0.29457,114.24,-0.069936,0.28731,0.95528,-44.04

> view matrix models
> #50,0.98767,0.15442,0.025863,-35.778,-0.14009,0.94531,-0.29457,112.94,-0.069936,0.28731,0.95528,-44.186

> view matrix models
> #50,0.98767,0.15442,0.025863,-35.817,-0.14009,0.94531,-0.29457,112.95,-0.069936,0.28731,0.95528,-44.22

> view matrix models
> #50,0.98767,0.15442,0.025863,-36.08,-0.14009,0.94531,-0.29457,113,-0.069936,0.28731,0.95528,-43.837

> ui mousemode right "rotate selected models"

> view matrix models
> #50,0.97608,0.19028,0.10514,-58.312,-0.15545,0.94898,-0.27436,110.99,-0.15198,0.25146,0.95586,-19.804

> view matrix models
> #50,0.9539,0.24132,0.17842,-80.68,-0.19058,0.94633,-0.26103,115.7,-0.23184,0.21499,0.9487,5.5368

> ui mousemode right "translate selected models"

> view matrix models
> #50,0.9539,0.24132,0.17842,-81.165,-0.19058,0.94633,-0.26103,115.93,-0.23184,0.21499,0.9487,7.0112

> ui mousemode right "rotate selected models"

> view matrix models
> #50,0.96787,0.22163,0.11877,-67.117,-0.18707,0.9503,-0.24887,111.84,-0.16802,0.21866,0.96123,-8.8643

> ui mousemode right "translate selected models"

> view matrix models
> #50,0.96787,0.22163,0.11877,-66.509,-0.18707,0.9503,-0.24887,111.75,-0.16802,0.21866,0.96123,-10.105

> select add #48

5168 atoms, 5164 bonds, 6 pseudobonds, 332 residues, 4 models selected  

> select subtract #50

2584 atoms, 2582 bonds, 3 pseudobonds, 166 residues, 2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #48,0.95628,0.29158,-0.022545,-48.169,-0.28983,0.93458,-0.20631,104.46,-0.039085,0.20382,0.97823,-37.131

> ui mousemode right "translate selected models"

> view matrix models
> #48,0.95628,0.29158,-0.022545,-48.247,-0.28983,0.93458,-0.20631,104.95,-0.039085,0.20382,0.97823,-36.432

> ui mousemode right "rotate selected models"

> view matrix models
> #48,0.96541,0.26066,-0.0058344,-46.462,-0.25655,0.94573,-0.19944,94.504,-0.046469,0.19404,0.97989,-33.116

> select add #47

5168 atoms, 5164 bonds, 6 pseudobonds, 332 residues, 4 models selected  

> select subtract #48

2584 atoms, 2582 bonds, 3 pseudobonds, 166 residues, 2 models selected  

> view matrix models
> #47,0.97604,0.21491,-0.034173,-34.595,-0.21559,0.93359,-0.28625,60.64,-0.029615,0.28676,0.95755,-52.102

> select add #49

5168 atoms, 5164 bonds, 6 pseudobonds, 332 residues, 4 models selected  

> select subtract #47

2584 atoms, 2582 bonds, 3 pseudobonds, 166 residues, 2 models selected  

> ui mousemode right "translate selected models"

> view matrix models
> #49,0.93591,0.34986,-0.040852,-58.467,-0.34738,0.89761,-0.27133,65.351,-0.058256,0.26813,0.96162,-42.07

> view matrix models
> #49,0.93591,0.34986,-0.040852,-58.672,-0.34738,0.89761,-0.27133,64.559,-0.058256,0.26813,0.96162,-43.454

> view matrix models
> #49,0.93591,0.34986,-0.040852,-57.921,-0.34738,0.89761,-0.27133,64.087,-0.058256,0.26813,0.96162,-43.357

> view matrix models
> #49,0.93591,0.34986,-0.040852,-57.016,-0.34738,0.89761,-0.27133,64.346,-0.058256,0.26813,0.96162,-43.226

> select add #47

5168 atoms, 5164 bonds, 6 pseudobonds, 332 residues, 4 models selected  

> select subtract #49

2584 atoms, 2582 bonds, 3 pseudobonds, 166 residues, 2 models selected  

> view matrix models
> #47,0.97604,0.21491,-0.034173,-34.561,-0.21559,0.93359,-0.28625,60.61,-0.029615,0.28676,0.95755,-52.095

> undo

> ui mousemode right "rotate selected models"

> view matrix models
> #47,0.95664,0.28616,-0.054367,-42.805,-0.28902,0.90937,-0.29919,83.141,-0.036176,0.30193,0.95264,-53.252

> view matrix models
> #47,0.96899,0.22331,-0.10579,-20.346,-0.2467,0.8497,-0.46599,122.83,-0.014167,0.47764,0.87844,-82.101

> undo

> view matrix models
> #47,0.9496,0.30788,-0.058949,-45.412,-0.31215,0.91148,-0.26791,80.723,-0.028752,0.27281,0.96164,-49.95

> view matrix models
> #47,0.94779,0.31415,-0.054815,-47.335,-0.31764,0.9147,-0.24985,77.338,-0.028352,0.25422,0.96673,-46.862

> ui mousemode right "translate selected models"

> view matrix models
> #47,0.94779,0.31415,-0.054815,-48.454,-0.31764,0.9147,-0.24985,77.697,-0.028352,0.25422,0.96673,-47.174

> view matrix models
> #47,0.94779,0.31415,-0.054815,-47.818,-0.31764,0.9147,-0.24985,78.325,-0.028352,0.25422,0.96673,-46.815

> ui mousemode right "rotate selected models"

> view matrix models
> #47,0.92658,0.36944,-0.070398,-53.007,-0.37407,0.8859,-0.27434,100.93,-0.038986,0.28053,0.95905,-49.123

> view matrix models
> #47,0.94208,0.29841,-0.15308,-22.856,-0.33442,0.87035,-0.36146,114.69,0.025372,0.39172,0.91973,-78.802

> ui mousemode right "translate selected models"

> view matrix models
> #47,0.94208,0.29841,-0.15308,-22.507,-0.33442,0.87035,-0.36146,114.68,0.025372,0.39172,0.91973,-79.867

> ui mousemode right "rotate selected models"

> view matrix models
> #47,0.93313,0.33363,-0.13399,-32.69,-0.35833,0.89345,-0.27082,95.408,0.02936,0.30073,0.95326,-66.919

> view matrix models
> #47,0.93573,0.32385,-0.13977,-29.787,-0.35161,0.88786,-0.29679,100.72,0.027978,0.32685,0.94466,-70.803

> ui mousemode right "translate selected models"

> view matrix models
> #47,0.93573,0.32385,-0.13977,-29.695,-0.35161,0.88786,-0.29679,100.87,0.027978,0.32685,0.94466,-70.949

> view matrix models
> #47,0.93573,0.32385,-0.13977,-28.817,-0.35161,0.88786,-0.29679,101.08,0.027978,0.32685,0.94466,-70.581

> view matrix models
> #47,0.93573,0.32385,-0.13977,-28.423,-0.35161,0.88786,-0.29679,100.74,0.027978,0.32685,0.94466,-70.43

> ui mousemode right "rotate selected models"

> view matrix models
> #47,0.93703,0.32058,-0.1386,-28.175,-0.34848,0.88474,-0.30952,103.46,0.023399,0.33833,0.94074,-71.329

> view matrix models
> #47,0.92464,0.38034,-0.019844,-63.817,-0.36712,0.87621,-0.31223,109.59,-0.10137,0.29598,0.9498,-39.234

> view matrix models
> #47,0.89452,0.44697,-0.0071838,-75.667,-0.42302,0.84116,-0.33692,133.55,-0.14455,0.30442,0.94151,-31.005

> view matrix models
> #47,0.88761,0.4605,-0.0089611,-77.021,-0.4421,0.84638,-0.29696,127.85,-0.12917,0.26755,0.95485,-28.397

> view matrix models
> #47,0.8814,0.46217,0.097591,-98.174,-0.41826,0.85962,-0.29344,119.46,-0.21951,0.21782,0.95098,1.3208

> ui mousemode right "translate selected models"

> view matrix models
> #47,0.8814,0.46217,0.097591,-98.508,-0.41826,0.85962,-0.29344,119.52,-0.21951,0.21782,0.95098,2.3605

> ui mousemode right "rotate selected models"

> view matrix models
> #47,0.96618,0.22264,0.13011,-67.426,-0.18919,0.95486,-0.22901,39.896,-0.17522,0.19665,0.96469,-4.3125

> color #50 black

> undo

[Repeated 1 time(s)]

> ui mousemode right "translate selected models"

> view matrix models
> #47,0.96618,0.22264,0.13011,-67.817,-0.18919,0.95486,-0.22901,35.945,-0.17522,0.19665,0.96469,-4.2705

> ui mousemode right "rotate selected models"

> view matrix models
> #47,0.93167,0.35238,0.088445,-81.918,-0.32096,0.91236,-0.25414,76.496,-0.17025,0.20838,0.96312,-7.5783

> ui mousemode right "translate selected models"

> view matrix models
> #47,0.93167,0.35238,0.088445,-81.571,-0.32096,0.91236,-0.25414,77.426,-0.17025,0.20838,0.96312,-7.3369

> hide #!8 models

> select clear

> hide #!14 models

> show #!14 models

> select add #14

451 atoms, 450 bonds, 1 pseudobond, 29 residues, 2 models selected  

> ui mousemode right "translate selected models"

> select add #13

547 atoms, 545 bonds, 2 pseudobonds, 37 residues, 4 models selected  

> show #!8 models

> view matrix models
> #13,0.93679,0.34915,0.022882,-68.6,-0.34379,0.93062,-0.12551,75.552,-0.065117,0.10971,0.99183,-11.297,#14,0.87715,0.42217,-0.22889,-23.422,-0.28741,0.84334,0.45405,-28.728,0.38472,-0.33249,0.86107,25.034

> ui mousemode right "rotate selected models"

> view matrix models
> #13,0.94055,0.33914,0.018883,-66.358,-0.33166,0.92894,-0.16454,81.136,-0.073345,0.1485,0.98619,-17.116,#14,0.87795,0.41538,-0.23803,-20.322,-0.29377,0.86001,0.41724,-24.051,0.37802,-0.29639,0.87707,15.311

> ui mousemode right "translate selected models"

> view matrix models
> #13,0.94055,0.33914,0.018883,-66.181,-0.33166,0.92894,-0.16454,80.618,-0.073345,0.1485,0.98619,-18.105,#14,0.87795,0.41538,-0.23803,-20.145,-0.29377,0.86001,0.41724,-24.569,0.37802,-0.29639,0.87707,14.322

> view matrix models
> #13,0.94055,0.33914,0.018883,-66.091,-0.33166,0.92894,-0.16454,81.081,-0.073345,0.1485,0.98619,-18.279,#14,0.87795,0.41538,-0.23803,-20.054,-0.29377,0.86001,0.41724,-24.106,0.37802,-0.29639,0.87707,14.147

> view matrix models
> #13,0.94055,0.33914,0.018883,-65.998,-0.33166,0.92894,-0.16454,81.173,-0.073345,0.1485,0.98619,-18.259,#14,0.87795,0.41538,-0.23803,-19.962,-0.29377,0.86001,0.41724,-24.015,0.37802,-0.29639,0.87707,14.168

> ui mousemode right "rotate selected models"

> select subtract #14

96 atoms, 95 bonds, 1 pseudobond, 8 residues, 2 models selected  

> view matrix models
> #13,0.83464,0.55052,-0.017495,-88.69,-0.54158,0.81448,-0.20811,159.23,-0.10032,0.18317,0.97795,-19.619

> ui mousemode right "translate selected models"

[Repeated 1 time(s)]

> view matrix models
> #13,0.83464,0.55052,-0.017495,-87.144,-0.54158,0.81448,-0.20811,160.2,-0.10032,0.18317,0.97795,-19.3

> view matrix models
> #13,0.83464,0.55052,-0.017495,-85.093,-0.54158,0.81448,-0.20811,160.46,-0.10032,0.18317,0.97795,-19.327

> ui mousemode right "rotate selected models"

> view matrix models
> #13,0.79314,0.60856,-0.024242,-89.469,-0.59978,0.77354,-0.20468,181.31,-0.10581,0.17688,0.97853,-16.825

> ui mousemode right "translate selected models"

> view matrix models
> #13,0.79314,0.60856,-0.024242,-89.873,-0.59978,0.77354,-0.20468,180.68,-0.10581,0.17688,0.97853,-15.513

> view matrix models
> #13,0.79314,0.60856,-0.024242,-90.259,-0.59978,0.77354,-0.20468,180.97,-0.10581,0.17688,0.97853,-15.349

> select add #14

547 atoms, 545 bonds, 2 pseudobonds, 37 residues, 4 models selected  

> select subtract #13

451 atoms, 450 bonds, 1 pseudobond, 29 residues, 2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #14,0.87549,0.41224,-0.25213,-16.11,-0.30018,0.87284,0.38477,-19.317,0.37869,-0.26118,0.88791,4.3902

> select clear

> combine #13,14,15,17,18

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '8'  

> hide #!47 models

> hide #!48 models

> hide #!49 models

> hide #!50 models

> hide #!51 models

> show #!51 models

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Fit14-9.cxs"

> combine #13,14,15,17,18

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '8'  

> hide #!51 models

> show #!51 models

> combine #13,14,15,17,18

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '8'  

> combine #13,14,15,17,18

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '8'  

> show #!48 models

> mmaker #51/8 to #48/8

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 8 (#48) with combination, chain 8 (#51),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> color #51 #00fdffff

> color #52 #73fa79ff

> color #53 #fffc79ff

> color #54 #531b93ff

> mmaker #51/8 to #47/8

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 8 (#47) with combination, chain 8 (#51),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> mmaker #52/8 to #48/8

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 8 (#48) with combination, chain 8 (#52),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> mmaker #53/8 to #49/8

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 8 (#49) with combination, chain 8 (#53),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> mmaker #54/8 to #50/8

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 8 (#50) with combination, chain 8 (#54),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> hide #!48 models

> select add #53

2584 atoms, 2582 bonds, 3 pseudobonds, 166 residues, 2 models selected  

> ui mousemode right "translate selected models"

> view matrix models
> #53,0.79283,0.60309,-0.08775,-79.524,-0.59187,0.72762,-0.34679,168.81,-0.1453,0.32688,0.93383,-31.228

> view matrix models
> #53,0.79283,0.60309,-0.08775,-81.065,-0.59187,0.72762,-0.34679,168.68,-0.1453,0.32688,0.93383,-31.509

> ui mousemode right "rotate selected models"

> view matrix models
> #53,0.78882,0.60994,-0.075722,-84.265,-0.60698,0.75369,-0.25204,146.43,-0.096659,0.24478,0.96475,-29.141

> view matrix models
> #53,0.78803,0.61129,-0.073005,-84.967,-0.60962,0.75827,-0.23107,141.63,-0.085894,0.2266,0.97019,-28.329

> view matrix models
> #53,0.77904,0.62492,-0.050785,-90.782,-0.62212,0.7604,-0.18641,134.48,-0.077876,0.17682,0.98116,-21.046

> ui mousemode right "translate selected models"

> view matrix models
> #53,0.77904,0.62492,-0.050785,-91.248,-0.62212,0.7604,-0.18641,136.03,-0.077876,0.17682,0.98116,-20.96

> view matrix models
> #53,0.77904,0.62492,-0.050785,-91.128,-0.62212,0.7604,-0.18641,136.1,-0.077876,0.17682,0.98116,-21.661

> select add #51

5168 atoms, 5164 bonds, 6 pseudobonds, 332 residues, 4 models selected  

> select subtract #53

2584 atoms, 2582 bonds, 3 pseudobonds, 166 residues, 2 models selected  

> view matrix models
> #51,0.78654,0.61619,0.040823,-106.01,-0.57112,0.75097,-0.33145,182.99,-0.23489,0.23738,0.94259,3.8618

> view matrix models
> #51,0.78654,0.61619,0.040823,-105.91,-0.57112,0.75097,-0.33145,182.99,-0.23489,0.23738,0.94259,3.5573

> select clear

> select add #54

2584 atoms, 2582 bonds, 3 pseudobonds, 166 residues, 2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #54,0.84403,0.53603,-0.017022,-88.104,-0.50918,0.79099,-0.33922,231.58,-0.16837,0.29498,0.94055,-22.126

> ui mousemode right "translate selected models"

> view matrix models
> #54,0.84403,0.53603,-0.017022,-87.786,-0.50918,0.79099,-0.33922,232.2,-0.16837,0.29498,0.94055,-23.324

> view matrix models
> #54,0.84403,0.53603,-0.017022,-87.749,-0.50918,0.79099,-0.33922,232.43,-0.16837,0.29498,0.94055,-23.375

> view matrix models
> #54,0.84403,0.53603,-0.017022,-86.705,-0.50918,0.79099,-0.33922,235.08,-0.16837,0.29498,0.94055,-22.186

> view matrix models
> #54,0.84403,0.53603,-0.017022,-85.367,-0.50918,0.79099,-0.33922,233.14,-0.16837,0.29498,0.94055,-21.896

> select clear

> select add #52

2584 atoms, 2582 bonds, 3 pseudobonds, 166 residues, 2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #52,0.8393,0.54154,-0.048038,-79.217,-0.53135,0.79838,-0.2833,201.22,-0.11506,0.2633,0.95783,-30.286

> select add #51

5168 atoms, 5164 bonds, 6 pseudobonds, 332 residues, 4 models selected  

> select subtract #52

2584 atoms, 2582 bonds, 3 pseudobonds, 166 residues, 2 models selected  

> view matrix models
> #51,0.78362,0.62062,-0.027806,-92.259,-0.59428,0.73582,-0.32467,189.57,-0.18103,0.27094,0.94542,-15.186

> select clear

> select add #53

2584 atoms, 2582 bonds, 3 pseudobonds, 166 residues, 2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #53,0.78778,0.61405,-0.048461,-90.908,-0.6044,0.75543,-0.25303,147.35,-0.11876,0.22862,0.96624,-22.076

> select add #51

5168 atoms, 5164 bonds, 6 pseudobonds, 332 residues, 4 models selected  

> view matrix models
> #51,0.78688,0.61561,-0.042924,-88.697,-0.59375,0.73633,-0.32445,189.31,-0.16813,0.28079,0.94493,-19.813,#53,0.79004,0.60971,-0.063966,-87.204,-0.60386,0.75593,-0.25283,147.09,-0.1058,0.23837,0.96539,-26.67

> undo

> ui mousemode right "translate selected models"

> view matrix models
> #51,0.78362,0.62062,-0.027806,-92.47,-0.59428,0.73582,-0.32467,189.61,-0.18103,0.27094,0.94542,-14.385,#53,0.78778,0.61405,-0.048461,-91.119,-0.6044,0.75543,-0.25303,147.39,-0.11876,0.22862,0.96624,-21.276

> undo

> select clear

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Fit14-9.cxs"

> select add #51

2584 atoms, 2582 bonds, 3 pseudobonds, 166 residues, 2 models selected  

> ui mousemode right "rotate selected models"

[Repeated 1 time(s)]

> view matrix models
> #51,0.7749,0.63074,-0.041243,-90.038,-0.62069,0.74697,-0.23828,174.61,-0.11948,0.21024,0.97032,-18.923

> view matrix models
> #51,0.7717,0.63474,-0.039902,-90.572,-0.62828,0.75111,-0.20273,167.91,-0.09871,0.18152,0.97842,-18.282

> ui mousemode right "translate selected models"

> view matrix models
> #51,0.7717,0.63474,-0.039902,-90.685,-0.62828,0.75111,-0.20273,168.04,-0.09871,0.18152,0.97842,-17.341

> select add #53

5168 atoms, 5164 bonds, 6 pseudobonds, 332 residues, 4 models selected  

> select subtract #51

2584 atoms, 2582 bonds, 3 pseudobonds, 166 residues, 2 models selected  

> ui mousemode right "rotate selected models"

[Repeated 1 time(s)]

> view matrix models
> #53,0.77177,0.63318,-0.058665,-89.92,-0.63332,0.75707,-0.1605,133.75,-0.057213,0.16102,0.98529,-23.073

> ui mousemode right "translate selected models"

> view matrix models
> #53,0.77177,0.63318,-0.058665,-90.403,-0.63332,0.75707,-0.1605,134,-0.057213,0.16102,0.98529,-21.421

> ui mousemode right "rotate selected models"

> view matrix models
> #53,0.76959,0.63614,-0.055379,-91.303,-0.63797,0.76235,-0.10868,123.12,-0.026917,0.11897,0.99253,-19.513

> ui mousemode right "translate selected models"

> view matrix models
> #53,0.76959,0.63614,-0.055379,-91.41,-0.63797,0.76235,-0.10868,121.99,-0.026917,0.11897,0.99253,-19.441

> view matrix models
> #53,0.76959,0.63614,-0.055379,-91.955,-0.63797,0.76235,-0.10868,121.83,-0.026917,0.11897,0.99253,-18.306

> ui mousemode right "rotate selected models"

> view matrix models
> #53,0.73827,0.67177,-0.060608,-92.641,-0.67365,0.72985,-0.11628,137.71,-0.033877,0.12667,0.99137,-18.409

> select add #51

5168 atoms, 5164 bonds, 6 pseudobonds, 332 residues, 4 models selected  

> select subtract #53

2584 atoms, 2582 bonds, 3 pseudobonds, 166 residues, 2 models selected  

> ui mousemode right "translate selected models"

> view matrix models
> #51,0.7717,0.63474,-0.039902,-91.085,-0.62828,0.75111,-0.20273,168.46,-0.09871,0.18152,0.97842,-16.003

> view matrix models
> #51,0.7717,0.63474,-0.039902,-91.07,-0.62828,0.75111,-0.20273,168.34,-0.09871,0.18152,0.97842,-16.324

> view matrix models
> #51,0.7717,0.63474,-0.039902,-91.467,-0.62828,0.75111,-0.20273,168.14,-0.09871,0.18152,0.97842,-16.415

> view matrix models
> #51,0.7717,0.63474,-0.039902,-91.445,-0.62828,0.75111,-0.20273,167.89,-0.09871,0.18152,0.97842,-16.415

> view matrix models
> #51,0.7717,0.63474,-0.039902,-91.668,-0.62828,0.75111,-0.20273,167.4,-0.09871,0.18152,0.97842,-16.374

> view matrix models
> #51,0.7717,0.63474,-0.039902,-91.369,-0.62828,0.75111,-0.20273,167.29,-0.09871,0.18152,0.97842,-17.414

> select add #53

5168 atoms, 5164 bonds, 6 pseudobonds, 332 residues, 4 models selected  

> select subtract #53

2584 atoms, 2582 bonds, 3 pseudobonds, 166 residues, 2 models selected  

> select subtract #51

Nothing selected  

> select add #52

2584 atoms, 2582 bonds, 3 pseudobonds, 166 residues, 2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #52,0.84464,0.53263,-0.053674,-77.131,-0.51956,0.79146,-0.32194,208.35,-0.129,0.29981,0.94524,-33.101

> ui mousemode right "translate selected models"

> view matrix models
> #52,0.84464,0.53263,-0.053674,-77.116,-0.51956,0.79146,-0.32194,209.44,-0.129,0.29981,0.94524,-32.04

> view matrix models
> #52,0.84464,0.53263,-0.053674,-77.078,-0.51956,0.79146,-0.32194,209.49,-0.129,0.29981,0.94524,-32.182

> ui mousemode right "rotate selected models"

> view matrix models
> #52,0.8218,0.56821,-0.042205,-82.85,-0.55789,0.78739,-0.26225,205.76,-0.11578,0.23906,0.96408,-25.092

> ui mousemode right "translate selected models"

> view matrix models
> #52,0.8218,0.56821,-0.042205,-82.336,-0.55789,0.78739,-0.26225,204.3,-0.11578,0.23906,0.96408,-24.894

> select clear

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Fit14-9.cxs"

> select add #53

2584 atoms, 2582 bonds, 3 pseudobonds, 166 residues, 2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #53,0.63932,0.76516,-0.076185,-90.706,-0.76749,0.62891,-0.12417,180.46,-0.047097,0.13786,0.98933,-17.871

> ui mousemode right "translate selected models"

> view matrix models
> #53,0.63932,0.76516,-0.076185,-90.392,-0.76749,0.62891,-0.12417,182.2,-0.047097,0.13786,0.98933,-17.82

> ui mousemode right "rotate selected models"

> view matrix models
> #53,0.66408,0.74537,-0.058529,-94.494,-0.73758,0.6403,-0.21447,192.24,-0.12238,0.1856,0.97497,-10.627

> ui mousemode right "translate selected models"

> view matrix models
> #53,0.66408,0.74537,-0.058529,-93.992,-0.73758,0.6403,-0.21447,192.56,-0.12238,0.1856,0.97497,-12.054

> view matrix models
> #53,0.66408,0.74537,-0.058529,-94.121,-0.73758,0.6403,-0.21447,192.83,-0.12238,0.1856,0.97497,-11.702

> ui mousemode right "rotate selected models"

> view matrix models
> #53,0.72318,0.68947,-0.040528,-97.031,-0.68114,0.70227,-0.20701,166.28,-0.11427,0.17731,0.9775,-11.977

> view matrix models
> #53,0.72381,0.6884,-0.046968,-95.597,-0.68158,0.70272,-0.20404,165.66,-0.10746,0.1797,0.97783,-13.928

> select add #51

5168 atoms, 5164 bonds, 6 pseudobonds, 332 residues, 4 models selected  

> ui mousemode right "translate selected models"

> view matrix models
> #51,0.7717,0.63474,-0.039902,-91.646,-0.62828,0.75111,-0.20273,168.71,-0.09871,0.18152,0.97842,-17.526,#53,0.72381,0.6884,-0.046968,-95.874,-0.68158,0.70272,-0.20404,167.08,-0.10746,0.1797,0.97783,-14.041

> view matrix models
> #51,0.7717,0.63474,-0.039902,-91.638,-0.62828,0.75111,-0.20273,168.71,-0.09871,0.18152,0.97842,-17.658,#53,0.72381,0.6884,-0.046968,-95.866,-0.68158,0.70272,-0.20404,167.08,-0.10746,0.1797,0.97783,-14.173

> select clear

> select add #52

2584 atoms, 2582 bonds, 3 pseudobonds, 166 residues, 2 models selected  

> ui mousemode right "rotate selected models"

[Repeated 1 time(s)]

> view matrix models
> #52,0.80921,0.58739,-0.012201,-90.275,-0.56858,0.77773,-0.26807,209.77,-0.14797,0.22386,0.96332,-14.968

> view matrix models
> #52,0.82047,0.57127,-0.022086,-86.878,-0.55597,0.78831,-0.26356,203.98,-0.13315,0.22852,0.96439,-19.163

> select clear

> select add #53

2584 atoms, 2582 bonds, 3 pseudobonds, 166 residues, 2 models selected  

> view matrix models
> #53,0.70954,0.70282,-0.050936,-95.447,-0.69516,0.6863,-0.21386,175.45,-0.11535,0.18715,0.97553,-13.803

> view matrix models
> #53,0.74331,0.65729,-0.12432,-76.929,-0.66139,0.69426,-0.28384,181.32,-0.10025,0.2932,0.95078,-35.406

> view matrix models
> #53,0.74955,0.65065,-0.12181,-77.194,-0.65484,0.70192,-0.28018,177.57,-0.096794,0.28977,0.95219,-35.614

> view matrix models
> #53,0.74392,0.66067,-0.10051,-82.683,-0.6641,0.71411,-0.22138,164.63,-0.074488,0.23144,0.96999,-30.652

> ui mousemode right "translate selected models"

> view matrix models
> #53,0.74392,0.66067,-0.10051,-82.889,-0.6641,0.71411,-0.22138,163.71,-0.074488,0.23144,0.96999,-31.095

> view matrix models
> #53,0.74392,0.66067,-0.10051,-82.439,-0.6641,0.71411,-0.22138,163.69,-0.074488,0.23144,0.96999,-32.785

> view matrix models
> #53,0.74392,0.66067,-0.10051,-82.332,-0.6641,0.71411,-0.22138,163.66,-0.074488,0.23144,0.96999,-33.089

> view matrix models
> #53,0.74392,0.66067,-0.10051,-82.667,-0.6641,0.71411,-0.22138,163.8,-0.074488,0.23144,0.96999,-33.79

> ui mousemode right "rotate selected models"

> view matrix models
> #53,0.74361,0.6622,-0.092393,-84.611,-0.6635,0.71378,-0.22425,164.35,-0.082551,0.22806,0.97014,-31.468

> view matrix models
> #53,0.72006,0.68669,-0.099875,-83.882,-0.68842,0.68885,-0.22707,175.43,-0.08713,0.23226,0.96874,-31.213

> ui mousemode right "translate selected models"

> view matrix models
> #53,0.72006,0.68669,-0.099875,-84.679,-0.68842,0.68885,-0.22707,176.37,-0.08713,0.23226,0.96874,-31.349

> select add #54

5168 atoms, 5164 bonds, 6 pseudobonds, 332 residues, 4 models selected  

> select subtract #53

2584 atoms, 2582 bonds, 3 pseudobonds, 166 residues, 2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #54,0.86908,0.49464,-0.0054776,-83.451,-0.46886,0.82015,-0.32791,216.32,-0.1577,0.28755,0.94469,-23.198

> ui mousemode right "translate selected models"

> view matrix models
> #54,0.86908,0.49464,-0.0054776,-84.839,-0.46886,0.82015,-0.32791,215.37,-0.1577,0.28755,0.94469,-23.484

> ui mousemode right "rotate selected models"

> view matrix models
> #54,0.84439,0.53513,-0.025307,-84.929,-0.50917,0.78694,-0.34852,235,-0.16659,0.30717,0.93696,-24.522

> view matrix models
> #54,0.83139,0.55516,0.024278,-96.989,-0.51209,0.78239,-0.35445,237.81,-0.21577,0.28225,0.93476,-8.7632

> select clear

> select add #54

2584 atoms, 2582 bonds, 3 pseudobonds, 166 residues, 2 models selected  

> ui mousemode right "translate selected models"

> view matrix models
> #54,0.83139,0.55516,0.024278,-95.442,-0.51209,0.78239,-0.35445,238.02,-0.21577,0.28225,0.93476,-8.4907

> view matrix models
> #54,0.83139,0.55516,0.024278,-94.586,-0.51209,0.78239,-0.35445,238.3,-0.21577,0.28225,0.93476,-8.3168

> ui mousemode right "rotate selected models"

> view matrix models
> #54,0.84979,0.52598,0.03465,-93.839,-0.48339,0.80381,-0.34673,226.24,-0.21023,0.2779,0.93733,-8.9685

> ui mousemode right "translate selected models"

> view matrix models
> #54,0.84979,0.52598,0.03465,-92.67,-0.48339,0.80381,-0.34673,225.8,-0.21023,0.2779,0.93733,-8.7668

> view matrix models
> #54,0.84979,0.52598,0.03465,-92.351,-0.48339,0.80381,-0.34673,225.88,-0.21023,0.2779,0.93733,-8.2537

> select clear

> hide #!8 models

> select add #53

2584 atoms, 2582 bonds, 3 pseudobonds, 166 residues, 2 models selected  

> view matrix models
> #53,0.72006,0.68669,-0.099875,-84.703,-0.68842,0.68885,-0.22707,176.39,-0.08713,0.23226,0.96874,-30.805

> view matrix models
> #53,0.72006,0.68669,-0.099875,-84.843,-0.68842,0.68885,-0.22707,176.53,-0.08713,0.23226,0.96874,-29.141

> select subtract #53

Nothing selected  

> show #!8 models

> select add #53

2584 atoms, 2582 bonds, 3 pseudobonds, 166 residues, 2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #53,0.72198,0.68668,-0.084993,-88.27,-0.68885,0.70177,-0.18169,164.43,-0.065116,0.18972,0.97968,-26.241

> ui mousemode right "translate selected models"

> view matrix models
> #53,0.72198,0.68668,-0.084993,-88.505,-0.68885,0.70177,-0.18169,163.29,-0.065116,0.18972,0.97968,-25.02

> view matrix models
> #53,0.72198,0.68668,-0.084993,-88.436,-0.68885,0.70177,-0.18169,163.3,-0.065116,0.18972,0.97968,-25.18

> view matrix models
> #53,0.72198,0.68668,-0.084993,-88.167,-0.68885,0.70177,-0.18169,163.24,-0.065116,0.18972,0.97968,-25.837

> select clear

[Repeated 1 time(s)]

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Fit14-9.cxs"

> combine #13,14,15,17,18

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '8'  

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter Lab/Diorge/Membranes/1.pdb"
> models 53 relModel 8

Invalid "models" argument: invalid models specifier  

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter Lab/Diorge/Membranes/1.pdb"
> models 53 relModel 8

Invalid "models" argument: invalid models specifier  

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter Lab/Diorge/Membranes/1.pdb"
> models 53 relModel #8

Invalid "models" argument: invalid models specifier  

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter Lab/Diorge/Membranes/1.pdb"
> models #53 relModel #8

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter Lab/Diorge/Membranes/2.pdb"
> models #51 relModel #8

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter Lab/Diorge/Membranes/2.pdb"
> models #55 relModel #8

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter Lab/Diorge/Membranes/2.pdb"
> models #51 relModel #8

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter Lab/Diorge/Membranes/3.pdb"
> models #55 relModel #8

[Repeated 1 time(s)]

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter Lab/Diorge/Membranes/4.pdb"
> models #52 relModel #8

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter Lab/Diorge/Membranes/5.pdb"
> models #54 relModel #8

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Fit14-9.cxs"

——— End of log from Mon Jan 8 19:50:54 2024 ———

opened ChimeraX session  

> open "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/pf1-fit2.pdb"

Chain information for pf1-fit2.pdb #56  
---  
Chain | Description  
A7 | No description available  
Ac | No description available  
Ae | No description available  
Af | No description available  
Am | No description available  
Ao | No description available  
Ar | No description available  
Av | No description available  
  

> hide #!13-15,17-18,51-56 atoms

> show #!13-15,17-18,51-56 cartoons

> select add #56

10951 atoms, 10971 bonds, 1 pseudobond, 700 residues, 2 models selected  

> ui mousemode right "translate selected models"

> view matrix models #56,1,0,0,75.213,0,1,0,69.997,0,0,1,35.898

> view matrix models #56,1,0,0,69.231,0,1,0,70.181,0,0,1,63.315

> ui tool show "Fit in Map"

> fitmap #56 inMap #8

Fit molecule pf1-fit2.pdb (#56) to map postprocess_masked330_onepf.mrc (#8)
using 10951 atoms  
average map value = 0.0101, steps = 84  
shifted from previous position = 9.35  
rotated from previous position = 11.9 degrees  
atoms outside contour = 7424, contour level = 0.013465  
  
Position of pf1-fit2.pdb (#56) relative to postprocess_masked330_onepf.mrc
(#8) coordinates:  
Matrix rotation and translation  
0.97925031 -0.20123117 -0.02397601 95.03291912  
0.20193494 0.97888119 0.03184184 45.67549080  
0.01706209 -0.03602273 0.99920531 62.48169484  
Axis -0.16516382 -0.09987550 0.98119611  
Axis point -191.51308972 525.69665493 0.00000000  
Rotation angle (degrees) 11.85562312  
Shift along axis 41.04893332  
  

> hide #!48-55 target m

> hide #!9-21 target m

> select clear

> show #!13 models

> hide #!13 models

> show #!14 models

> show #!15 models

> show #!17 models

> hide #!17 models

> show #!18 models

> select add #18

1330 atoms, 1329 bonds, 1 pseudobond, 84 residues, 2 models selected  

> ui mousemode right "translate selected models"

> view matrix models
> #18,0.97592,-0.21595,-0.030694,51.365,0.21587,0.9764,-0.006095,-12.687,0.031286,-0.00067755,0.99951,-5.4017

> select add #15

1780 atoms, 1778 bonds, 1 pseudobond, 114 residues, 3 models selected  

> select subtract #18

450 atoms, 449 bonds, 30 residues, 1 model selected  

> view matrix models
> #15,0.96754,0.025808,-0.2514,54.643,-0.054053,0.99289,-0.1061,31.106,0.24688,0.11624,0.96205,-64.627

> hide #!8 models

> show #!16 models

> hide #!16 models

> close #16

> combine #15

> hide #!16 models

> show #!16 models

> hide #!14 models

> hide #!15 models

> hide #!18 models

> hide #!56 models

Drag select of 15 residues  

> delete atoms sel

> delete bonds sel

> show #!15 models

> hide #!16 models

> select #15/6:102

17 atoms, 16 bonds, 1 residue, 1 model selected  

> select add #15/6:103

32 atoms, 30 bonds, 2 residues, 1 model selected  
Drag select of 13 residues  

> delete atoms sel

> delete bonds sel

> show #!13 models

> show #!14 models

> hide #!14 models

> hide #!13 models

> show #!16 models

> show #!17 models

> hide #!17 models

> show #!14 models

> hide #!14 models

> show #!13 models

> hide #!13 models

> show #!18 models

> hide #!18 models

> show #!17 models

> hide #!17 models

> show #!56 models

> select add #16

241 atoms, 240 bonds, 15 residues, 1 model selected  

> select #16/6:116

16 atoms, 15 bonds, 1 residue, 1 model selected  

> cofr sel

> ui mousemode right "rotate selected models"

> view matrix models
> #16,0.85622,0.36853,-0.36203,22.659,-0.45882,0.86455,-0.20505,154.04,0.23743,0.34168,0.90933,-101.51

> ui mousemode right "translate selected models"

> view matrix models
> #16,0.85622,0.36853,-0.36203,20.435,-0.45882,0.86455,-0.20505,154.04,0.23743,0.34168,0.90933,-102.86

> ui mousemode right "rotate selected models"

> select add #15

225 atoms, 223 bonds, 16 residues, 2 models selected  

> select add #16

450 atoms, 448 bonds, 30 residues, 2 models selected  

> select subtract #16

209 atoms, 208 bonds, 15 residues, 1 model selected  

> view matrix models
> #15,0.97088,-0.068756,-0.22948,68.183,0.053269,0.99591,-0.073019,3.0315,0.23357,0.058669,0.97057,-52.435

> ui mousemode right "translate selected models"

> view matrix models
> #15,0.97088,-0.068756,-0.22948,64.168,0.053269,0.99591,-0.073019,3.2088,0.23357,0.058669,0.97057,-54.887

> view matrix models
> #15,0.97088,-0.068756,-0.22948,64.781,0.053269,0.99591,-0.073019,2.1974,0.23357,0.058669,0.97057,-54.372

> view matrix models
> #15,0.97088,-0.068756,-0.22948,63.512,0.053269,0.99591,-0.073019,3.1284,0.23357,0.058669,0.97057,-55.219

> view matrix models
> #15,0.97088,-0.068756,-0.22948,62.866,0.053269,0.99591,-0.073019,4.3688,0.23357,0.058669,0.97057,-54.45

> view matrix models
> #15,0.97088,-0.068756,-0.22948,63.068,0.053269,0.99591,-0.073019,4.1194,0.23357,0.058669,0.97057,-54.477

> view matrix models
> #15,0.97088,-0.068756,-0.22948,61.683,0.053269,0.99591,-0.073019,4.9255,0.23357,0.058669,0.97057,-54.801

> show #!17 models

> show #!8 models

> show #!18 models

> select subtract #15

Nothing selected  

> select add #14

451 atoms, 450 bonds, 1 pseudobond, 29 residues, 2 models selected  

> select subtract #14

Nothing selected  

> select add #13

96 atoms, 95 bonds, 1 pseudobond, 8 residues, 2 models selected  

> select subtract #13

Nothing selected  

> select add #18

1330 atoms, 1329 bonds, 1 pseudobond, 84 residues, 2 models selected  

> select subtract #18

Nothing selected  

> select add #17

257 atoms, 259 bonds, 15 residues, 1 model selected  

> ui mousemode right "translate selected models"

> view matrix models
> #17,0.66001,-0.74079,0.125,175.5,0.73369,0.67136,0.10476,-77.72,-0.16153,0.022564,0.98661,29.825

> ui mousemode right "rotate selected models"

> view matrix models
> #17,0.70804,-0.70132,0.082622,167.92,0.69467,0.71276,0.096989,-76.893,-0.12691,-0.011277,0.99185,28.882

> ui mousemode right "translate selected models"

> view matrix models
> #17,0.70804,-0.70132,0.082622,168.04,0.69467,0.71276,0.096989,-76.611,-0.12691,-0.011277,0.99185,28.022

> view matrix models
> #17,0.70804,-0.70132,0.082622,168.49,0.69467,0.71276,0.096989,-76.269,-0.12691,-0.011277,0.99185,27.69

> view matrix models
> #17,0.70804,-0.70132,0.082622,168.62,0.69467,0.71276,0.096989,-76.394,-0.12691,-0.011277,0.99185,27.345

> view matrix models
> #17,0.70804,-0.70132,0.082622,168.34,0.69467,0.71276,0.096989,-76.529,-0.12691,-0.011277,0.99185,28.022

> view matrix models
> #17,0.70804,-0.70132,0.082622,168.27,0.69467,0.71276,0.096989,-77.308,-0.12691,-0.011277,0.99185,27.919

> view matrix models
> #17,0.70804,-0.70132,0.082622,168.25,0.69467,0.71276,0.096989,-76.994,-0.12691,-0.011277,0.99185,27.805

> view matrix models
> #17,0.70804,-0.70132,0.082622,168.27,0.69467,0.71276,0.096989,-76.951,-0.12691,-0.011277,0.99185,27.608

> show #!14 models

> select add #14

708 atoms, 709 bonds, 1 pseudobond, 44 residues, 3 models selected  

> select subtract #17

451 atoms, 450 bonds, 1 pseudobond, 29 residues, 2 models selected  

> ui mousemode right "translate selected models"

> view matrix models
> #14,0.87549,0.41224,-0.25213,-14.712,-0.30018,0.87284,0.38477,-15.451,0.37869,-0.26118,0.88791,4.3848

> view matrix models
> #14,0.87549,0.41224,-0.25213,-14.248,-0.30018,0.87284,0.38477,-13.565,0.37869,-0.26118,0.88791,4.8421

> ui mousemode right "rotate selected models"

> view matrix models
> #14,0.93163,0.30624,0.19565,-88.022,-0.33765,0.92852,0.15445,25.807,-0.13437,-0.20995,0.96844,78.324

> view matrix models
> #14,0.95401,0.25473,0.15805,-74.104,-0.27291,0.95616,0.10625,16.47,-0.12406,-0.1445,0.9817,59.697

> view matrix models
> #14,0.96467,0.25756,0.055467,-57.167,-0.26278,0.95581,0.1318,9.6842,-0.019068,-0.14172,0.98972,37.118

> view matrix models
> #14,0.97104,0.23351,0.050627,-52.305,-0.23813,0.96319,0.12475,4.6456,-0.019633,-0.13319,0.9909,35.168

> view matrix models
> #14,0.87617,0.35776,-0.32302,10.903,-0.31479,0.9322,0.17864,15.935,0.36503,-0.054835,0.92938,-44.833

> ui mousemode right "translate selected models"

> view matrix models
> #14,0.87617,0.35776,-0.32302,9.3196,-0.31479,0.9322,0.17864,15.021,0.36503,-0.054835,0.92938,-46.182

> view matrix models
> #14,0.87617,0.35776,-0.32302,9.967,-0.31479,0.9322,0.17864,15.245,0.36503,-0.054835,0.92938,-46.521

> ui mousemode right "rotate selected models"

> view matrix models
> #14,0.85864,0.42986,-0.2792,-10.516,-0.36649,0.89567,0.2519,19.159,0.35835,-0.11397,0.9266,-31.965

> view matrix models
> #14,0.88594,0.4137,-0.20968,-25.652,-0.36043,0.89863,0.2501,17.688,0.29189,-0.146,0.94524,-15.696

> view matrix models
> #14,0.86936,0.42437,-0.25322,-16.391,-0.36489,0.89681,0.25019,18.932,0.33326,-0.12511,0.9345,-26.192

> view matrix models
> #14,0.89913,0.33098,-0.2864,4.254,-0.27704,0.93694,0.21305,0.2925,0.33885,-0.11221,0.93412,-29.984

> ui mousemode right "translate selected models"

> view matrix models
> #14,0.89913,0.33098,-0.2864,6.1951,-0.27704,0.93694,0.21305,1.0147,0.33885,-0.11221,0.93412,-30.539

> view matrix models
> #14,0.89913,0.33098,-0.2864,6.0839,-0.27704,0.93694,0.21305,1.2734,0.33885,-0.11221,0.93412,-30.396

> view matrix models
> #14,0.89913,0.33098,-0.2864,4.5975,-0.27704,0.93694,0.21305,-1.1072,0.33885,-0.11221,0.93412,-31.003

> show #!13 models

> ui mousemode right "translate selected models"

> select add #13

547 atoms, 545 bonds, 2 pseudobonds, 37 residues, 4 models selected  

> select subtract #14

96 atoms, 95 bonds, 1 pseudobond, 8 residues, 2 models selected  

> view matrix models
> #13,0.79314,0.60856,-0.024242,-90.928,-0.59978,0.77354,-0.20468,184.11,-0.10581,0.17688,0.97853,-15.33

> view matrix models
> #13,0.79314,0.60856,-0.024242,-90.625,-0.59978,0.77354,-0.20468,184.78,-0.10581,0.17688,0.97853,-15.21

> select add #14

547 atoms, 545 bonds, 2 pseudobonds, 37 residues, 4 models selected  

> view matrix models
> #13,0.79314,0.60856,-0.024242,-90.688,-0.59978,0.77354,-0.20468,184.52,-0.10581,0.17688,0.97853,-15.236,#14,0.89913,0.33098,-0.2864,4.5343,-0.27704,0.93694,0.21305,-1.3609,0.33885,-0.11221,0.93412,-31.029

> select subtract #14

96 atoms, 95 bonds, 1 pseudobond, 8 residues, 2 models selected  

> select subtract #13

Nothing selected  

> select add #14

451 atoms, 450 bonds, 1 pseudobond, 29 residues, 2 models selected  

> select subtract #14

Nothing selected  

> select add #13

96 atoms, 95 bonds, 1 pseudobond, 8 residues, 2 models selected  

> view matrix models
> #13,0.79314,0.60856,-0.024242,-90.618,-0.59978,0.77354,-0.20468,182.65,-0.10581,0.17688,0.97853,-15.276

> view matrix models
> #13,0.79314,0.60856,-0.024242,-90.805,-0.59978,0.77354,-0.20468,182.23,-0.10581,0.17688,0.97853,-15.387

> select subtract #13

Nothing selected  

> select add #16

241 atoms, 240 bonds, 15 residues, 1 model selected  

> select subtract #16

Nothing selected  

> select add #17

257 atoms, 259 bonds, 15 residues, 1 model selected  

> select subtract #17

Nothing selected  

> select add #18

1330 atoms, 1329 bonds, 1 pseudobond, 84 residues, 2 models selected  

> select subtract #18

Nothing selected  

> select add #19

2584 atoms, 2582 bonds, 3 pseudobonds, 166 residues, 2 models selected  

> select subtract #19

Nothing selected  

> select add #13

96 atoms, 95 bonds, 1 pseudobond, 8 residues, 2 models selected  

> select subtract #13

Nothing selected  

> select add #14

451 atoms, 450 bonds, 1 pseudobond, 29 residues, 2 models selected  

> select subtract #14

Nothing selected  

> select add #15

209 atoms, 208 bonds, 15 residues, 1 model selected  

> view sel

> ui mousemode right "translate selected models"

> ui mousemode right "rotate selected models"

> view matrix models
> #15,0.96514,-0.13655,-0.2233,74.886,0.12943,0.99051,-0.046291,-14.168,0.22751,0.015775,0.97365,-45.81

> ui mousemode right "translate selected models"

> view matrix models
> #15,0.96514,-0.13655,-0.2233,79.154,0.12943,0.99051,-0.046291,-13.019,0.22751,0.015775,0.97365,-43.135

> ui mousemode right "rotate selected models"

> view matrix models
> #15,0.9589,-0.17873,-0.22037,88.069,0.17664,0.98384,-0.029323,-24.282,0.22205,-0.010809,0.97498,-37.116

> select add #14

660 atoms, 658 bonds, 1 pseudobond, 44 residues, 3 models selected  

> select subtract #14

209 atoms, 208 bonds, 15 residues, 1 model selected  

> select subtract #15

Nothing selected  

> select add #16

241 atoms, 240 bonds, 15 residues, 1 model selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #16,0.85061,0.38736,-0.35555,16.147,-0.41446,0.91007,-4.9863e-05,96.109,0.32355,0.1474,0.93466,-81.8

> ui mousemode right "translate selected models"

> view matrix models
> #16,0.85061,0.38736,-0.35555,16.272,-0.41446,0.91007,-4.9863e-05,96.062,0.32355,0.1474,0.93466,-80.652

> ui mousemode right "rotate selected models"

> view matrix models
> #16,0.86131,0.36145,-0.35707,20.178,-0.39728,0.91721,-0.029831,97.064,0.31672,0.16755,0.9336,-83.535

> view matrix models
> #16,0.89397,0.27219,-0.356,33.2,-0.33598,0.93278,-0.13051,101.71,0.29655,0.23628,0.92533,-93.048

> view matrix models
> #16,0.92278,0.21933,-0.31681,31.658,-0.28636,0.94048,-0.18299,100.91,0.25782,0.25959,0.93067,-91.872

> ui mousemode right "translate selected models"

> view matrix models
> #16,0.92278,0.21933,-0.31681,30.966,-0.28636,0.94048,-0.18299,101.27,0.25782,0.25959,0.93067,-91.696

> view matrix models
> #16,0.92278,0.21933,-0.31681,31.2,-0.28636,0.94048,-0.18299,101.33,0.25782,0.25959,0.93067,-92.342

> view matrix models
> #16,0.92278,0.21933,-0.31681,31.05,-0.28636,0.94048,-0.18299,101.38,0.25782,0.25959,0.93067,-92.311

> select add #15

450 atoms, 448 bonds, 30 residues, 2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #15,0.95904,-0.17784,-0.22048,87.877,0.17569,0.984,-0.029495,-24.096,0.22219,-0.010448,0.97495,-37.213,#16,0.9225,0.22016,-0.31705,30.977,-0.2873,0.94019,-0.18306,101.64,0.25778,0.25996,0.93057,-92.364

> select subtract #15

241 atoms, 240 bonds, 15 residues, 1 model selected  

> select add #15

450 atoms, 448 bonds, 30 residues, 2 models selected  

> select subtract #15

241 atoms, 240 bonds, 15 residues, 1 model selected  

> select subtract #16

Nothing selected  

> select add #16

241 atoms, 240 bonds, 15 residues, 1 model selected  

> select subtract #16

Nothing selected  

> select add #15

209 atoms, 208 bonds, 15 residues, 1 model selected  

> view matrix models
> #15,0.94254,-0.2585,-0.21166,105.17,0.26165,0.96507,-0.013484,-40.278,0.20775,-0.04267,0.97725,-28.536

> select clear

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Fit14-10.cxs"

——— End of log from Tue Jan 9 11:58:46 2024 ———

opened ChimeraX session  

> hide #!56 models

> hide #!18 models

> show #!18 models

> hide #!13 models

> show #!13 models

> hide #!14 models

> show #!14 models

> combine #14

> hide #!13 models

> show #!13 models

> hide #!8 models

> hide #!14-18 target m

> hide #!13 models

> show #!13 models

> hide #!13 models

> show #!14 models

> hide #!14 models

Drag select of 16 residues  

> delete atoms sel

> delete bonds sel

> show #!14 models

> hide #!57 models

Drag select of 12 residues  

> delete atoms sel

> delete bonds sel

> show #!57 models

> show #!8 models

> select add #14

261 atoms, 260 bonds, 1 pseudobond, 17 residues, 2 models selected  

> select add #57

458 atoms, 455 bonds, 2 pseudobonds, 30 residues, 4 models selected  

> ui mousemode right "translate selected models"

> ui mousemode right "rotate selected models"

> view matrix models
> #14,0.88983,0.40916,-0.20197,-26.585,-0.31757,0.87317,0.36977,-9.727,0.32764,-0.26489,0.90691,9.1474,#57,0.88983,0.40916,-0.20197,-26.585,-0.31757,0.87317,0.36977,-9.727,0.32764,-0.26489,0.90691,9.1474

> ui mousemode right "translate selected models"

> view matrix models
> #14,0.88983,0.40916,-0.20197,-27.435,-0.31757,0.87317,0.36977,-9.7574,0.32764,-0.26489,0.90691,10.366,#57,0.88983,0.40916,-0.20197,-27.435,-0.31757,0.87317,0.36977,-9.7574,0.32764,-0.26489,0.90691,10.366

> select subtract #14

197 atoms, 195 bonds, 1 pseudobond, 13 residues, 2 models selected  

> select add #14

458 atoms, 455 bonds, 2 pseudobonds, 30 residues, 4 models selected  

> select subtract #57

261 atoms, 260 bonds, 1 pseudobond, 17 residues, 2 models selected  

> ui mousemode right "rotate selected models"

> select #8

4 models selected  

> select #14/o:123

24 atoms, 23 bonds, 1 residue, 1 model selected  

> view matrix models
> #14,0.86171,0.50704,-0.018976,-76.961,-0.39038,0.68641,0.61356,-3.2765,0.32412,-0.5213,0.78942,86.388

> ui mousemode right "translate selected models"

> view matrix models
> #14,0.86171,0.50704,-0.018976,-78.64,-0.39038,0.68641,0.61356,-1.4301,0.32412,-0.5213,0.78942,89.958

> view matrix models
> #14,0.86171,0.50704,-0.018976,-78.504,-0.39038,0.68641,0.61356,-1.167,0.32412,-0.5213,0.78942,90.391

> ui mousemode right "rotate selected models"

> view matrix models
> #14,0.89914,0.40318,0.17029,-100.2,-0.37525,0.50992,0.77406,1.9431,0.22526,-0.75989,0.60978,193.01

> ui mousemode right "translate selected models"

> view matrix models
> #14,0.89914,0.40318,0.17029,-99.227,-0.37525,0.50992,0.77406,3.5664,0.22526,-0.75989,0.60978,195.14

> ui mousemode right "rotate selected models"

> view matrix models
> #14,0.95336,0.29553,0.061333,-66.796,-0.23784,0.61048,0.75547,-40.356,0.18582,-0.73483,0.6523,189.53

> ui mousemode right "translate selected models"

> view matrix models
> #14,0.95336,0.29553,0.061333,-65.126,-0.23784,0.61048,0.75547,-42.198,0.18582,-0.73483,0.6523,189.18

> select add #14

261 atoms, 260 bonds, 1 pseudobond, 17 residues, 2 models selected  

> select add #57

458 atoms, 455 bonds, 2 pseudobonds, 30 residues, 4 models selected  

> ui mousemode right "translate selected models"

> view matrix models
> #14,0.95336,0.29553,0.061333,-64.858,-0.23784,0.61048,0.75547,-41.394,0.18582,-0.73483,0.6523,189.23,#57,0.88983,0.40916,-0.20197,-27.167,-0.31757,0.87317,0.36977,-8.9541,0.32764,-0.26489,0.90691,10.413

> view matrix models
> #14,0.95336,0.29553,0.061333,-65.125,-0.23784,0.61048,0.75547,-41.433,0.18582,-0.73483,0.6523,189.16,#57,0.88983,0.40916,-0.20197,-27.434,-0.31757,0.87317,0.36977,-8.9928,0.32764,-0.26489,0.90691,10.342

> select subtract #57

261 atoms, 260 bonds, 1 pseudobond, 17 residues, 2 models selected  

> select add #57

458 atoms, 455 bonds, 2 pseudobonds, 30 residues, 4 models selected  

> select subtract #14

197 atoms, 195 bonds, 1 pseudobond, 13 residues, 2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #57,0.79339,0.58536,-0.16699,-54.989,-0.51524,0.79187,0.32782,56.401,0.32413,-0.17405,0.92986,-13.917

> view matrix models
> #57,0.79205,0.58727,-0.16665,-55.223,-0.5174,0.79068,0.32729,57.196,0.32397,-0.17301,0.93011,-14.169

> view matrix models
> #57,0.81687,0.5501,-0.17355,-50.384,-0.47547,0.81248,0.33735,42.073,0.32658,-0.19306,0.92524,-9.2143

> ui mousemode right "translate selected models"

> view matrix models
> #57,0.81687,0.5501,-0.17355,-50.067,-0.47547,0.81248,0.33735,41.397,0.32658,-0.19306,0.92524,-8.041

> view matrix models
> #57,0.81687,0.5501,-0.17355,-49.458,-0.47547,0.81248,0.33735,41.124,0.32658,-0.19306,0.92524,-8.3866

> view matrix models
> #57,0.81687,0.5501,-0.17355,-49.632,-0.47547,0.81248,0.33735,40.656,0.32658,-0.19306,0.92524,-7.829

> show #!13 models

> show #!15 models

> show #!16 models

> show #!17 models

> show #!18 models

> hide #!14 models

> show #!14 models

> hide #!16 models

> show #!16 models

> hide #!17 models

> show #!17 models

> hide #!18 models

> show #!18 models

> hide #!15 models

> show #!15 models

> hide #!16 models

> show #!16 models

> hide #!15 models

> show #!15 models

> select clear

> select add #13

96 atoms, 95 bonds, 1 pseudobond, 8 residues, 2 models selected  

> select subtract #13

Nothing selected  

> select add #14

261 atoms, 260 bonds, 1 pseudobond, 17 residues, 2 models selected  

> select subtract #14

Nothing selected  

> select add #15

209 atoms, 208 bonds, 15 residues, 1 model selected  

> select add #16

450 atoms, 448 bonds, 30 residues, 2 models selected  

> view matrix models
> #15,0.94254,-0.2585,-0.21166,106.09,0.26165,0.96507,-0.013484,-16.952,0.20775,-0.04267,0.97725,-27.973,#16,0.9225,0.22016,-0.31705,31.896,-0.2873,0.94019,-0.18306,124.96,0.25778,0.25996,0.93057,-91.801

> view matrix models
> #15,0.94254,-0.2585,-0.21166,105.98,0.26165,0.96507,-0.013484,-18.181,0.20775,-0.04267,0.97725,-26.886,#16,0.9225,0.22016,-0.31705,31.79,-0.2873,0.94019,-0.18306,123.73,0.25778,0.25996,0.93057,-90.714

> view matrix models
> #15,0.94254,-0.2585,-0.21166,104.58,0.26165,0.96507,-0.013484,-19.257,0.20775,-0.04267,0.97725,-27.845,#16,0.9225,0.22016,-0.31705,30.385,-0.2873,0.94019,-0.18306,122.66,0.25778,0.25996,0.93057,-91.673

> view matrix models
> #15,0.94254,-0.2585,-0.21166,104.16,0.26165,0.96507,-0.013484,-18.417,0.20775,-0.04267,0.97725,-27.982,#16,0.9225,0.22016,-0.31705,29.972,-0.2873,0.94019,-0.18306,123.5,0.25778,0.25996,0.93057,-91.81

> ui mousemode right "rotate selected models"

> view matrix models
> #15,0.95533,-0.19734,-0.22,90.68,0.217,0.97374,0.068836,-27.758,0.20064,-0.1135,0.97307,-11.133,#16,0.90063,0.27636,-0.3354,26.02,-0.32474,0.94084,-0.096789,113.59,0.28881,0.19609,0.93709,-85.683

> ui mousemode right "translate selected models"

> view matrix models
> #15,0.95533,-0.19734,-0.22,92.286,0.217,0.97374,0.068836,-27.584,0.20064,-0.1135,0.97307,-11.084,#16,0.90063,0.27636,-0.3354,27.626,-0.32474,0.94084,-0.096789,113.77,0.28881,0.19609,0.93709,-85.633

> view matrix models
> #15,0.95533,-0.19734,-0.22,92.442,0.217,0.97374,0.068836,-27.728,0.20064,-0.1135,0.97307,-11.789,#16,0.90063,0.27636,-0.3354,27.782,-0.32474,0.94084,-0.096789,113.62,0.28881,0.19609,0.93709,-86.338

> ui mousemode right "translate selected models"

> view matrix models
> #15,0.95533,-0.19734,-0.22,92.237,0.217,0.97374,0.068836,-27.96,0.20064,-0.1135,0.97307,-12.738,#16,0.90063,0.27636,-0.3354,27.577,-0.32474,0.94084,-0.096789,113.39,0.28881,0.19609,0.93709,-87.288

> view matrix models
> #15,0.95533,-0.19734,-0.22,92.072,0.217,0.97374,0.068836,-27.528,0.20064,-0.1135,0.97307,-12.74,#16,0.90063,0.27636,-0.3354,27.412,-0.32474,0.94084,-0.096789,113.82,0.28881,0.19609,0.93709,-87.289

> view matrix models
> #15,0.95533,-0.19734,-0.22,92.761,0.217,0.97374,0.068836,-27.231,0.20064,-0.1135,0.97307,-12.439,#16,0.90063,0.27636,-0.3354,28.101,-0.32474,0.94084,-0.096789,114.12,0.28881,0.19609,0.93709,-86.989

> ui mousemode right "rotate selected models"

> view matrix models
> #15,0.96281,-0.13437,-0.23441,81.125,0.15032,0.9873,0.051493,-13.735,0.22451,-0.084815,0.97077,-22.535,#16,0.87293,0.3302,-0.35912,26.825,-0.38946,0.915,-0.10536,133.68,0.2938,0.23183,0.92733,-93.516

> ui mousemode right "translate selected models"

> view matrix models
> #15,0.96281,-0.13437,-0.23441,81.889,0.15032,0.9873,0.051493,-13.559,0.22451,-0.084815,0.97077,-22.191,#16,0.87293,0.3302,-0.35912,27.589,-0.38946,0.915,-0.10536,133.86,0.2938,0.23183,0.92733,-93.171

> view matrix models
> #15,0.96281,-0.13437,-0.23441,82.152,0.15032,0.9873,0.051493,-13.443,0.22451,-0.084815,0.97077,-22.295,#16,0.87293,0.3302,-0.35912,27.852,-0.38946,0.915,-0.10536,133.97,0.2938,0.23183,0.92733,-93.276

> view matrix models
> #15,0.96281,-0.13437,-0.23441,81.877,0.15032,0.9873,0.051493,-13.52,0.22451,-0.084815,0.97077,-22.451,#16,0.87293,0.3302,-0.35912,27.577,-0.38946,0.915,-0.10536,133.9,0.2938,0.23183,0.92733,-93.432

> view matrix models
> #15,0.96281,-0.13437,-0.23441,81.439,0.15032,0.9873,0.051493,-13.386,0.22451,-0.084815,0.97077,-22.156,#16,0.87293,0.3302,-0.35912,27.139,-0.38946,0.915,-0.10536,134.03,0.2938,0.23183,0.92733,-93.136

> view matrix models
> #15,0.96281,-0.13437,-0.23441,81.328,0.15032,0.9873,0.051493,-13.242,0.22451,-0.084815,0.97077,-22.268,#16,0.87293,0.3302,-0.35912,27.028,-0.38946,0.915,-0.10536,134.17,0.2938,0.23183,0.92733,-93.248

> select subtract #15

241 atoms, 240 bonds, 15 residues, 1 model selected  

> ui mousemode right zoom

> ui mousemode right "translate selected models"

> view matrix models
> #16,0.87293,0.3302,-0.35912,27.172,-0.38946,0.915,-0.10536,134.37,0.2938,0.23183,0.92733,-91.571

> view matrix models
> #16,0.87293,0.3302,-0.35912,27.644,-0.38946,0.915,-0.10536,134.51,0.2938,0.23183,0.92733,-91.568

> ui mousemode right "rotate selected models"

> view matrix models
> #16,0.88888,0.29929,-0.34688,28.982,-0.38645,0.89646,-0.21683,159.58,0.24607,0.32679,0.9125,-100.33

> ui mousemode right "translate selected models"

> view matrix models
> #16,0.88888,0.29929,-0.34688,28.571,-0.38645,0.89646,-0.21683,159.91,0.24607,0.32679,0.9125,-99.177

> select add #15

450 atoms, 448 bonds, 30 residues, 2 models selected  

> select add #17

707 atoms, 707 bonds, 45 residues, 3 models selected  

> select subtract #17

450 atoms, 448 bonds, 30 residues, 2 models selected  

> select subtract #16

209 atoms, 208 bonds, 15 residues, 1 model selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #15,0.99459,-0.09133,-0.049407,29.533,0.094008,0.99406,0.054905,-4.324,0.044099,-0.059252,0.99727,2.4103

> undo

> view matrix models
> #15,0.9599,-0.16055,-0.2298,86.113,0.15787,0.987,-0.030145,1.7496,0.23165,-0.0073413,0.97277,-39.287

> view matrix models
> #15,0.96407,-0.15914,-0.21271,81.595,0.14804,0.98669,-0.067237,11.169,0.22058,0.033331,0.9748,-45.542

> ui mousemode right "translate selected models"

> view matrix models
> #15,0.96407,-0.15914,-0.21271,81.296,0.14804,0.98669,-0.067237,11.313,0.22058,0.033331,0.9748,-44.501

> select add #16

450 atoms, 448 bonds, 30 residues, 2 models selected  

> select subtract #15

241 atoms, 240 bonds, 15 residues, 1 model selected  

> ui mousemode right "translate selected models"

> view matrix models
> #16,0.88888,0.29929,-0.34688,28.265,-0.38645,0.89646,-0.21683,160.12,0.24607,0.32679,0.9125,-97.522

> view matrix models
> #16,0.88888,0.29929,-0.34688,28.463,-0.38645,0.89646,-0.21683,160.29,0.24607,0.32679,0.9125,-97.563

> view matrix models
> #16,0.88888,0.29929,-0.34688,28.462,-0.38645,0.89646,-0.21683,160.29,0.24607,0.32679,0.9125,-97.552

> ui mousemode right "rotate selected models"

> view matrix models
> #16,0.88487,0.24463,-0.39643,50.671,-0.25973,0.96555,0.016098,76.381,0.38671,0.08872,0.91792,-73.365

> ui mousemode right "translate selected models"

> view matrix models
> #16,0.88487,0.24463,-0.39643,50.558,-0.25973,0.96555,0.016098,74.97,0.38671,0.08872,0.91792,-75.873

> select add #15

450 atoms, 448 bonds, 30 residues, 2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #15,0.9587,-0.16887,-0.22885,87.509,0.16509,0.98563,-0.035736,2.0449,0.2316,-0.0035204,0.97281,-38.653,#16,0.88045,0.23406,-0.41233,56.725,-0.23748,0.97041,0.043768,64.276,0.41037,0.059385,0.90998,-72.723

> ui mousemode right "translate selected models"

> view matrix models
> #15,0.9587,-0.16887,-0.22885,87.465,0.16509,0.98563,-0.035736,1.684,0.2316,-0.0035204,0.97281,-39.452,#16,0.88045,0.23406,-0.41233,56.681,-0.23748,0.97041,0.043768,63.915,0.41037,0.059385,0.90998,-73.522

> view matrix models
> #15,0.9587,-0.16887,-0.22885,87.526,0.16509,0.98563,-0.035736,1.3469,0.2316,-0.0035204,0.97281,-39.724,#16,0.88045,0.23406,-0.41233,56.742,-0.23748,0.97041,0.043768,63.578,0.41037,0.059385,0.90998,-73.794

> view matrix models
> #15,0.9587,-0.16887,-0.22885,87.648,0.16509,0.98563,-0.035736,1.5497,0.2316,-0.0035204,0.97281,-39.702,#16,0.88045,0.23406,-0.41233,56.864,-0.23748,0.97041,0.043768,63.781,0.41037,0.059385,0.90998,-73.773

> ui mousemode right "rotate selected models"

> view matrix models
> #15,0.95697,-0.18167,-0.22631,90.119,0.17235,0.98318,-0.060427,5.4965,0.23348,0.018822,0.97218,-44.544,#16,0.88433,0.22157,-0.41094,58.457,-0.23509,0.97181,0.018061,68.067,0.40335,0.080635,0.91149,-77.158

> ui mousemode right "translate selected models"

> view matrix models
> #15,0.95697,-0.18167,-0.22631,89.933,0.17235,0.98318,-0.060427,5.4732,0.23348,0.018822,0.97218,-43.767,#16,0.88433,0.22157,-0.41094,58.272,-0.23509,0.97181,0.018061,68.043,0.40335,0.080635,0.91149,-76.382

> view matrix models
> #15,0.95697,-0.18167,-0.22631,89.688,0.17235,0.98318,-0.060427,5.8145,0.23348,0.018822,0.97218,-43.764,#16,0.88433,0.22157,-0.41094,58.027,-0.23509,0.97181,0.018061,68.385,0.40335,0.080635,0.91149,-76.379

> view matrix models
> #15,0.95697,-0.18167,-0.22631,89.439,0.17235,0.98318,-0.060427,5.7958,0.23348,0.018822,0.97218,-43.543,#16,0.88433,0.22157,-0.41094,57.777,-0.23509,0.97181,0.018061,68.366,0.40335,0.080635,0.91149,-76.158

> select subtract #15

241 atoms, 240 bonds, 15 residues, 1 model selected  

> ui mousemode right "translate selected models"

> view matrix models
> #16,0.88433,0.22157,-0.41094,57.638,-0.23509,0.97181,0.018061,68.642,0.40335,0.080635,0.91149,-76.199

> ui mousemode right "rotate selected models"

> view matrix models
> #16,0.89602,0.18235,-0.40485,62.77,-0.21216,0.97679,-0.029592,72.499,0.39006,0.11241,0.9139,-81.063

> ui mousemode right "translate selected models"

> view matrix models
> #16,0.89602,0.18235,-0.40485,62.511,-0.21216,0.97679,-0.029592,72.643,0.39006,0.11241,0.9139,-80.871

> view matrix models
> #16,0.89602,0.18235,-0.40485,62.566,-0.21216,0.97679,-0.029592,72.291,0.39006,0.11241,0.9139,-81.585

> undo

> select up

126806 atoms, 126759 bonds, 8142 residues, 64 models selected  

> select down

241 atoms, 240 bonds, 15 residues, 1 model selected  

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Fit14-11.cxs"

> select subtract #16

Nothing selected  

> select clear

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> select add #58

2591 atoms, 2586 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> ui mousemode right "translate selected models"

> view matrix models
> #58,0.79314,0.60856,-0.024242,-95.323,-0.59978,0.77354,-0.20468,157.94,-0.10581,0.17688,0.97853,-16.06

> ui tool show "Fit in Map"

> fitmap #58 inMap #8

Fit molecule combination (#58) to map postprocess_masked330_onepf.mrc (#8)
using 2591 atoms  
average map value = 0.01219, steps = 84  
shifted from previous position = 3.83  
rotated from previous position = 6.16 degrees  
atoms outside contour = 1581, contour level = 0.013465  
  
Position of combination (#58) relative to postprocess_masked330_onepf.mrc (#8)
coordinates:  
Matrix rotation and translation  
0.74409403 0.65978717 -0.10490455 -77.06679466  
-0.66504473 0.71659150 -0.21026679 186.37388579  
-0.06355762 0.22622448 0.97199944 -34.09603723  
Axis 0.31278538 -0.02962881 -0.94936160  
Axis point 197.40563079 194.67149122 0.00000000  
Rotation angle (degrees) 44.24667073  
Shift along axis 2.74206582  
  

> color #58 #009051ff

> color #58 #00fa92ff

> select add #59

5182 atoms, 5172 bonds, 8 pseudobonds, 334 residues, 4 models selected  

> select subtract #58

2591 atoms, 2586 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> view matrix models
> #59,0.79314,0.60856,-0.024242,-89.671,-0.59978,0.77354,-0.20468,207.18,-0.10581,0.17688,0.97853,-14.419

> fitmap #58 inMap #8

Fit molecule combination (#58) to map postprocess_masked330_onepf.mrc (#8)
using 2591 atoms  
average map value = 0.01219, steps = 48  
shifted from previous position = 0.0352  
rotated from previous position = 0.0214 degrees  
atoms outside contour = 1580, contour level = 0.013465  
  
Position of combination (#58) relative to postprocess_masked330_onepf.mrc (#8)
coordinates:  
Matrix rotation and translation  
0.74431563 0.65953113 -0.10494250 -77.05170774  
-0.66481427 0.71683946 -0.21015038 186.25749825  
-0.06337379 0.22618549 0.97202052 -34.09591496  
Axis 0.31278696 -0.02979849 -0.94935576  
Axis point 197.38522678 194.63863604 0.00000000  
Rotation angle (degrees) 44.22652310  
Shift along axis 2.71819168  
  

> fitmap #58 inMap #8

Fit molecule combination (#58) to map postprocess_masked330_onepf.mrc (#8)
using 2591 atoms  
average map value = 0.01219, steps = 44  
shifted from previous position = 0.00343  
rotated from previous position = 0.00408 degrees  
atoms outside contour = 1580, contour level = 0.013465  
  
Position of combination (#58) relative to postprocess_masked330_onepf.mrc (#8)
coordinates:  
Matrix rotation and translation  
0.74428462 0.65955729 -0.10499806 -77.04179519  
-0.66485343 0.71680997 -0.21012708 186.26905601  
-0.06332718 0.22620267 0.97201956 -34.10651762  
Axis 0.31276842 -0.02987038 -0.94935961  
Axis point 197.38782958 194.62657242 0.00000000  
Rotation angle (degrees) 44.22904731  
Shift along axis 2.71918300  
  

> fitmap #58 inMap #8

Fit molecule combination (#58) to map postprocess_masked330_onepf.mrc (#8)
using 2591 atoms  
average map value = 0.01219, steps = 44  
shifted from previous position = 0.00666  
rotated from previous position = 0.00457 degrees  
atoms outside contour = 1582, contour level = 0.013465  
  
Position of combination (#58) relative to postprocess_masked330_onepf.mrc (#8)
coordinates:  
Matrix rotation and translation  
0.74426514 0.65958972 -0.10493238 -77.05645631  
-0.66486851 0.71678955 -0.21014900 186.27849395  
-0.06339769 0.22617281 0.97202191 -34.09139816  
Axis 0.31275407 -0.02977193 -0.94936743  
Axis point 197.38388845 194.64370350 0.00000000  
Rotation angle (degrees) 44.23058954  
Shift along axis 2.71967187  
  

> fitmap #58 inMap #8

Fit molecule combination (#58) to map postprocess_masked330_onepf.mrc (#8)
using 2591 atoms  
average map value = 0.01219, steps = 44  
shifted from previous position = 0.027  
rotated from previous position = 0.0124 degrees  
atoms outside contour = 1583, contour level = 0.013465  
  
Position of combination (#58) relative to postprocess_masked330_onepf.mrc (#8)
coordinates:  
Matrix rotation and translation  
0.74424362 0.65964149 -0.10475941 -77.09427479  
-0.66487218 0.71675279 -0.21026275 186.30248217  
-0.06361143 0.22613833 0.97201597 -34.06416347  
Axis 0.31279611 -0.02949335 -0.94936228  
Axis point 197.38454756 194.69740993 0.00000000  
Rotation angle (degrees) 44.23322655  
Shift along axis 2.72975893  
  

> fitmap #59 inMap #8

Fit molecule combination (#59) to map postprocess_masked330_onepf.mrc (#8)
using 2591 atoms  
average map value = 0.01318, steps = 84  
shifted from previous position = 2.27  
rotated from previous position = 6.34 degrees  
atoms outside contour = 1484, contour level = 0.013465  
  
Position of combination (#59) relative to postprocess_masked330_onepf.mrc (#8)
coordinates:  
Matrix rotation and translation  
0.80707685 0.59042814 -0.00464339 -93.49300607  
-0.58784796 0.80276323 -0.10002985 175.12832501  
-0.05533290 0.08346138 0.99497360 -7.32182999  
Axis 0.15373507 0.04246936 -0.98719901  
Axis point 220.55786790 230.49154909 0.00000000  
Rotation angle (degrees) 36.63944250  
Shift along axis 0.29253791  
  

> color #58 #0433ffff

> select add #60

5182 atoms, 5172 bonds, 8 pseudobonds, 334 residues, 4 models selected  

> select subtract #59

2591 atoms, 2586 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> view matrix models
> #60,0.79314,0.60856,-0.024242,-99.326,-0.59978,0.77354,-0.20468,132.47,-0.10581,0.17688,0.97853,-9.568

> fitmap #59 inMap #8

Fit molecule combination (#59) to map postprocess_masked330_onepf.mrc (#8)
using 2591 atoms  
average map value = 0.01318, steps = 44  
shifted from previous position = 0.0227  
rotated from previous position = 0.025 degrees  
atoms outside contour = 1483, contour level = 0.013465  
  
Position of combination (#59) relative to postprocess_masked330_onepf.mrc (#8)
coordinates:  
Matrix rotation and translation  
0.80692514 0.59063700 -0.00444416 -93.55278983  
-0.58805526 0.80264751 -0.09973958 175.12338785  
-0.05534279 0.08309578 0.99500365 -7.25869046  
Axis 0.15314462 0.04263317 -0.98728372  
Axis point 220.41444142 230.52405964 0.00000000  
Rotation angle (degrees) 36.65083649  
Shift along axis 0.30534633  
  

> fitmap #60 inMap #8

Fit molecule combination (#60) to map postprocess_masked330_onepf.mrc (#8)
using 2591 atoms  
average map value = 0.008678, steps = 216  
shifted from previous position = 9.11  
rotated from previous position = 13.1 degrees  
atoms outside contour = 1871, contour level = 0.013465  
  
Position of combination (#60) relative to postprocess_masked330_onepf.mrc (#8)
coordinates:  
Matrix rotation and translation  
0.67036005 0.71954272 -0.18131653 -60.63700394  
-0.74203580 0.64986466 -0.16449559 181.02162202  
-0.00053040 0.24481463 0.96956976 -49.81749717  
Axis 0.26777879 -0.11827384 -0.95619340  
Axis point 167.76162340 164.84419696 0.00000000  
Rotation angle (degrees) 49.84202942  
Shift along axis 9.98773667  
  

> color #58 #ff8ad8ff

> color #60 #00fdffff

> select clear

> color #59 #d783ffff

> color #59 #941751ff

> color #59 #00f900ff

> select clear

> ui windowfill toggle

[Repeated 1 time(s)]

> volume #8 level 0.008765

> hide #!8 models

> show #!8 models

> select add #57

197 atoms, 195 bonds, 1 pseudobond, 13 residues, 2 models selected  

> select subtract #57

Nothing selected  

> select add #15

209 atoms, 208 bonds, 15 residues, 1 model selected  

> select subtract #15

Nothing selected  

> select add #14

261 atoms, 260 bonds, 1 pseudobond, 17 residues, 2 models selected  

> hide #!8 models

> select #57/o:132

24 atoms, 23 bonds, 1 residue, 1 model selected  

> select #14/o:131

17 atoms, 16 bonds, 1 residue, 1 model selected  

> show sel atoms

> select #14/o:131

17 atoms, 16 bonds, 1 residue, 1 model selected  

> select #14/o:131

17 atoms, 16 bonds, 1 residue, 1 model selected  

> select #57/o:132

24 atoms, 23 bonds, 1 residue, 1 model selected  

> select #14/o:131

17 atoms, 16 bonds, 1 residue, 1 model selected  

> select #14/o:131@HB3

1 atom, 1 residue, 1 model selected  

> cofr sel

> ui mousemode right "rotate selected models"

> view matrix models
> #14,0.95749,0.28726,0.026545,-57.611,-0.21687,0.65605,0.72288,-48.743,0.19024,-0.69791,0.69046,173.42

> view matrix models
> #14,0.98052,0.19259,-0.03849,-30.151,-0.12852,0.77739,0.61576,-70.642,0.14851,-0.59882,0.787,142.69

> select #14/o:131

17 atoms, 16 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select clear

> select #14/o:131

17 atoms, 16 bonds, 1 residue, 1 model selected  

> view matrix models
> #14,0.96641,0.14721,-0.21066,14.651,-0.035919,0.88902,0.45645,-81.457,0.25447,-0.43356,0.86445,73.257

> ui mousemode right "translate selected models"

> view matrix models
> #14,0.96641,0.14721,-0.21066,14.243,-0.035919,0.88902,0.45645,-81.703,0.25447,-0.43356,0.86445,71.325

> view matrix models
> #14,0.96641,0.14721,-0.21066,15.814,-0.035919,0.88902,0.45645,-84.024,0.25447,-0.43356,0.86445,71.223

> view matrix models
> #14,0.96641,0.14721,-0.21066,15.938,-0.035919,0.88902,0.45645,-83.939,0.25447,-0.43356,0.86445,71.056

> view matrix models
> #14,0.96641,0.14721,-0.21066,15.95,-0.035919,0.88902,0.45645,-84.151,0.25447,-0.43356,0.86445,70.966

> view matrix models
> #14,0.96641,0.14721,-0.21066,15.984,-0.035919,0.88902,0.45645,-84.115,0.25447,-0.43356,0.86445,70.827

> view matrix models
> #14,0.96641,0.14721,-0.21066,16.014,-0.035919,0.88902,0.45645,-84.136,0.25447,-0.43356,0.86445,70.816

> view matrix models
> #14,0.96641,0.14721,-0.21066,16.117,-0.035919,0.88902,0.45645,-84.15,0.25447,-0.43356,0.86445,71.057

> show #!8 models

> close #58-60

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> select add #58

2608 atoms, 2602 bonds, 4 pseudobonds, 168 residues, 3 models selected  

> ui mousemode right "translate selected models"

> view matrix models
> #14,0.96641,0.14721,-0.21066,11.039,-0.035919,0.88902,0.45645,-109.06,0.25447,-0.43356,0.86445,68.987,#58,0.79314,0.60856,-0.024242,-95.884,-0.59978,0.77354,-0.20468,157.32,-0.10581,0.17688,0.97853,-17.457

> fitmap #58 inMap #8

Fit molecule combination (#58) to map postprocess_masked330_onepf.mrc (#8)
using 2591 atoms  
average map value = 0.01184, steps = 104  
shifted from previous position = 4.53  
rotated from previous position = 7.3 degrees  
atoms outside contour = 1318, contour level = 0.0087645  
  
Position of combination (#58) relative to postprocess_masked330_onepf.mrc (#8)
coordinates:  
Matrix rotation and translation  
0.72340790 0.68298775 -0.10103836 -79.88425710  
-0.68733769 0.69860901 -0.19877716 193.46185285  
-0.06517606 0.21324444 0.97482249 -31.41129711  
Axis 0.28784984 -0.02505441 -0.95734777  
Axis point 195.18686452 196.94825878 0.00000000  
Rotation angle (degrees) 45.69964666  
Shift along axis 2.22979268  
  

> select add #59

5199 atoms, 5188 bonds, 8 pseudobonds, 335 residues, 5 models selected  

> select subtract #58

2608 atoms, 2602 bonds, 4 pseudobonds, 168 residues, 3 models selected  

> view matrix models
> #14,0.96641,0.14721,-0.21066,5.673,-0.035919,0.88902,0.45645,-161.64,0.25447,-0.43356,0.86445,65.462,#59,0.79314,0.60856,-0.024242,-96.171,-0.59978,0.77354,-0.20468,129.66,-0.10581,0.17688,0.97853,-18.912

> fitmap #59 inMap #8

Fit molecule combination (#59) to map postprocess_masked330_onepf.mrc (#8)
using 2591 atoms  
average map value = 0.008645, steps = 176  
shifted from previous position = 6.32  
rotated from previous position = 13.3 degrees  
atoms outside contour = 1637, contour level = 0.0087645  
  
Position of combination (#59) relative to postprocess_masked330_onepf.mrc (#8)
coordinates:  
Matrix rotation and translation  
0.65941397 0.73380172 -0.16342658 -65.76048439  
-0.75171214 0.64066505 -0.15645173 183.70936762  
-0.01010285 0.22601621 0.97407115 -44.43283811  
Axis 0.24809748 -0.09945731 -0.96361605  
Axis point 164.75436769 168.86761848 0.00000000  
Rotation angle (degrees) 50.42593976  
Shift along axis 8.22994619  
  

> select add #60

5199 atoms, 5188 bonds, 8 pseudobonds, 335 residues, 5 models selected  

> select subtract #59

2608 atoms, 2602 bonds, 4 pseudobonds, 168 residues, 3 models selected  

> view matrix models
> #14,0.96641,0.14721,-0.21066,3.9812,-0.035919,0.88902,0.45645,-135.7,0.25447,-0.43356,0.86445,66.518,#60,0.79314,0.60856,-0.024242,-92.497,-0.59978,0.77354,-0.20468,208.18,-0.10581,0.17688,0.97853,-14.332

> undo

[Repeated 7 time(s)]

> ui mousemode right "translate selected models"

> view matrix models
> #14,0.96641,0.14721,-0.21066,15.819,-0.035919,0.88902,0.45645,-84.136,0.25447,-0.43356,0.86445,70.511

> view matrix models
> #14,0.96641,0.14721,-0.21066,15.997,-0.035919,0.88902,0.45645,-83.964,0.25447,-0.43356,0.86445,70.134

> view matrix models
> #14,0.96641,0.14721,-0.21066,15.658,-0.035919,0.88902,0.45645,-83.786,0.25447,-0.43356,0.86445,69.803

> hide #!60 models

> hide #!59 models

> hide #!58 models

> select add #57

214 atoms, 211 bonds, 1 pseudobond, 14 residues, 3 models selected  

> select subtract #57

17 atoms, 16 bonds, 1 residue, 1 model selected  

> select add #14

261 atoms, 260 bonds, 1 pseudobond, 17 residues, 2 models selected  

> select subtract #14

Nothing selected  

> select add #14

261 atoms, 260 bonds, 1 pseudobond, 17 residues, 2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #14,0.92754,0.36705,-0.070313,-48.918,-0.28584,0.81795,0.49925,-28.74,0.24076,-0.44298,0.8636,74.573

> ui mousemode right "translate selected models"

> view matrix models
> #14,0.92754,0.36705,-0.070313,-50.785,-0.28584,0.81795,0.49925,-26.44,0.24076,-0.44298,0.8636,74.752

> view matrix models
> #14,0.92754,0.36705,-0.070313,-50.585,-0.28584,0.81795,0.49925,-26.516,0.24076,-0.44298,0.8636,74.743

> ui mousemode right "translate selected models"

> ui mousemode right "rotate selected models"

> view matrix models
> #14,0.86984,0.47181,-0.14417,-47.047,-0.39183,0.83826,0.37919,12.628,0.29975,-0.27334,0.91402,18.642

> ui mousemode right "translate selected models"

> view matrix models
> #14,0.86984,0.47181,-0.14417,-47.56,-0.39183,0.83826,0.37919,12.717,0.29975,-0.27334,0.91402,15.127

> view matrix models
> #14,0.86984,0.47181,-0.14417,-48.097,-0.39183,0.83826,0.37919,12.406,0.29975,-0.27334,0.91402,15.105

> view matrix models
> #14,0.86984,0.47181,-0.14417,-47.937,-0.39183,0.83826,0.37919,11.702,0.29975,-0.27334,0.91402,15.923

> view matrix models
> #14,0.86984,0.47181,-0.14417,-48.036,-0.39183,0.83826,0.37919,12.11,0.29975,-0.27334,0.91402,15.699

> view matrix models
> #14,0.86984,0.47181,-0.14417,-48.702,-0.39183,0.83826,0.37919,12.145,0.29975,-0.27334,0.91402,16.298

> select subtract #14

Nothing selected  

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> close #58-60

> select add #61

2591 atoms, 2586 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> ui mousemode right "translate selected models"

> view matrix models
> #61,0.79314,0.60856,-0.024242,-95.157,-0.59978,0.77354,-0.20468,157.93,-0.10581,0.17688,0.97853,-17.598

> fitmap #61 inMap #8

Fit molecule combination (#61) to map postprocess_masked330_onepf.mrc (#8)
using 2591 atoms  
average map value = 0.01167, steps = 88  
shifted from previous position = 4.84  
rotated from previous position = 6.45 degrees  
atoms outside contour = 1329, contour level = 0.0087645  
  
Position of combination (#61) relative to postprocess_masked330_onepf.mrc (#8)
coordinates:  
Matrix rotation and translation  
0.72716296 0.68550167 -0.03635234 -93.25529172  
-0.68175550 0.71496871 -0.15501352 178.17364319  
-0.08027124 0.13750350 0.98724329 -12.51901719  
Axis 0.20910684 0.03139559 -0.97738869  
Axis point 175.54784471 205.39983784 0.00000000  
Rotation angle (degrees) 44.38240726  
Shift along axis -1.67050748  
  

> select add #62

5182 atoms, 5172 bonds, 8 pseudobonds, 334 residues, 4 models selected  

> select subtract #61

2591 atoms, 2586 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> view matrix models
> #62,0.79314,0.60856,-0.024242,-98.708,-0.59978,0.77354,-0.20468,129.38,-0.10581,0.17688,0.97853,-20.221

> fitmap #62 inMap #8

Fit molecule combination (#62) to map postprocess_masked330_onepf.mrc (#8)
using 2591 atoms  
average map value = 0.006763, steps = 68  
shifted from previous position = 5.31  
rotated from previous position = 3.67 degrees  
atoms outside contour = 1772, contour level = 0.0087645  
  
Position of combination (#62) relative to postprocess_masked330_onepf.mrc (#8)
coordinates:  
Matrix rotation and translation  
0.82415686 0.56537942 -0.03334032 -91.74786585  
-0.56199508 0.80908875 -0.17186309 109.60395796  
-0.07019258 0.16037924 0.98455650 -20.41642587  
Axis 0.28254552 0.03133990 -0.95874180  
Axis point 127.12652693 200.35905569 0.00000000  
Rotation angle (degrees) 36.01129952  
Shift along axis -2.91389029  
  

> select add #63

5182 atoms, 5172 bonds, 8 pseudobonds, 334 residues, 4 models selected  

> select subtract #62

2591 atoms, 2586 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> view matrix models
> #63,0.79314,0.60856,-0.024242,-89.308,-0.59978,0.77354,-0.20468,207.53,-0.10581,0.17688,0.97853,-13.035

> fitmap #63 inMap #8

Fit molecule combination (#63) to map postprocess_masked330_onepf.mrc (#8)
using 2591 atoms  
average map value = 0.01285, steps = 132  
shifted from previous position = 3.23  
rotated from previous position = 9.96 degrees  
atoms outside contour = 1265, contour level = 0.0087645  
  
Position of combination (#63) relative to postprocess_masked330_onepf.mrc (#8)
coordinates:  
Matrix rotation and translation  
0.79088704 0.61115294 0.03146071 -102.31801641  
-0.60987973 0.79139101 -0.04179699 170.11847511  
-0.05044208 0.01386945 0.99863068 7.70878222  
Axis 0.04544044 0.06685713 -0.99672729  
Axis point 198.56302310 235.28730403 0.00000000  
Rotation angle (degrees) 37.77200725  
Shift along axis -0.95929534  
  

> color #61 #73fdffff

> color #62 #76d6ffff

> color #63 #ff85ffff

> select clear

> hide #!57,61-63 target m

> hide #!13-19 target m

> show #!9 models

> hide #!8 models

> hide #!9 models

> show #!61-63 target m

> show #!57 models

> show #!13-18 target m

> hide #!14 models

> show #!14 models

> select add #14

261 atoms, 260 bonds, 1 pseudobond, 17 residues, 2 models selected  

> select add #13

357 atoms, 355 bonds, 2 pseudobonds, 25 residues, 4 models selected  

> select subtract #13

261 atoms, 260 bonds, 1 pseudobond, 17 residues, 2 models selected  

> select add #15

470 atoms, 468 bonds, 1 pseudobond, 32 residues, 3 models selected  

> select subtract #15

261 atoms, 260 bonds, 1 pseudobond, 17 residues, 2 models selected  

> select add #16

502 atoms, 500 bonds, 1 pseudobond, 32 residues, 3 models selected  

> select subtract #16

261 atoms, 260 bonds, 1 pseudobond, 17 residues, 2 models selected  

> select add #17

518 atoms, 519 bonds, 1 pseudobond, 32 residues, 3 models selected  

> select subtract #17

261 atoms, 260 bonds, 1 pseudobond, 17 residues, 2 models selected  

> select add #18

1591 atoms, 1589 bonds, 2 pseudobonds, 101 residues, 4 models selected  

> select subtract #18

261 atoms, 260 bonds, 1 pseudobond, 17 residues, 2 models selected  

> select add #33

2845 atoms, 2842 bonds, 4 pseudobonds, 183 residues, 4 models selected  

> select subtract #33

261 atoms, 260 bonds, 1 pseudobond, 17 residues, 2 models selected  

> select add #57

458 atoms, 455 bonds, 2 pseudobonds, 30 residues, 4 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #14,0.89894,0.3731,-0.22959,-16.973,-0.34639,0.9262,0.14888,28.376,0.26819,-0.054303,0.96183,-33.524,#57,0.85589,0.45056,-0.25389,-20.479,-0.43938,0.89243,0.10252,61.216,0.27277,0.023807,0.96178,-50.992

> view matrix models
> #14,0.92224,0.26952,-0.27719,9.7336,-0.25555,0.96296,0.086052,14.731,0.29011,-0.0085242,0.95695,-46.68,#57,0.88966,0.34755,-0.29617,3.195,-0.35281,0.93495,0.037345,47.628,0.28989,0.071269,0.9544,-63.14

> ui mousemode right "translate selected models"

> view matrix models
> #14,0.92224,0.26952,-0.27719,10.856,-0.25555,0.96296,0.086052,15.487,0.29011,-0.0085242,0.95695,-49.797,#57,0.88966,0.34755,-0.29617,4.3175,-0.35281,0.93495,0.037345,48.385,0.28989,0.071269,0.9544,-66.256

> view matrix models
> #14,0.92224,0.26952,-0.27719,10.764,-0.25555,0.96296,0.086052,15.006,0.29011,-0.0085242,0.95695,-50.12,#57,0.88966,0.34755,-0.29617,4.2251,-0.35281,0.93495,0.037345,47.903,0.28989,0.071269,0.9544,-66.58

> select add #43

3042 atoms, 3037 bonds, 5 pseudobonds, 196 residues, 6 models selected  

> select subtract #43

458 atoms, 455 bonds, 2 pseudobonds, 30 residues, 4 models selected  

> select add #43

3042 atoms, 3037 bonds, 5 pseudobonds, 196 residues, 6 models selected  

> select subtract #43

458 atoms, 455 bonds, 2 pseudobonds, 30 residues, 4 models selected  

> select add #8

458 atoms, 455 bonds, 2 pseudobonds, 30 residues, 6 models selected  

> select subtract #8

458 atoms, 455 bonds, 2 pseudobonds, 30 residues, 4 models selected  

> show #!8 models

> ui mousemode right "translate selected models"

> view matrix models
> #14,0.92224,0.26952,-0.27719,11.219,-0.25555,0.96296,0.086052,15.331,0.29011,-0.0085242,0.95695,-50.53,#57,0.88966,0.34755,-0.29617,4.6807,-0.35281,0.93495,0.037345,48.229,0.28989,0.071269,0.9544,-66.99

> ui mousemode right "rotate selected models"

> view matrix models
> #14,0.95166,0.27886,-0.12876,-24.959,-0.2684,0.95883,0.092822,17.437,0.14935,-0.053775,0.98732,-19.07,#57,0.91803,0.3676,-0.14861,-33.431,-0.36516,0.92988,0.044396,50.382,0.15451,0.01351,0.9879,-34.523

> view matrix models
> #14,0.95256,0.27914,-0.12125,-26.633,-0.26906,0.95861,0.093105,17.559,0.14222,-0.056064,0.98825,-17.361,#57,0.9189,0.36837,-0.14113,-35.197,-0.3658,0.92962,0.044694,50.507,0.14766,0.010556,0.98898,-32.755

> close #61-63

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> select subtract #57

261 atoms, 260 bonds, 1 pseudobond, 17 residues, 2 models selected  

> select subtract #14

Nothing selected  

> select add #58

2591 atoms, 2586 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> ui mousemode right "translate selected models"

> view matrix models
> #58,0.79314,0.60856,-0.024242,-94.408,-0.59978,0.77354,-0.20468,155.13,-0.10581,0.17688,0.97853,-15.561

> fitmap #58 inMap #8

Fit molecule combination (#58) to map postprocess_masked330_onepf.mrc (#8)
using 2591 atoms  
average map value = 0.01093, steps = 196  
shifted from previous position = 4.5  
rotated from previous position = 9.81 degrees  
atoms outside contour = 1421, contour level = 0.0087645  
  
Position of combination (#58) relative to postprocess_masked330_onepf.mrc (#8)
coordinates:  
Matrix rotation and translation  
0.70179770 0.71218639 0.01644775 -105.26319200  
-0.70639620 0.69870627 -0.11319873 178.53008290  
-0.09211074 0.06782398 0.99343622 5.43930489  
Axis 0.12621857 0.07569269 -0.98911045  
Axis point 161.74746308 214.61555211 0.00000000  
Rotation angle (degrees) 45.81558297  
Shift along axis -5.15281979  
  

> select add #59

5182 atoms, 5172 bonds, 8 pseudobonds, 334 residues, 4 models selected  

> select subtract #58

2591 atoms, 2586 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> view matrix models
> #59,0.79314,0.60856,-0.024242,-97.069,-0.59978,0.77354,-0.20468,131.35,-0.10581,0.17688,0.97853,-15.562

> fitmap #59 inMap #8

Fit molecule combination (#59) to map postprocess_masked330_onepf.mrc (#8)
using 2591 atoms  
average map value = 0.00833, steps = 316  
shifted from previous position = 5.66  
rotated from previous position = 13.8 degrees  
atoms outside contour = 1627, contour level = 0.0087645  
  
Position of combination (#59) relative to postprocess_masked330_onepf.mrc (#8)
coordinates:  
Matrix rotation and translation  
0.63607578 0.77094077 -0.03252577 -96.00329035  
-0.76833478 0.62890988 -0.11888659 181.19905140  
-0.07119874 0.10061156 0.99237496 -5.65834605  
Axis 0.14112662 0.02486484 -0.98967925  
Axis point 143.40902540 191.59368369 0.00000000  
Rotation angle (degrees) 51.04717499  
Shift along axis -3.44318661  
  

> select add #60

5182 atoms, 5172 bonds, 8 pseudobonds, 334 residues, 4 models selected  

> select subtract #59

2591 atoms, 2586 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> view matrix models
> #60,0.79314,0.60856,-0.024242,-90.375,-0.59978,0.77354,-0.20468,207.25,-0.10581,0.17688,0.97853,-16.1

> fitmap #60 inMap #8

Fit molecule combination (#60) to map postprocess_masked330_onepf.mrc (#8)
using 2591 atoms  
average map value = 0.01256, steps = 140  
shifted from previous position = 2.67  
rotated from previous position = 13.2 degrees  
atoms outside contour = 1300, contour level = 0.0087645  
  
Position of combination (#60) relative to postprocess_masked330_onepf.mrc (#8)
coordinates:  
Matrix rotation and translation  
0.77356630 0.62976959 0.07060767 -111.40537602  
-0.63143613 0.77542609 0.00167044 169.42512779  
-0.05369904 -0.04587643 0.99750277 22.88459313  
Axis -0.03749137 0.09801757 -0.99447823  
Axis point 182.34880026 242.57971802 0.00000000  
Rotation angle (degrees) 39.35357911  
Shift along axis -1.97485047  
  

> color #58 #00fa92ff

> color #59 #7a81ffff

> color #60 #ff8ad8ff

> select clear

> select add #15

209 atoms, 208 bonds, 15 residues, 1 model selected  

> select add #16

450 atoms, 448 bonds, 30 residues, 2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #15,0.94641,-0.22975,-0.227,101.52,0.15981,0.94389,-0.28903,61.199,0.28066,0.23726,0.93002,-89.408,#16,0.90376,0.13377,-0.4066,71.502,-0.25256,0.93359,-0.25423,133.41,0.34559,0.33245,0.87752,-111.1

> ui mousemode right "translate selected models"

> view matrix models
> #15,0.94641,-0.22975,-0.227,100.65,0.15981,0.94389,-0.28903,61.18,0.28066,0.23726,0.93002,-87.113,#16,0.90376,0.13377,-0.4066,70.623,-0.25256,0.93359,-0.25423,133.39,0.34559,0.33245,0.87752,-108.81

> view matrix models
> #15,0.94641,-0.22975,-0.227,101.51,0.15981,0.94389,-0.28903,61.005,0.28066,0.23726,0.93002,-87.053,#16,0.90376,0.13377,-0.4066,71.482,-0.25256,0.93359,-0.25423,133.22,0.34559,0.33245,0.87752,-108.75

> view matrix models
> #15,0.94641,-0.22975,-0.227,101.23,0.15981,0.94389,-0.28903,61.137,0.28066,0.23726,0.93002,-86.019,#16,0.90376,0.13377,-0.4066,71.206,-0.25256,0.93359,-0.25423,133.35,0.34559,0.33245,0.87752,-107.72

> ui mousemode right "rotate selected models"

> view matrix models
> #15,0.94816,-0.21835,-0.2309,99.309,0.15621,0.95297,-0.25971,54.211,0.27675,0.21018,0.93767,-81.186,#16,0.90047,0.14496,-0.41004,70.175,-0.25359,0.94096,-0.22424,126.14,0.35333,0.30591,0.88407,-104.95

> ui mousemode right "translate selected models"

> view matrix models
> #15,0.94816,-0.21835,-0.2309,99.455,0.15621,0.95297,-0.25971,54.159,0.27675,0.21018,0.93767,-81.804,#16,0.90047,0.14496,-0.41004,70.321,-0.25359,0.94096,-0.22424,126.09,0.35333,0.30591,0.88407,-105.57

> select clear

> close #58-60

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> select add #58

2591 atoms, 2586 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> ui mousemode right "translate selected models"

> view matrix models
> #58,0.79314,0.60856,-0.024242,-95.542,-0.59978,0.77354,-0.20468,155.55,-0.10581,0.17688,0.97853,-17.551

> fitmap #58 inMap #8

Fit molecule combination (#58) to map postprocess_masked330_onepf.mrc (#8)
using 2591 atoms  
average map value = 0.01094, steps = 196  
shifted from previous position = 5.44  
rotated from previous position = 12.8 degrees  
atoms outside contour = 1420, contour level = 0.0087645  
  
Position of combination (#58) relative to postprocess_masked330_onepf.mrc (#8)
coordinates:  
Matrix rotation and translation  
0.69470061 0.71864394 0.03069124 -108.86444101  
-0.71706453 0.69527244 -0.04913949 168.48052427  
-0.05665257 0.01212964 0.99832027 9.93059036  
Axis 0.04255785 0.06066944 -0.99725024  
Axis point 144.89683606 212.78650569 0.00000000  
Rotation angle (degrees) 46.04074395  
Shift along axis -4.31470019  
  

> select add #59

5182 atoms, 5172 bonds, 8 pseudobonds, 334 residues, 4 models selected  

> select subtract #58

2591 atoms, 2586 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> view matrix models
> #59,0.79314,0.60856,-0.024242,-99.148,-0.59978,0.77354,-0.20468,133.17,-0.10581,0.17688,0.97853,-19.296

> fitmap #59 inMap #8

Fit molecule combination (#59) to map postprocess_masked330_onepf.mrc (#8)
using 2591 atoms  
average map value = 0.006696, steps = 100  
shifted from previous position = 4.35  
rotated from previous position = 7.81 degrees  
atoms outside contour = 1774, contour level = 0.0087645  
  
Position of combination (#59) relative to postprocess_masked330_onepf.mrc (#8)
coordinates:  
Matrix rotation and translation  
0.82253175 0.56630384 -0.05235917 -87.83539594  
-0.56869658 0.81818493 -0.08460269 90.38881120  
-0.00507134 0.09936488 0.99503814 -21.31995137  
Axis 0.15986267 -0.04109181 -0.98628363  
Axis point 99.34135261 187.15810156 0.00000000  
Rotation angle (degrees) 35.12712443  
Shift along axis 3.27167819  
  

> select add #60

5182 atoms, 5172 bonds, 8 pseudobonds, 334 residues, 4 models selected  

> select subtract #59

2591 atoms, 2586 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> view matrix models
> #60,0.79314,0.60856,-0.024242,-87.493,-0.59978,0.77354,-0.20468,203.73,-0.10581,0.17688,0.97853,-13.741

> fitmap #60 inMap #8

Fit molecule combination (#60) to map postprocess_masked330_onepf.mrc (#8)
using 2591 atoms  
average map value = 0.01248, steps = 144  
shifted from previous position = 4.36  
rotated from previous position = 15.2 degrees  
atoms outside contour = 1312, contour level = 0.0087645  
  
Position of combination (#60) relative to postprocess_masked330_onepf.mrc (#8)
coordinates:  
Matrix rotation and translation  
0.77162500 0.63217433 0.07035958 -111.69461591  
-0.63538685 0.77121095 0.03895143 163.56425317  
-0.02963798 -0.07476145 0.99676091 24.74095134  
Axis -0.08907660 0.07833275 -0.99293975  
Axis point 171.61250867 238.93307512 0.00000000  
Rotation angle (degrees) 39.66420820  
Shift along axis -1.80445926  
  

> color #58 #fffc79ff

> color #59 #73fdffff

> color #60 #73fa79ff

> select clear

> select add #60

2591 atoms, 2586 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #60,0.76644,0.64208,-0.01737,-95.081,-0.63465,0.75285,-0.17444,211.37,-0.098925,0.14472,0.98452,-9.4526

> view matrix models
> #60,0.78224,0.62215,-0.032074,-90.612,-0.61063,0.75553,-0.23732,218.89,-0.12341,0.20522,0.9709,-15.72

> ui mousemode right "translate selected models"

> view matrix models
> #60,0.78224,0.62215,-0.032074,-90.726,-0.61063,0.75553,-0.23732,220.16,-0.12341,0.20522,0.9709,-15.903

> view matrix models
> #60,0.78224,0.62215,-0.032074,-91.582,-0.61063,0.75553,-0.23732,220.51,-0.12341,0.20522,0.9709,-15.058

> view matrix models
> #60,0.78224,0.62215,-0.032074,-91.596,-0.61063,0.75553,-0.23732,220.48,-0.12341,0.20522,0.9709,-15.154

> select add #58

5182 atoms, 5172 bonds, 8 pseudobonds, 334 residues, 4 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #58,0.76349,0.64522,0.027778,-102.62,-0.64546,0.7638,-0.00054434,128.74,-0.021568,-0.017514,0.99961,10.695,#60,0.84052,0.54153,-0.016423,-90.155,-0.53389,0.82273,-0.19514,181.06,-0.092164,0.17279,0.98064,-16.954

> undo

> select subtract #60

2591 atoms, 2586 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> view matrix models
> #58,0.75322,0.65735,0.023632,-105.03,-0.63531,0.73633,-0.23279,180.52,-0.17043,0.16033,0.97224,3.7415

> ui mousemode right "translate selected models"

> view matrix models
> #58,0.75322,0.65735,0.023632,-104.82,-0.63531,0.73633,-0.23279,180.29,-0.17043,0.16033,0.97224,3.2248

> view matrix models
> #58,0.75322,0.65735,0.023632,-104.8,-0.63531,0.73633,-0.23279,180.28,-0.17043,0.16033,0.97224,3.2378

> view matrix models
> #58,0.75322,0.65735,0.023632,-104.88,-0.63531,0.73633,-0.23279,180.4,-0.17043,0.16033,0.97224,3.6709

> view matrix models
> #58,0.75322,0.65735,0.023632,-105.28,-0.63531,0.73633,-0.23279,180.28,-0.17043,0.16033,0.97224,4.4527

> ui mousemode right "rotate selected models"

> view matrix models
> #58,0.72544,0.6871,-0.040396,-93.497,-0.688,0.72221,-0.071165,160.81,-0.019723,0.079419,0.99665,-11.76

> ui mousemode right "translate selected models"

> view matrix models
> #58,0.72544,0.6871,-0.040396,-93.039,-0.688,0.72221,-0.071165,161.08,-0.019723,0.079419,0.99665,-13.573

> ui mousemode right "rotate selected models"

> view matrix models
> #58,0.78301,0.62196,-0.008341,-96.028,-0.61375,0.77035,-0.17283,156.19,-0.10107,0.14045,0.98492,-9.105

> view matrix models
> #58,0.77058,0.63702,-0.020547,-94.527,-0.63452,0.76372,-0.11886,150.75,-0.060024,0.10463,0.9927,-10.587

> show #!9 models

> select add #9

17829 atoms, 17833 bonds, 11 pseudobonds, 1145 residues, 4 models selected  

> ui mousemode right "translate selected models"

> view matrix models
> #9,1,0,0,9.0202,0,1,0,0.10633,0,0,1,-34.159,#58,0.77058,0.63702,-0.020547,-85.507,-0.63452,0.76372,-0.11886,150.86,-0.060024,0.10463,0.9927,-44.746

> show #!7 models

> volume #7 level 0.0122

> hide #!9 models

> show #!9 models

> hide #!9 models

> select subtract #9

2591 atoms, 2586 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> view matrix models
> #58,0.77058,0.63702,-0.020547,-95.293,-0.63452,0.76372,-0.11886,151.46,-0.060024,0.10463,0.9927,-10.285

> fitmap #58 inMap #8

Fit molecule combination (#58) to map postprocess_masked330_onepf.mrc (#8)
using 2591 atoms  
average map value = 0.01094, steps = 128  
shifted from previous position = 1.5  
rotated from previous position = 8.13 degrees  
atoms outside contour = 1427, contour level = 0.0087645  
  
Position of combination (#58) relative to postprocess_masked330_onepf.mrc (#8)
coordinates:  
Matrix rotation and translation  
0.69460507 0.71873611 0.03069528 -108.85965070  
-0.71715590 0.69517716 -0.04915416 168.52136127  
-0.05666753 0.01212942 0.99831942 9.90464958  
Axis 0.04256242 0.06067485 -0.99724972  
Axis point 144.90811951 212.77829601 0.00000000  
Rotation angle (degrees) 46.04837141  
Shift along axis -4.28572979  
  

> hide #!8 models

> hide #!7 models

> show #!9 models

> select add #28

5175 atoms, 5168 bonds, 7 pseudobonds, 333 residues, 4 models selected  

> select subtract #28

2591 atoms, 2586 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> select subtract #58

Nothing selected  

> select add #59

2591 atoms, 2586 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> ui mousemode right "translate selected models"

[Repeated 1 time(s)]

> view matrix models
> #59,0.82255,0.56636,-0.051519,-76.456,-0.56867,0.8182,-0.084669,89.174,-0.0058001,0.098942,0.99508,-19.46

> view matrix models
> #59,0.82255,0.56636,-0.051519,-81.049,-0.56867,0.8182,-0.084669,89.967,-0.0058001,0.098942,0.99508,-20.794

> view matrix models
> #59,0.82255,0.56636,-0.051519,-82.254,-0.56867,0.8182,-0.084669,88.666,-0.0058001,0.098942,0.99508,-20.929

> hide #!9 models

> select add #58

5182 atoms, 5172 bonds, 8 pseudobonds, 334 residues, 4 models selected  

> select subtract #59

2591 atoms, 2586 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #58,0.72477,0.68835,0.029732,-107.77,-0.67578,0.71862,-0.16406,178.5,-0.1343,0.098816,0.986,7.8793

> ui mousemode right "translate selected models"

> view matrix models
> #58,0.72477,0.68835,0.029732,-107.35,-0.67578,0.71862,-0.16406,175.65,-0.1343,0.098816,0.986,6.3154

> view matrix models
> #58,0.72477,0.68835,0.029732,-107.48,-0.67578,0.71862,-0.16406,174.22,-0.1343,0.098816,0.986,6.3212

> ui mousemode right "rotate selected models"

> view matrix models
> #58,0.76418,0.64362,0.042124,-107.54,-0.63511,0.76225,-0.12495,148.14,-0.11253,0.068728,0.99127,7.8485

> ui mousemode right "translate selected models"

> view matrix models
> #58,0.76418,0.64362,0.042124,-107.1,-0.63511,0.76225,-0.12495,149.09,-0.11253,0.068728,0.99127,8.0655

> show #!8 models

> select add #59

5182 atoms, 5172 bonds, 8 pseudobonds, 334 residues, 4 models selected  

> select subtract #58

2591 atoms, 2586 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #59,0.78812,0.61254,-0.060414,-84.235,-0.61503,0.77978,-0.11696,113.28,-0.024533,0.12933,0.9913,-23.433

> ui mousemode right "rotate selected models"

> view matrix models
> #59,0.80814,0.58582,-0.060994,-81.934,-0.58875,0.80056,-0.11173,102.24,-0.016626,0.12621,0.99186,-24.394

> ui mousemode right "translate selected models"

> ui mousemode right "rotate selected models"

> view matrix models
> #59,0.80255,0.59647,0.011305,-98.099,-0.59127,0.79779,-0.118,104.65,-0.0794,0.088014,0.99295,-3.4311

> ui mousemode right "translate selected models"

> view matrix models
> #59,0.80255,0.59647,0.011305,-98.614,-0.59127,0.79779,-0.118,104.78,-0.0794,0.088014,0.99295,-1.8343

> hide #!8 models

> ui mousemode right "translate selected models"

> view matrix models
> #59,0.80255,0.59647,0.011305,-97.972,-0.59127,0.79779,-0.118,104.89,-0.0794,0.088014,0.99295,-4.0716

> view matrix models
> #59,0.80255,0.59647,0.011305,-98.009,-0.59127,0.79779,-0.118,104.94,-0.0794,0.088014,0.99295,-4.3401

> view matrix models
> #59,0.80255,0.59647,0.011305,-97.938,-0.59127,0.79779,-0.118,104.91,-0.0794,0.088014,0.99295,-4.2923

> view matrix models
> #59,0.80255,0.59647,0.011305,-97.771,-0.59127,0.79779,-0.118,104.93,-0.0794,0.088014,0.99295,-4.6797

> view matrix models
> #59,0.80255,0.59647,0.011305,-98.514,-0.59127,0.79779,-0.118,105.05,-0.0794,0.088014,0.99295,-4.9197

> view matrix models
> #59,0.80255,0.59647,0.011305,-97.328,-0.59127,0.79779,-0.118,104.46,-0.0794,0.088014,0.99295,-4.6085

> show #!8 models

> select add #58

5182 atoms, 5172 bonds, 8 pseudobonds, 334 residues, 4 models selected  

> view matrix models
> #58,0.76418,0.64362,0.042124,-104.28,-0.63511,0.76225,-0.12495,148.82,-0.11253,0.068728,0.99127,9.09,#59,0.80255,0.59647,0.011305,-94.511,-0.59127,0.79779,-0.118,104.19,-0.0794,0.088014,0.99295,-3.584

> view matrix models
> #58,0.76418,0.64362,0.042124,-104.44,-0.63511,0.76225,-0.12495,148.02,-0.11253,0.068728,0.99127,9.1218,#59,0.80255,0.59647,0.011305,-94.672,-0.59127,0.79779,-0.118,103.39,-0.0794,0.088014,0.99295,-3.5522

> select subtract #58

2591 atoms, 2586 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> view matrix models
> #59,0.80255,0.59647,0.011305,-90.294,-0.59127,0.79779,-0.118,100.69,-0.0794,0.088014,0.99295,-2.366

> view matrix models
> #59,0.80255,0.59647,0.011305,-89.418,-0.59127,0.79779,-0.118,100.48,-0.0794,0.088014,0.99295,-2.1495

> view matrix models
> #59,0.80255,0.59647,0.011305,-89.429,-0.59127,0.79779,-0.118,100.09,-0.0794,0.088014,0.99295,-2.1479

> view matrix models
> #59,0.80255,0.59647,0.011305,-89.662,-0.59127,0.79779,-0.118,99.895,-0.0794,0.088014,0.99295,-1.4508

> select clear

> hide #!8 models

> show #!8 models

> hide #!8 models

> show #!8 models

> hide #!8 models

> select add #15

209 atoms, 208 bonds, 15 residues, 1 model selected  

> ui mousemode right "translate selected models"

> view matrix models
> #15,0.94816,-0.21835,-0.2309,99.187,0.15621,0.95297,-0.25971,54.235,0.27675,0.21018,0.93767,-80.986

> show #!8 models

> select add #14

470 atoms, 468 bonds, 1 pseudobond, 32 residues, 3 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #14,0.92065,0.39039,-0.0026041,-69.241,-0.37857,0.89435,0.23838,23.821,0.09539,-0.21848,0.97117,31.442,#15,0.98433,-0.072634,-0.16068,52.708,0.057113,0.99343,-0.099193,33.844,0.16683,0.088462,0.98201,-47.628

> undo

> select subtract #15

261 atoms, 260 bonds, 1 pseudobond, 17 residues, 2 models selected  

> view matrix models
> #14,0.91445,0.40437,0.015951,-71.189,-0.39452,0.88199,0.25778,26.484,0.09017,-0.24202,0.96607,35.409

> ui mousemode right "translate selected models"

> view matrix models
> #14,0.91445,0.40437,0.015951,-72.761,-0.39452,0.88199,0.25778,27.784,0.09017,-0.24202,0.96607,37.99

> view matrix models
> #14,0.91445,0.40437,0.015951,-72.639,-0.39452,0.88199,0.25778,27.291,0.09017,-0.24202,0.96607,37.774

> hide #!58-60 target m

> select subtract #14

Nothing selected  

> select add #18

1330 atoms, 1329 bonds, 1 pseudobond, 84 residues, 2 models selected  

> select subtract #18

Nothing selected  

> select add #17

257 atoms, 259 bonds, 15 residues, 1 model selected  

> select add #16

498 atoms, 499 bonds, 30 residues, 2 models selected  

> select subtract #17

241 atoms, 240 bonds, 15 residues, 1 model selected  

> select add #15

450 atoms, 448 bonds, 30 residues, 2 models selected  

> ui mousemode right "translate selected models"

> view matrix models
> #15,0.94816,-0.21835,-0.2309,100.58,0.15621,0.95297,-0.25971,54.077,0.27675,0.21018,0.93767,-81.23,#16,0.90047,0.14496,-0.41004,71.719,-0.25359,0.94096,-0.22424,125.93,0.35333,0.30591,0.88407,-105.81

> ui mousemode right "rotate selected models"

> view matrix models
> #15,0.95774,-0.13636,-0.25328,86.225,0.078837,0.97122,-0.22476,58.456,0.27663,0.19529,0.94092,-78.778,#16,0.87512,0.2245,-0.42868,63.632,-0.32419,0.92968,-0.17493,132.13,0.35926,0.29206,0.88636,-104.5

> ui mousemode right "translate selected models"

> view matrix models
> #15,0.95774,-0.13636,-0.25328,86.229,0.078837,0.97122,-0.22476,59.16,0.27663,0.19529,0.94092,-78.793,#16,0.87512,0.2245,-0.42868,63.635,-0.32419,0.92968,-0.17493,132.83,0.35926,0.29206,0.88636,-104.52

> view matrix models
> #15,0.95774,-0.13636,-0.25328,86.361,0.078837,0.97122,-0.22476,58.842,0.27663,0.19529,0.94092,-78.884,#16,0.87512,0.2245,-0.42868,63.767,-0.32419,0.92968,-0.17493,132.52,0.35926,0.29206,0.88636,-104.61

> ui mousemode right "rotate selected models"

> view matrix models
> #15,0.9604,-0.12848,-0.24724,83.04,0.075884,0.97441,-0.2116,56.178,0.2681,0.18446,0.94557,-75.912,#16,0.87583,0.23285,-0.42274,60.722,-0.32555,0.93167,-0.16129,129.68,0.3563,0.27889,0.89178,-102.36

> view matrix models
> #15,0.94047,-0.14485,-0.30746,102.07,0.095352,0.98075,-0.17038,43.025,0.32623,0.13092,0.93618,-74.272,#16,0.85221,0.20975,-0.47931,81.182,-0.30231,0.94512,-0.12391,115.08,0.42702,0.2505,0.86885,-105.45

> ui mousemode right "translate selected models"

> view matrix models
> #15,0.94047,-0.14485,-0.30746,102.55,0.095352,0.98075,-0.17038,42.535,0.32623,0.13092,0.93618,-75.904,#16,0.85221,0.20975,-0.47931,81.661,-0.30231,0.94512,-0.12391,114.59,0.42702,0.2505,0.86885,-107.08

> view matrix models
> #15,0.94047,-0.14485,-0.30746,102.8,0.095352,0.98075,-0.17038,43.13,0.32623,0.13092,0.93618,-75.967,#16,0.85221,0.20975,-0.47931,81.907,-0.30231,0.94512,-0.12391,115.18,0.42702,0.2505,0.86885,-107.15

> view matrix models
> #15,0.94047,-0.14485,-0.30746,102.79,0.095352,0.98075,-0.17038,43.253,0.32623,0.13092,0.93618,-75.892,#16,0.85221,0.20975,-0.47931,81.905,-0.30231,0.94512,-0.12391,115.31,0.42702,0.2505,0.86885,-107.07

> view matrix models
> #15,0.94047,-0.14485,-0.30746,102.65,0.095352,0.98075,-0.17038,43.616,0.32623,0.13092,0.93618,-75.983,#16,0.85221,0.20975,-0.47931,81.763,-0.30231,0.94512,-0.12391,115.67,0.42702,0.2505,0.86885,-107.16

> select clear

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Fit14-12.cxs"

[Repeated 1 time(s)]

> select add #62

2591 atoms, 2586 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> ui mousemode right "rotate selected models"

> ui mousemode right "translate selected models"

> view matrix models
> #62,0.79314,0.60856,-0.024242,-92.079,-0.59978,0.77354,-0.20468,155.23,-0.10581,0.17688,0.97853,-13.838

> fitmap #61 inMap #8

Fit molecule combination (#61) to map postprocess_masked330_onepf.mrc (#8)
using 2591 atoms  
average map value = 0.01405, steps = 84  
shifted from previous position = 0.95  
rotated from previous position = 6.55 degrees  
atoms outside contour = 1074, contour level = 0.0087645  
  
Position of combination (#61) relative to postprocess_masked330_onepf.mrc (#8)
coordinates:  
Matrix rotation and translation  
0.77599338 0.63073408 0.00296557 -98.49221931  
-0.62744331 0.77240784 -0.09849378 167.06073955  
-0.06441402 0.07456979 0.99513325 -2.84625734  
Axis 0.13607657 0.05297928 -0.98928073  
Axis point 185.94282828 221.81838968 0.00000000  
Rotation angle (degrees) 39.48714882  
Shift along axis -1.73597830  
  

> select add #61

5182 atoms, 5172 bonds, 8 pseudobonds, 334 residues, 4 models selected  

> fitmap #62 inMap #8

Fit molecule combination (#62) to map postprocess_masked330_onepf.mrc (#8)
using 2591 atoms  
average map value = 0.01144, steps = 116  
shifted from previous position = 2.97  
rotated from previous position = 8.78 degrees  
atoms outside contour = 1340, contour level = 0.0087645  
  
Position of combination (#62) relative to postprocess_masked330_onepf.mrc (#8)
coordinates:  
Matrix rotation and translation  
0.72753599 0.68589596 0.01543072 -104.86672200  
-0.68156357 0.72514839 -0.09813724 164.21387837  
-0.07850150 0.06088136 0.99505325 3.66900088  
Axis 0.11524129 0.06807299 -0.99100228  
Axis point 155.18371807 213.77181298 0.00000000  
Rotation angle (degrees) 43.62517215  
Shift along axis -4.54243519  
  

> select subtract #62

2591 atoms, 2586 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> view matrix models
> #61,0.77596,0.63077,0.003806,-104.41,-0.62741,0.77242,-0.098558,112.81,-0.065107,0.074089,0.99512,0.089586

> fitmap #61 inMap #8

Fit molecule combination (#61) to map postprocess_masked330_onepf.mrc (#8)
using 2591 atoms  
average map value = 0.008545, steps = 164  
shifted from previous position = 5.54  
rotated from previous position = 10.5 degrees  
atoms outside contour = 1640, contour level = 0.0087645  
  
Position of combination (#61) relative to postprocess_masked330_onepf.mrc (#8)
coordinates:  
Matrix rotation and translation  
0.64858494 0.76108270 -0.00952371 -101.72613501  
-0.75872616 0.64547932 -0.08769874 169.41495003  
-0.06059864 0.06410597 0.99610152 -0.36979116  
Axis 0.09933399 0.03342107 -0.99449273  
Axis point 132.64528401 194.37426694 0.00000000  
Rotation angle (degrees) 49.82810951  
Shift along axis -4.07507869  
  

> select add #63

5182 atoms, 5172 bonds, 8 pseudobonds, 334 residues, 4 models selected  

> view matrix models
> #61,0.64856,0.76111,-0.0086828,-102.91,-0.7587,0.6455,-0.087764,191.95,-0.061193,0.063508,0.9961,-1.6785,#63,0.79314,0.60856,-0.024242,-91.693,-0.59978,0.77354,-0.20468,204.79,-0.10581,0.17688,0.97853,-16.964

> undo

> select subtract #61

2591 atoms, 2586 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> view matrix models
> #63,0.79314,0.60856,-0.024242,-91.114,-0.59978,0.77354,-0.20468,208.14,-0.10581,0.17688,0.97853,-17.096

> fitmap #63 inMap #8

Fit molecule combination (#63) to map postprocess_masked330_onepf.mrc (#8)
using 2591 atoms  
average map value = 0.01271, steps = 124  
shifted from previous position = 3.75  
rotated from previous position = 12.9 degrees  
atoms outside contour = 1293, contour level = 0.0087645  
  
Position of combination (#63) relative to postprocess_masked330_onepf.mrc (#8)
coordinates:  
Matrix rotation and translation  
0.78836097 0.61210402 0.06177094 -108.54152155  
-0.61332134 0.78983292 0.00095034 162.40386879  
-0.04820701 -0.03863465 0.99808990 19.81797474  
Axis -0.03215711 0.08934127 -0.99548182  
Axis point 182.61439774 240.55624574 0.00000000  
Rotation angle (degrees) 37.98779403  
Shift along axis -1.72868454  
  

> select clear

> color #62 #fffb00ff

> color #63 #73fa79ff

> color #61 #ff8ad8ff

> select add #62

2591 atoms, 2586 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> select add #61

5182 atoms, 5172 bonds, 8 pseudobonds, 334 residues, 4 models selected  

> ui mousemode right "translate selected models"

> view matrix models
> #61,0.64856,0.76111,-0.0086828,-97.721,-0.7587,0.6455,-0.087764,166.2,-0.061193,0.063508,0.9961,0.54194,#62,0.72749,0.68592,0.016271,-100.86,-0.68153,0.72517,-0.098201,161,-0.079158,0.060351,0.99503,4.583

> view matrix models
> #61,0.64856,0.76111,-0.0086828,-101.51,-0.7587,0.6455,-0.087764,168.17,-0.061193,0.063508,0.9961,-0.31003,#62,0.72749,0.68592,0.016271,-104.64,-0.68153,0.72517,-0.098201,162.97,-0.079158,0.060351,0.99503,3.7311

> select subtract #62

2591 atoms, 2586 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> view matrix models
> #61,0.64856,0.76111,-0.0086828,-98.239,-0.7587,0.6455,-0.087764,167.27,-0.061193,0.063508,0.9961,0.58471

> select add #59

5182 atoms, 5172 bonds, 8 pseudobonds, 334 residues, 4 models selected  

> select subtract #59

2591 atoms, 2586 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> select add #60

5182 atoms, 5172 bonds, 8 pseudobonds, 334 residues, 4 models selected  

> select subtract #60

2591 atoms, 2586 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> show #!59 models

> hide #!59 models

> show #!60 models

> hide #!60 models

> show #!59 models

> hide #!59 models

> show #!58 models

> hide #!58 models

> hide #!57 models

> show #!57 models

> select add #62

5182 atoms, 5172 bonds, 8 pseudobonds, 334 residues, 4 models selected  

> select subtract #61

2591 atoms, 2586 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> view matrix models
> #62,0.72749,0.68592,0.016271,-102.45,-0.68153,0.72517,-0.098201,163.92,-0.079158,0.060351,0.99503,4.8475

> ui mousemode right "rotate selected models"

> view matrix models
> #62,0.75572,0.6503,-0.077463,-80.777,-0.64916,0.72821,-0.21976,181.48,-0.086498,0.21636,0.97247,-25.166

> view matrix models
> #62,0.75845,0.6478,-0.071526,-81.949,-0.64784,0.73737,-0.19131,173.31,-0.071187,0.19143,0.97892,-23.765

> select add #61

5182 atoms, 5172 bonds, 8 pseudobonds, 334 residues, 4 models selected  

> select subtract #62

2591 atoms, 2586 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> view matrix models
> #61,0.81371,0.58073,0.02499,-96.289,-0.58021,0.81407,-0.025376,80.063,-0.035081,0.0061493,0.99937,7.9783

> ui mousemode right "translate selected models"

> view matrix models
> #61,0.81371,0.58073,0.02499,-96.774,-0.58021,0.81407,-0.025376,76.326,-0.035081,0.0061493,0.99937,8.1563

> view matrix models
> #61,0.81371,0.58073,0.02499,-98.211,-0.58021,0.81407,-0.025376,76.426,-0.035081,0.0061493,0.99937,8.8286

> view matrix models
> #61,0.81371,0.58073,0.02499,-93.912,-0.58021,0.81407,-0.025376,77.267,-0.035081,0.0061493,0.99937,12.772

> view matrix models
> #61,0.81371,0.58073,0.02499,-94.12,-0.58021,0.81407,-0.025376,76.076,-0.035081,0.0061493,0.99937,12.564

> ui mousemode right "rotate selected models"

> view matrix models
> #61,0.7597,0.6498,0.024986,-99.323,-0.64792,0.75966,-0.055845,108.34,-0.055268,0.026236,0.99813,12.194

> ui mousemode right "translate selected models"

> view matrix models
> #61,0.7597,0.6498,0.024986,-98.876,-0.64792,0.75966,-0.055845,110.72,-0.055268,0.026236,0.99813,11.567

> view matrix models
> #61,0.7597,0.6498,0.024986,-100.06,-0.64792,0.75966,-0.055845,110.08,-0.055268,0.026236,0.99813,11.562

> view matrix models
> #61,0.7597,0.6498,0.024986,-99.137,-0.64792,0.75966,-0.055845,108.67,-0.055268,0.026236,0.99813,11.482

> ui mousemode right "rotate selected models"

[Repeated 1 time(s)]

> view matrix models
> #61,0.76344,0.64482,-0.037071,-86.114,-0.64588,0.76201,-0.046745,105.87,-0.0018936,0.05963,0.99822,-6.8892

> ui mousemode right "translate selected models"

> view matrix models
> #61,0.76344,0.64482,-0.037071,-87.283,-0.64588,0.76201,-0.046745,105.78,-0.0018936,0.05963,0.99822,-8.75

> select add #62

5182 atoms, 5172 bonds, 8 pseudobonds, 334 residues, 4 models selected  

> select subtract #61

2591 atoms, 2586 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #62,0.75318,0.62487,0.20554,-131.94,-0.57236,0.77654,-0.26342,163.88,-0.32422,0.080757,0.94253,59.624

> view matrix models
> #62,0.76542,0.62564,0.15073,-123.4,-0.58094,0.77251,-0.2564,165.1,-0.27685,0.10869,0.95475,41.247

> view matrix models
> #62,0.778,0.62403,0.072857,-109.71,-0.59241,0.76726,-0.24567,166.41,-0.20921,0.14797,0.96661,16.28

> view matrix models
> #62,0.76588,0.637,0.087467,-113.26,-0.61818,0.76691,-0.17236,156.72,-0.17687,0.077937,0.98114,23.073

> view matrix models
> #62,0.76212,0.641,0.091061,-114.17,-0.62535,0.76523,-0.15283,154.57,-0.16765,0.05953,0.98405,24.899

> view matrix models
> #62,0.79249,0.60829,0.044147,-103.12,-0.57952,0.77361,-0.25631,164.54,-0.19006,0.17754,0.96559,5.8395

> view matrix models
> #62,0.7742,0.63057,0.054646,-106.76,-0.61166,0.76759,-0.19152,159.16,-0.16271,0.11485,0.97997,11.958

> select add #61

5182 atoms, 5172 bonds, 8 pseudobonds, 334 residues, 4 models selected  

> view matrix models
> #61,0.7807,0.62485,0.0085679,-94.791,-0.59501,0.74747,-0.29538,150.04,-0.19097,0.2255,0.95534,-4.9438,#62,0.78334,0.61291,0.10347,-114.84,-0.52142,0.73856,-0.42738,195.78,-0.33837,0.28083,0.89813,29.162

> undo

> select subtract #62

2591 atoms, 2586 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> view matrix models
> #61,0.76465,0.59953,-0.23638,-36.53,-0.64438,0.71647,-0.26729,160.85,0.0091135,0.3567,0.93417,-66.591

> view matrix models
> #61,0.76122,0.64661,0.049395,-104.84,-0.6171,0.74569,-0.25127,145.4,-0.19931,0.16079,0.96666,13.61

> view matrix models
> #61,0.85065,0.52175,0.064492,-96.861,-0.49615,0.8373,-0.22971,95.748,-0.17385,0.16341,0.97112,7.027

> view matrix models
> #61,0.84784,0.52812,0.047456,-94.308,-0.44096,0.75196,-0.49001,157.41,-0.29447,0.39453,0.87042,-1.8958

> view matrix models
> #61,0.85835,0.51007,0.055445,-93.851,-0.42265,0.7642,-0.4872,150.36,-0.29088,0.39476,0.87153,-2.8887

> view matrix models
> #61,0.88423,0.4643,0.050615,-87.447,-0.38665,0.7885,-0.4783,135.76,-0.26198,0.40336,0.87674,-11.692

> view matrix models
> #61,0.87901,0.4749,-0.042561,-69.911,-0.43817,0.76937,-0.46484,147.71,-0.18801,0.42725,0.88437,-33.504

> view matrix models
> #61,0.89003,0.45485,-0.031015,-69.82,-0.41703,0.78474,-0.45856,138.67,-0.18424,0.42106,0.88812,-33.588

> view matrix models
> #61,0.83235,0.55362,0.02651,-92.857,-0.54327,0.82438,-0.15891,93.723,-0.10983,0.11786,0.98694,1.5846

> view matrix models
> #61,0.77949,0.6252,0.03897,-101.41,-0.60973,0.77152,-0.18161,123.8,-0.14361,0.1178,0.9826,9.2107

> view matrix models
> #61,0.8215,0.56723,0.058222,-100.29,-0.55722,0.82026,-0.12915,91.405,-0.12101,0.073652,0.98991,13.427

> select add #63

5182 atoms, 5172 bonds, 8 pseudobonds, 334 residues, 4 models selected  

> select subtract #61

2591 atoms, 2586 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> view matrix models
> #63,0.61208,0.7899,0.03769,-109.75,-0.78545,0.61278,-0.086977,255.48,-0.091798,0.023633,0.9955,14.651

> undo

> view matrix models
> #63,0.82988,0.55675,0.036327,-98.969,-0.53723,0.81497,-0.21729,185.79,-0.15058,0.16081,0.97543,-1.2687

> undo

> view matrix models
> #63,0.81315,0.57985,0.050676,-103.89,-0.57032,0.81112,-0.12967,175.46,-0.11629,0.07654,0.99026,8.3652

> ui mousemode right "translate selected models"

> view matrix models
> #63,0.81315,0.57985,0.050676,-104.23,-0.57032,0.81112,-0.12967,178.23,-0.11629,0.07654,0.99026,7.554

> ui mousemode right "rotate selected models"

> view matrix models
> #63,0.78029,0.62409,0.040757,-105.89,-0.61282,0.77595,-0.14953,198.86,-0.12494,0.091697,0.98792,6.25

> view matrix models
> #63,0.78978,0.60728,-0.086326,-78.056,-0.61277,0.77487,-0.15519,200.25,-0.027352,0.17546,0.98411,-31.78

> ui mousemode right "translate selected models"

> view matrix models
> #63,0.78978,0.60728,-0.086326,-82.297,-0.61277,0.77487,-0.15519,203.74,-0.027352,0.17546,0.98411,-32.342

> undo

> select add #61

5182 atoms, 5172 bonds, 8 pseudobonds, 334 residues, 4 models selected  

> select subtract #63

2591 atoms, 2586 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> view matrix models
> #61,0.8215,0.56723,0.058222,-102.81,-0.55722,0.82026,-0.12915,93.468,-0.12101,0.073652,0.98991,13.093

> view matrix models
> #61,0.8215,0.56723,0.058222,-101.08,-0.55722,0.82026,-0.12915,96.52,-0.12101,0.073652,0.98991,13.12

> ui mousemode right "rotate selected models"

> view matrix models
> #61,0.75539,0.65364,0.046285,-105.46,-0.6417,0.75219,-0.14975,133.27,-0.1327,0.083416,0.98764,13.653

> ui mousemode right "translate selected models"

> view matrix models
> #61,0.75539,0.65364,0.046285,-109.03,-0.6417,0.75219,-0.14975,132.75,-0.1327,0.083416,0.98764,12.472

> ui mousemode right "rotate selected models"

> view matrix models
> #61,0.71508,0.6986,0.024882,-107.04,-0.68502,0.70739,-0.17421,156.71,-0.1393,0.10753,0.98439,8.874

> hide #!61 models

> hide #!62 models

> hide #!63 models

> hide #!54-63 target m

> hide #!10-21 target m

> hide #!8 models

> show #!9 models

> hide #!9 models

> show #!13-18 target m

> show #!55 models

> hide #!55 models

> show #!57 models

> show #!61 models

> show #!62 models

> show #!63 models

> hide #!55-63 target m

> hide #!11-21 target m

> show #!9 models

> hide #!9 models

> show #!13-18 target m

> show #!57 models

> show #!61 models

> hide #!61 models

> show #!8 models

> select add #14

2852 atoms, 2846 bonds, 5 pseudobonds, 184 residues, 4 models selected  

> select subtract #14

2591 atoms, 2586 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> select add #15

2800 atoms, 2794 bonds, 4 pseudobonds, 182 residues, 3 models selected  

> select subtract #15

2591 atoms, 2586 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> select add #16

2832 atoms, 2826 bonds, 4 pseudobonds, 182 residues, 3 models selected  

> view matrix models
> #16,0.86074,0.23566,-0.45121,69.095,-0.26632,0.96387,-0.0046236,81.728,0.43382,0.12415,0.89241,-85.608,#61,0.69709,0.71482,0.055666,-114.8,-0.71296,0.6993,-0.05161,141.06,-0.075819,-0.0037103,0.99711,30.404

> ui mousemode right "translate selected models"

> view matrix models
> #16,0.86074,0.23566,-0.45121,68.887,-0.26632,0.96387,-0.0046236,81.486,0.43382,0.12415,0.89241,-86.586,#61,0.69709,0.71482,0.055666,-115.01,-0.71296,0.6993,-0.05161,140.82,-0.075819,-0.0037103,0.99711,29.426

> view matrix models
> #16,0.86074,0.23566,-0.45121,68.559,-0.26632,0.96387,-0.0046236,81.579,0.43382,0.12415,0.89241,-86.73,#61,0.69709,0.71482,0.055666,-115.33,-0.71296,0.6993,-0.05161,140.91,-0.075819,-0.0037103,0.99711,29.282

> view matrix models
> #16,0.86074,0.23566,-0.45121,68.504,-0.26632,0.96387,-0.0046236,81.581,0.43382,0.12415,0.89241,-86.735,#61,0.69709,0.71482,0.055666,-115.39,-0.71296,0.6993,-0.05161,140.91,-0.075819,-0.0037103,0.99711,29.277

> view matrix models
> #16,0.86074,0.23566,-0.45121,68.517,-0.26632,0.96387,-0.0046236,81.629,0.43382,0.12415,0.89241,-86.062,#61,0.69709,0.71482,0.055666,-115.37,-0.71296,0.6993,-0.05161,140.96,-0.075819,-0.0037103,0.99711,29.95

> ui mousemode right "rotate selected models"

> view matrix models
> #16,0.87498,0.20071,-0.4406,71.37,-0.21782,0.97592,0.012008,66.696,0.4324,0.085466,0.89762,-78.421,#61,0.72246,0.68798,0.068827,-113.3,-0.68895,0.7247,-0.012203,123.46,-0.058274,-0.038602,0.99755,37.644

> ui mousemode right "translate selected models"

> view matrix models
> #16,0.87498,0.20071,-0.4406,70.383,-0.21782,0.97592,0.012008,66.454,0.4324,0.085466,0.89762,-78.787,#61,0.72246,0.68798,0.068827,-114.28,-0.68895,0.7247,-0.012203,123.22,-0.058274,-0.038602,0.99755,37.278

> ui mousemode right "rotate selected models"

> view matrix models
> #16,0.90366,0.077388,-0.42119,87.979,-0.11298,0.99177,-0.060167,57.342,0.41307,0.10196,0.90497,-80.162,#61,0.80247,0.59001,0.089044,-100.11,-0.59068,0.80662,-0.021433,88.141,-0.08447,-0.035397,0.9958,40.13

> ui mousemode right "translate selected models"

> view matrix models
> #16,0.90366,0.077388,-0.42119,87.467,-0.11298,0.99177,-0.060167,57.78,0.41307,0.10196,0.90497,-80.147,#61,0.80247,0.59001,0.089044,-100.62,-0.59068,0.80662,-0.021433,88.579,-0.08447,-0.035397,0.9958,40.145

> view matrix models
> #16,0.90366,0.077388,-0.42119,86.937,-0.11298,0.99177,-0.060167,58.047,0.41307,0.10196,0.90497,-80.363,#61,0.80247,0.59001,0.089044,-101.15,-0.59068,0.80662,-0.021433,88.845,-0.08447,-0.035397,0.9958,39.929

> view matrix models
> #16,0.90366,0.077388,-0.42119,86.898,-0.11298,0.99177,-0.060167,58.482,0.41307,0.10196,0.90497,-80.571,#61,0.80247,0.59001,0.089044,-101.19,-0.59068,0.80662,-0.021433,89.281,-0.08447,-0.035397,0.9958,39.721

> view matrix models
> #16,0.90366,0.077388,-0.42119,86.963,-0.11298,0.99177,-0.060167,58.191,0.41307,0.10196,0.90497,-80.565,#61,0.80247,0.59001,0.089044,-101.12,-0.59068,0.80662,-0.021433,88.989,-0.08447,-0.035397,0.9958,39.727

> select clear

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> select add #14

261 atoms, 260 bonds, 1 pseudobond, 17 residues, 2 models selected  

> select subtract #14

Nothing selected  

> select add #13

96 atoms, 95 bonds, 1 pseudobond, 8 residues, 2 models selected  

> select subtract #13

Nothing selected  

> select add #16

241 atoms, 240 bonds, 15 residues, 1 model selected  

> select subtract #16

Nothing selected  

> select add #17

257 atoms, 259 bonds, 15 residues, 1 model selected  

> select subtract #17

Nothing selected  

> select add #15

209 atoms, 208 bonds, 15 residues, 1 model selected  

> select subtract #15

Nothing selected  

> select add #18

1330 atoms, 1329 bonds, 1 pseudobond, 84 residues, 2 models selected  

> select subtract #18

Nothing selected  

> mmaker #64/9 to #18/9

No 'to' model specified  

> mmaker #64/9 #18/9

> matchmaker #64/9 #18/9

Missing required "to" argument  

> mmaker #64/9 to #18/9

No 'to' model specified  

> hide #!64 models

> hide #!65 models

> hide #!66 models

> mmaker #64/9 to #18/6

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker copy of copy of copy of pointy-1pf.pdb, chain 6 (#18) with
combination, chain 9 (#64), sequence alignment score = 670.7  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> hide #!18 models

> show #!18 models

> ui tool show Matchmaker

> matchmaker #18/6 to #64/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#64) with copy of copy of copy of
pointy-1pf.pdb, chain 6 (#18), sequence alignment score = 670.7  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> hide #!57 models

> show #!57 models

> hide #!18 models

> show #!18 models

> show #!60 models

> hide #!60 models

> show #!61 models

> hide #!61 models

> show #!61 models

> hide #!61 models

> show #!62 models

> show #!63 models

> show #!61 models

> select add #61

2591 atoms, 2586 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> view matrix models
> #61,0.80247,0.59001,0.089044,-113.29,-0.59068,0.80662,-0.021433,80.056,-0.08447,-0.035397,0.9958,33.742

> view matrix models
> #61,0.80247,0.59001,0.089044,-111.28,-0.59068,0.80662,-0.021433,80.098,-0.08447,-0.035397,0.9958,27.586

> view matrix models
> #61,0.80247,0.59001,0.089044,-111.32,-0.59068,0.80662,-0.021433,82.794,-0.08447,-0.035397,0.9958,27.752

> ui mousemode right "rotate selected models"

> view matrix models
> #61,0.67078,0.73602,0.09121,-119.28,-0.73113,0.67689,-0.08524,153.74,-0.12448,-0.0095093,0.99218,30.474

> ui mousemode right "translate selected models"

> view matrix models
> #61,0.67078,0.73602,0.09121,-115.61,-0.73113,0.67689,-0.08524,153.19,-0.12448,-0.0095093,0.99218,31.299

> ui mousemode right "rotate selected models"

> view matrix models
> #61,0.70613,0.70806,-0.0047673,-96.678,-0.68782,0.68431,-0.24213,174.75,-0.16818,0.17426,0.97023,1.9886

> view matrix models
> #61,0.70865,0.70523,0.021645,-101.89,-0.68254,0.69298,-0.23223,169.68,-0.17877,0.14979,0.97242,9.3073

> view matrix models
> #61,0.72125,0.68186,0.12193,-119.39,-0.65458,0.7285,-0.20202,149.75,-0.22657,0.065891,0.97176,38.358

> view matrix models
> #61,0.7177,0.68651,0.11666,-118.69,-0.66495,0.7254,-0.17787,147.63,-0.20673,0.050084,0.97711,36.972

> view matrix models
> #61,0.73054,0.67663,0.092164,-113.98,-0.66231,0.73493,-0.14568,138.36,-0.16631,0.045384,0.98503,28.396

> view matrix models
> #61,0.72451,0.67788,0.12475,-119.7,-0.65586,0.73367,-0.1777,143.87,-0.21198,0.046924,0.97615,38.945

> view matrix models
> #61,0.73381,0.67463,0.079964,-111.69,-0.65822,0.73518,-0.16206,140.81,-0.16812,0.066285,0.98354,24.228

> ui mousemode right "translate selected models"

> view matrix models
> #61,0.73381,0.67463,0.079964,-112.07,-0.65822,0.73518,-0.16206,140.97,-0.16812,0.066285,0.98354,25.38

> ui mousemode right "rotate selected models"

> view matrix models
> #61,0.75321,0.65307,0.078546,-110.67,-0.63785,0.75434,-0.15532,131.11,-0.16068,0.066887,0.98474,23.516

> view matrix models
> #61,0.75867,0.64925,0.05383,-105.84,-0.63571,0.75585,-0.15673,130.62,-0.14244,0.084687,0.98617,15.476

> view matrix models
> #61,0.75812,0.6495,0.058332,-106.71,-0.63563,0.75598,-0.15639,130.51,-0.14568,0.081487,0.98597,16.9

> select add #62

5182 atoms, 5172 bonds, 8 pseudobonds, 334 residues, 4 models selected  

> view matrix models
> #61,0.76141,0.64762,0.029126,-101.06,-0.63617,0.75508,-0.15857,131.26,-0.12469,0.10221,0.98692,7.7311,#62,0.77801,0.62773,0.025581,-100.93,-0.61218,0.76663,-0.19368,159.93,-0.14119,0.13503,0.98073,2.8523

> mmaker #64/9 to #61/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#61) with combination, chain 9 (#64),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> show #!64 models

> hide #!61 models

> show #!61 models

> close #64-66

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 389, in _items_change  
item_names = self._item_names()  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 47, in _item_names  
values = [v for v in self.list_func() if self.filter_func(v)]  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 47, in   
values = [v for v in self.list_func() if self.filter_func(v)]  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/match_maker/tool.py", line 497, in   
filter_func=lambda c, ref=chain: c.structure != ref.structure)  
AttributeError: 'Sequence' object has no attribute 'structure'  
  
Error processing trigger "changes":  
AttributeError: 'Sequence' object has no attribute 'structure'  
  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/match_maker/tool.py", line 497, in  
filter_func=lambda c, ref=chain: c.structure != ref.structure)  
  
See log for complete Python traceback.  
  

> select add #18

6512 atoms, 6501 bonds, 9 pseudobonds, 418 residues, 6 models selected  

> select subtract #61

3921 atoms, 3915 bonds, 5 pseudobonds, 251 residues, 4 models selected  

> select subtract #62

1330 atoms, 1329 bonds, 1 pseudobond, 84 residues, 2 models selected  

> select subtract #18

Nothing selected  

> select add #17

257 atoms, 259 bonds, 15 residues, 1 model selected  

> select subtract #17

Nothing selected  

> select add #16

241 atoms, 240 bonds, 15 residues, 1 model selected  

> select subtract #16

Nothing selected  

> select add #15

209 atoms, 208 bonds, 15 residues, 1 model selected  

> select subtract #15

Nothing selected  

> select add #14

261 atoms, 260 bonds, 1 pseudobond, 17 residues, 2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #14,0.88118,0.45265,0.13652,-99.055,-0.47062,0.81219,0.34476,39.981,0.045177,-0.36804,0.92871,79.66

> ui mousemode right "translate selected models"

> view matrix models
> #14,0.88118,0.45265,0.13652,-99.604,-0.47062,0.81219,0.34476,41.351,0.045177,-0.36804,0.92871,81.705

> view matrix models
> #14,0.88118,0.45265,0.13652,-99.427,-0.47062,0.81219,0.34476,41.268,0.045177,-0.36804,0.92871,81.867

> select add #13

357 atoms, 355 bonds, 2 pseudobonds, 25 residues, 4 models selected  

> select subtract #13

261 atoms, 260 bonds, 1 pseudobond, 17 residues, 2 models selected  

> select add #15

470 atoms, 468 bonds, 1 pseudobond, 32 residues, 3 models selected  

> select subtract #15

261 atoms, 260 bonds, 1 pseudobond, 17 residues, 2 models selected  

> select add #16

502 atoms, 500 bonds, 1 pseudobond, 32 residues, 3 models selected  

> select subtract #16

261 atoms, 260 bonds, 1 pseudobond, 17 residues, 2 models selected  

> select add #17

518 atoms, 519 bonds, 1 pseudobond, 32 residues, 3 models selected  

> select subtract #17

261 atoms, 260 bonds, 1 pseudobond, 17 residues, 2 models selected  

> select add #57

458 atoms, 455 bonds, 2 pseudobonds, 30 residues, 4 models selected  

> select subtract #14

197 atoms, 195 bonds, 1 pseudobond, 13 residues, 2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #57,0.89406,0.44602,-0.041505,-67.072,-0.44085,0.89254,0.095015,63.951,0.079423,-0.066652,0.99461,-2.9614

> ui mousemode right "translate selected models"

> view matrix models
> #57,0.89406,0.44602,-0.041505,-66.695,-0.44085,0.89254,0.095015,64.304,0.079423,-0.066652,0.99461,-2.7655

> view matrix models
> #57,0.89406,0.44602,-0.041505,-66.715,-0.44085,0.89254,0.095015,64.039,0.079423,-0.066652,0.99461,-2.6853

> view matrix models
> #57,0.89406,0.44602,-0.041505,-66.709,-0.44085,0.89254,0.095015,64.333,0.079423,-0.066652,0.99461,-2.5051

> view matrix models
> #57,0.89406,0.44602,-0.041505,-66.806,-0.44085,0.89254,0.095015,64.317,0.079423,-0.066652,0.99461,-2.6626

> view matrix models
> #57,0.89406,0.44602,-0.041505,-66.735,-0.44085,0.89254,0.095015,64.24,0.079423,-0.066652,0.99461,-3.0032

> view matrix models
> #57,0.89406,0.44602,-0.041505,-66.648,-0.44085,0.89254,0.095015,64.337,0.079423,-0.066652,0.99461,-2.9852

> select clear

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> mmaker #64/9 to #61/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#61) with combination, chain 9 (#64),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> mmaker #64/9 to #63/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#63) with combination, chain 9 (#64),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> mmaker #65/9 to #61/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#61) with combination, chain 9 (#65),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> close #64-65

> select add #18

1330 atoms, 1329 bonds, 1 pseudobond, 84 residues, 2 models selected  

> select subtract #18

Nothing selected  

> select add #15

209 atoms, 208 bonds, 15 residues, 1 model selected  

> select subtract #15

Nothing selected  

> select add #57

197 atoms, 195 bonds, 1 pseudobond, 13 residues, 2 models selected  

> select subtract #57

Nothing selected  

> select add #15

209 atoms, 208 bonds, 15 residues, 1 model selected  

> select subtract #15

Nothing selected  

> select add #14

261 atoms, 260 bonds, 1 pseudobond, 17 residues, 2 models selected  

> select subtract #14

Nothing selected  

> select add #14

261 atoms, 260 bonds, 1 pseudobond, 17 residues, 2 models selected  

> select add #13

357 atoms, 355 bonds, 2 pseudobonds, 25 residues, 4 models selected  

> select subtract #13

261 atoms, 260 bonds, 1 pseudobond, 17 residues, 2 models selected  

> select add #13

357 atoms, 355 bonds, 2 pseudobonds, 25 residues, 4 models selected  

> select subtract #13

261 atoms, 260 bonds, 1 pseudobond, 17 residues, 2 models selected  

> select add #15

470 atoms, 468 bonds, 1 pseudobond, 32 residues, 3 models selected  

> select subtract #15

261 atoms, 260 bonds, 1 pseudobond, 17 residues, 2 models selected  

> select add #16

502 atoms, 500 bonds, 1 pseudobond, 32 residues, 3 models selected  

> select subtract #16

261 atoms, 260 bonds, 1 pseudobond, 17 residues, 2 models selected  

> select add #17

518 atoms, 519 bonds, 1 pseudobond, 32 residues, 3 models selected  

> select subtract #17

261 atoms, 260 bonds, 1 pseudobond, 17 residues, 2 models selected  

> select add #18

1591 atoms, 1589 bonds, 2 pseudobonds, 101 residues, 4 models selected  

> select subtract #18

261 atoms, 260 bonds, 1 pseudobond, 17 residues, 2 models selected  

> select add #57

458 atoms, 455 bonds, 2 pseudobonds, 30 residues, 4 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #14,0.91262,0.38944,0.12437,-89.746,-0.40622,0.82961,0.38306,17.626,0.046,-0.40011,0.91531,91.121,#57,0.92383,0.38121,-0.034748,-59.811,-0.37453,0.91892,0.12373,40.196,0.0791,-0.1013,0.99171,5.0922

> view matrix models
> #14,0.87622,0.37688,0.30034,-113.93,-0.481,0.72235,0.49684,33.106,-0.029699,-0.5798,0.81422,163.65,#57,0.89497,0.42433,0.13775,-97.003,-0.44611,0.85403,0.26763,40.112,-0.0040752,-0.30097,0.95362,71.615

> view matrix models
> #14,0.87626,0.35732,0.32324,-114.19,-0.47706,0.73757,0.47792,32.747,-0.067649,-0.57299,0.81677,169.11,#57,0.89568,0.41274,0.16555,-100.05,-0.44274,0.86258,0.24481,42.051,-0.041753,-0.29257,0.95533,76.807

> view matrix models
> #14,0.83337,0.35589,0.4229,-124.75,-0.51011,0.78982,0.34056,54.585,-0.21281,-0.49954,0.83975,177.35,#57,0.85717,0.44323,0.2623,-117.93,-0.48086,0.87115,0.099343,75.923,-0.18447,-0.21128,0.95986,86.221

> view matrix models
> #14,0.8555,0.3476,0.38379,-119.75,-0.47648,0.81861,0.32069,45.737,-0.2027,-0.45722,0.86594,161.31,#57,0.87742,0.42269,0.22686,-110.56,-0.44764,0.89144,0.070374,70.737,-0.17248,-0.1633,0.97138,71.332

> ui mousemode right "translate selected models"

> view matrix models
> #14,0.8555,0.3476,0.38379,-120.36,-0.47648,0.81861,0.32069,46.23,-0.2027,-0.45722,0.86594,162.61,#57,0.87742,0.42269,0.22686,-111.16,-0.44764,0.89144,0.070374,71.23,-0.17248,-0.1633,0.97138,72.63

> view matrix models
> #14,0.8555,0.3476,0.38379,-119.89,-0.47648,0.81861,0.32069,46.122,-0.2027,-0.45722,0.86594,162.87,#57,0.87742,0.42269,0.22686,-110.7,-0.44764,0.89144,0.070374,71.121,-0.17248,-0.1633,0.97138,72.883

> ui mousemode right "rotate selected models"

> view matrix models
> #14,0.9039,0.29023,0.3142,-103.68,-0.39835,0.83876,0.37121,16.84,-0.1558,-0.4607,0.87377,152.95,#57,0.92172,0.34531,0.17658,-92.893,-0.36703,0.92376,0.10936,40.901,-0.12536,-0.16561,0.97819,62.887

> view matrix models
> #14,0.90391,0.24173,0.35288,-100.81,-0.38375,0.82269,0.41943,8.087,-0.18892,-0.51454,0.8364,178.08,#57,0.92258,0.31103,0.22828,-95.742,-0.35061,0.92282,0.15962,28.114,-0.16101,-0.2273,0.96042,86.541

> view matrix models
> #14,0.89761,0.26248,0.35413,-104.25,-0.39471,0.83626,0.38063,14.827,-0.19623,-0.48143,0.85423,169.01,#57,0.9167,0.33135,0.22331,-98.001,-0.36302,0.92416,0.11896,38.152,-0.16696,-0.19012,0.96746,78.331

> view matrix models
> #14,0.92213,0.1702,0.34742,-88.081,-0.32964,0.81573,0.47532,-11.768,-0.2025,-0.55283,0.80831,194.31,#57,0.9393,0.24077,0.24444,-87.023,-0.29423,0.93171,0.21294,4.8657,-0.17648,-0.27194,0.946,101.96

> view matrix models
> #14,0.92431,0.24536,0.29233,-93.873,-0.35847,0.82101,0.44433,-1.2942,-0.13099,-0.51549,0.84682,164.98,#57,0.94036,0.29531,0.16885,-84.257,-0.3243,0.9281,0.1829,17.33,-0.1027,-0.22675,0.96852,73.51

> view matrix models
> #14,0.91484,0.28929,0.28175,-99.337,-0.38332,0.84158,0.38053,11.492,-0.12703,-0.45613,0.8808,145.01,#57,0.93121,0.33414,0.14562,-86.306,-0.35156,0.92885,0.11681,35.331,-0.096227,-0.15997,0.98242,55.184

> view matrix models
> #14,0.91038,0.27654,0.30779,-100.78,-0.38712,0.83192,0.39755,11.002,-0.14612,-0.48107,0.86442,157.21,#57,0.92767,0.33013,0.17447,-90.371,-0.35477,0.92499,0.1361,33.031,-0.11645,-0.18816,0.97521,66.581

> view matrix models
> #14,0.91335,0.28175,0.29395,-99.799,-0.38284,0.84008,0.38431,10.988,-0.13866,-0.46355,0.87516,149.95,#57,0.93012,0.33075,0.15959,-88.087,-0.35094,0.92857,0.12085,34.486,-0.10822,-0.16841,0.97976,59.85

> select subtract #57

261 atoms, 260 bonds, 1 pseudobond, 17 residues, 2 models selected  

> select subtract #14

Nothing selected  

> select add #13

96 atoms, 95 bonds, 1 pseudobond, 8 residues, 2 models selected  

> ui mousemode right "translate selected models"

> view matrix models
> #13,0.79314,0.60856,-0.024242,-90.601,-0.59978,0.77354,-0.20468,182.51,-0.10581,0.17688,0.97853,-16.135

> ui mousemode right "rotate selected models"

> view matrix models
> #13,0.80774,0.58433,-0.078183,-77.194,-0.57444,0.75028,-0.32727,206.88,-0.13257,0.30926,0.94169,-35.529

> view matrix models
> #13,0.72714,0.68586,-0.029519,-95.003,-0.66467,0.69261,-0.28017,229.68,-0.17171,0.22334,0.9595,-10.45

> ui mousemode right "translate selected models"

> view matrix models
> #13,0.72714,0.68586,-0.029519,-94.145,-0.66467,0.69261,-0.28017,229.53,-0.17171,0.22334,0.9595,-10.907

> select clear

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> mmaker #64/9 to #63/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#63) with combination, chain 9 (#64),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> mmaker #65/9 to #61/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#61) with combination, chain 9 (#65),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> mmaker #66/9 to #62/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#62) with combination, chain 9 (#66),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> hide #!63 models

> hide #!62 models

> hide #!61 models

> color #64 #7a81ffff

> color #65 #fffc79ff

> color #66 #ff2600ff

> select add #65

2591 atoms, 2586 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #65,0.65127,0.75885,-0.0017609,-98.418,-0.73511,0.63031,-0.24965,198.33,-0.18834,0.16389,0.96833,8.1389

> ui mousemode right "translate selected models"

> view matrix models
> #65,0.65127,0.75885,-0.0017609,-99.824,-0.73511,0.63031,-0.24965,198.49,-0.18834,0.16389,0.96833,7.7273

> ui mousemode right "rotate selected models"

> view matrix models
> #65,0.62871,0.77751,-0.014537,-97.096,-0.75366,0.6046,-0.25778,209.66,-0.19164,0.17303,0.96609,6.7326

> view matrix models
> #65,0.63333,0.77368,-0.017653,-96.491,-0.74453,0.60292,-0.28664,214.12,-0.21112,0.19468,0.95788,7.2483

> view matrix models
> #65,0.64973,0.76013,-0.0079853,-98.553,-0.73081,0.62171,-0.28176,206.14,-0.20921,0.18891,0.95945,7.8778

> view matrix models
> #65,0.72701,0.68626,0.022361,-102.9,-0.66288,0.70999,-0.23771,163.69,-0.179,0.15799,0.97108,6.6946

> ui mousemode right "translate selected models"

> view matrix models
> #65,0.72701,0.68626,0.022361,-102.24,-0.66288,0.70999,-0.23771,166.13,-0.179,0.15799,0.97108,6.5295

> ui mousemode right "rotate selected models"

> view matrix models
> #65,0.66483,0.74683,-0.015534,-96.276,-0.72231,0.63742,-0.26824,200.58,-0.19043,0.18955,0.96323,3.1244

> view matrix models
> #65,0.67851,0.73322,-0.044915,-89.872,-0.71279,0.64234,-0.28166,200.31,-0.17766,0.22312,0.95846,-6.0977

> view matrix models
> #65,0.68127,0.73076,-0.043174,-90.202,-0.71028,0.6456,-0.28054,198.85,-0.17714,0.22179,0.95887,-5.9786

> ui mousemode right "translate selected models"

> view matrix models
> #65,0.68127,0.73076,-0.043174,-91.267,-0.71028,0.6456,-0.28054,198.17,-0.17714,0.22179,0.95887,-6.2279

> view matrix models
> #65,0.68127,0.73076,-0.043174,-91.432,-0.71028,0.6456,-0.28054,198.12,-0.17714,0.22179,0.95887,-6.1027

> view matrix models
> #65,0.68127,0.73076,-0.043174,-91.427,-0.71028,0.6456,-0.28054,198.15,-0.17714,0.22179,0.95887,-6.0206

> ui mousemode right "rotate selected models"

> view matrix models
> #65,0.67991,0.73212,-0.041569,-91.798,-0.70946,0.64241,-0.28977,200.59,-0.18544,0.22651,0.95619,-4.9346

> select add #64

5182 atoms, 5172 bonds, 8 pseudobonds, 334 residues, 4 models selected  

> select subtract #65

2591 atoms, 2586 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> view matrix models
> #64,0.69608,0.7106,-0.10252,-79.62,-0.71018,0.66052,-0.24362,264.1,-0.1054,0.24239,0.96444,-29.492

> ui mousemode right "translate selected models"

> view matrix models
> #64,0.69608,0.7106,-0.10252,-78.66,-0.71018,0.66052,-0.24362,263.94,-0.1054,0.24239,0.96444,-29.123

> view matrix models
> #64,0.69608,0.7106,-0.10252,-78.689,-0.71018,0.66052,-0.24362,263.92,-0.1054,0.24239,0.96444,-29.123

> ui mousemode right "rotate selected models"

> view matrix models
> #64,0.68493,0.72832,-0.020524,-97.199,-0.70909,0.65983,-0.24862,264.88,-0.16754,0.18484,0.96838,-4.5834

> view matrix models
> #64,0.69017,0.72075,-0.064687,-87.532,-0.71179,0.66004,-0.24021,263.66,-0.13044,0.21183,0.96856,-18.061

> color #66 #00f900ff

> select add #66

5182 atoms, 5172 bonds, 8 pseudobonds, 334 residues, 4 models selected  

> select subtract #66

2591 atoms, 2586 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> select add #66

5182 atoms, 5172 bonds, 8 pseudobonds, 334 residues, 4 models selected  

> select subtract #64

2591 atoms, 2586 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #66,0.71162,0.70176,-0.033617,-92.589,-0.68367,0.68066,-0.26323,208.44,-0.16184,0.2103,0.96415,-8.6448

> view matrix models
> #66,0.71519,0.69581,-0.065988,-85.357,-0.68572,0.68027,-0.25889,208.05,-0.13525,0.2304,0.96365,-18.352

> select add #64

5182 atoms, 5172 bonds, 8 pseudobonds, 334 residues, 4 models selected  

> select subtract #66

2591 atoms, 2586 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> view matrix models
> #64,0.71771,0.6935,-0.062833,-87.05,-0.6792,0.6773,-0.28276,261.96,-0.15354,0.24562,0.95713,-18.966

> select clear

> select add #66

2591 atoms, 2586 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #66,0.70859,0.70522,-0.023773,-94.785,-0.68574,0.68029,-0.25878,208.03,-0.16632,0.19967,0.96564,-5.6356

> view matrix models
> #66,0.71165,0.70213,-0.023838,-94.663,-0.67806,0.67758,-0.28481,212.43,-0.18382,0.21885,0.95829,-5.1159

> view matrix models
> #66,0.71132,0.70251,-0.02238,-94.981,-0.68042,0.68027,-0.27251,209.78,-0.17621,0.20907,0.96189,-5.0943

> view matrix models
> #66,0.70801,0.70574,-0.025664,-94.407,-0.6841,0.67637,-0.27301,211.49,-0.17531,0.21085,0.96167,-5.6328

> view matrix models
> #66,0.74426,0.66662,-0.041079,-89.408,-0.64997,0.70878,-0.27416,197.63,-0.15365,0.23075,0.96081,-14.255

> view matrix models
> #66,0.74481,0.6661,-0.039716,-89.67,-0.64723,0.70666,-0.28589,199.95,-0.16236,0.23864,0.95744,-13.676

> view matrix models
> #66,0.74344,0.66722,-0.045934,-88.4,-0.64967,0.70416,-0.28651,201.13,-0.15882,0.24285,0.95697,-15.239

> view matrix models
> #66,0.73972,0.6721,-0.033066,-91.4,-0.65145,0.70296,-0.28539,201.53,-0.16856,0.23265,0.95784,-11.172

> view matrix models
> #66,0.74006,0.67177,-0.032193,-91.567,-0.6496,0.70161,-0.29284,202.98,-0.17413,0.23763,0.95562,-10.774

> view matrix models
> #66,0.741,0.67081,-0.030418,-91.893,-0.65094,0.70645,-0.27786,199.1,-0.1649,0.2257,0.96014,-10.761

> view matrix models
> #66,0.7409,0.67092,-0.030636,-91.852,-0.65079,0.70591,-0.27957,199.54,-0.16594,0.22707,0.95964,-10.771

> hide #!64-66 target m

> hide #!57 models

> hide #!1-21 target m

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Fit14-13.cxs"

> show #!9 models

> hide #!9 models

> show #!64-66 target m

> show #!13-18 target m

> show #!57 models

> select clear

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Fit14-13.cxs"

> show #!8 models

> select add #65

2591 atoms, 2586 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> ui mousemode right "translate selected models"

> ui mousemode right "rotate selected models"

> view matrix models
> #65,0.69751,0.71515,-0.045195,-90.617,-0.68891,0.65189,-0.31694,199.91,-0.1972,0.25221,0.94737,-6.7335

> view matrix models
> #65,0.69389,0.71916,-0.036435,-92.604,-0.69389,0.65427,-0.30075,197.05,-0.19245,0.23397,0.95301,-4.6272

> select clear

> volume #8 level 0.01403

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Fit14-13.cxs"

> select add #16

241 atoms, 240 bonds, 15 residues, 1 model selected  

> select subtract #16

Nothing selected  

> select add #15

209 atoms, 208 bonds, 15 residues, 1 model selected  

> select subtract #15

Nothing selected  

> select add #14

261 atoms, 260 bonds, 1 pseudobond, 17 residues, 2 models selected  

> select subtract #14

Nothing selected  

> select add #18

1330 atoms, 1329 bonds, 1 pseudobond, 84 residues, 2 models selected  

> select subtract #18

Nothing selected  

> select add #18

1330 atoms, 1329 bonds, 1 pseudobond, 84 residues, 2 models selected  

> select subtract #18

Nothing selected  

> select add #17

257 atoms, 259 bonds, 15 residues, 1 model selected  

> ui mousemode right "translate selected models"

> view matrix models
> #17,0.70804,-0.70132,0.082622,168.16,0.69467,0.71276,0.096989,-76.736,-0.12691,-0.011277,0.99185,28.781

> view matrix models
> #17,0.70804,-0.70132,0.082622,168.23,0.69467,0.71276,0.096989,-76.405,-0.12691,-0.011277,0.99185,28.729

> view matrix models
> #17,0.70804,-0.70132,0.082622,167.91,0.69467,0.71276,0.096989,-76.185,-0.12691,-0.011277,0.99185,28.322

> view matrix models
> #17,0.70804,-0.70132,0.082622,167.27,0.69467,0.71276,0.096989,-76.426,-0.12691,-0.011277,0.99185,28.105

> view matrix models
> #17,0.70804,-0.70132,0.082622,167.23,0.69467,0.71276,0.096989,-76.466,-0.12691,-0.011277,0.99185,28.35

> view matrix models
> #17,0.70804,-0.70132,0.082622,166.79,0.69467,0.71276,0.096989,-76.456,-0.12691,-0.011277,0.99185,28.099

> ui mousemode right "rotate selected models"

> view matrix models
> #17,0.68388,-0.70654,0.18197,151.97,0.70559,0.70393,0.081404,-73.597,-0.18561,0.072728,0.97993,25.274

> ui mousemode right "translate selected models"

> view matrix models
> #17,0.68388,-0.70654,0.18197,151.99,0.70559,0.70393,0.081404,-73.278,-0.18561,0.072728,0.97993,26.367

> ui mousemode right "rotate selected models"

> view matrix models
> #17,0.65604,-0.7464,0.11179,178.87,0.74143,0.66505,0.089367,-74.044,-0.14105,0.024253,0.98971,25.467

> ui mousemode right "translate selected models"

> view matrix models
> #17,0.65604,-0.7464,0.11179,178.99,0.74143,0.66505,0.089367,-74.076,-0.14105,0.024253,0.98971,24.89

> view matrix models
> #17,0.65604,-0.7464,0.11179,178.98,0.74143,0.66505,0.089367,-74.532,-0.14105,0.024253,0.98971,24.942

> view matrix models
> #17,0.65604,-0.7464,0.11179,179.02,0.74143,0.66505,0.089367,-74.638,-0.14105,0.024253,0.98971,24.648

> view matrix models
> #17,0.65604,-0.7464,0.11179,178.97,0.74143,0.66505,0.089367,-74.562,-0.14105,0.024253,0.98971,24.978

> select subtract #17

Nothing selected  

> select add #16

241 atoms, 240 bonds, 15 residues, 1 model selected  

> select subtract #16

Nothing selected  

> select add #15

209 atoms, 208 bonds, 15 residues, 1 model selected  

> select subtract #15

Nothing selected  

> select add #14

261 atoms, 260 bonds, 1 pseudobond, 17 residues, 2 models selected  

> select subtract #14

Nothing selected  

> select add #14

261 atoms, 260 bonds, 1 pseudobond, 17 residues, 2 models selected  

> select add #57

458 atoms, 455 bonds, 2 pseudobonds, 30 residues, 4 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #14,0.92186,0.27679,0.27122,-96.012,-0.36411,0.85824,0.36173,7.8327,-0.13265,-0.43222,0.89196,138.86,#57,0.93754,0.3188,0.1392,-82.993,-0.3329,0.93835,0.093116,34.271,-0.10094,-0.13364,0.98588,49.765

> view matrix models
> #14,0.93771,0.25851,0.23211,-87.662,-0.33091,0.86808,0.37004,-2.3373,-0.10583,-0.4238,0.89955,130.37,#57,0.95134,0.28894,0.10706,-73.006,-0.29921,0.94927,0.096777,24.659,-0.073665,-0.1241,0.98953,41.7

> view matrix models
> #14,0.91968,0.24302,0.30842,-95.576,-0.35236,0.85739,0.37513,3.138,-0.17327,-0.45368,0.87416,154.78,#57,0.93641,0.29816,0.18503,-87.245,-0.3206,0.9413,0.10569,28.799,-0.14266,-0.15829,0.97703,64.899

> view matrix models
> #14,0.91681,0.2407,0.31861,-96.493,-0.35884,0.84667,0.39292,3.2451,-0.17518,-0.47456,0.86261,161.83,#57,0.93395,0.29916,0.19554,-89.029,-0.32647,0.93675,0.12614,26.939,-0.14544,-0.18164,0.97255,71.335

> select add #66

3049 atoms, 3041 bonds, 6 pseudobonds, 197 residues, 6 models selected  

> select subtract #57

2852 atoms, 2846 bonds, 5 pseudobonds, 184 residues, 4 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #14,0.90834,0.21562,0.35836,-97.688,-0.35397,0.85272,0.38415,2.7982,-0.22275,-0.47579,0.85088,174.05,#66,0.73382,0.67916,0.015876,-101.79,-0.64656,0.70539,-0.29048,201.04,-0.20848,0.20289,0.95675,3.6741

> view matrix models
> #14,0.89052,0.25646,0.37577,-105.67,-0.39537,0.84489,0.36034,17.483,-0.22507,-0.46946,0.85379,172.68,#66,0.7022,0.71198,0.001349,-100.18,-0.67938,0.6706,-0.29789,216.94,-0.213,0.20826,0.9546,3.7646

> ui mousemode right "translate selected models"

> view matrix models
> #14,0.89052,0.25646,0.37577,-108.87,-0.39537,0.84489,0.36034,17.767,-0.22507,-0.46946,0.85379,172.19,#66,0.7022,0.71198,0.001349,-103.37,-0.67938,0.6706,-0.29789,217.22,-0.213,0.20826,0.9546,3.2724

> ui mousemode right "rotate selected models"

> view matrix models
> #14,0.87052,0.2974,0.39212,-116.22,-0.43631,0.83497,0.33535,33.009,-0.22767,-0.46301,0.85661,170.87,#66,0.66866,0.74344,-0.013796,-100.95,-0.71095,0.63379,-0.30473,233.22,-0.2178,0.21357,0.95234,3.454

> hide #!8 models

> select add #13

2948 atoms, 2941 bonds, 6 pseudobonds, 192 residues, 6 models selected  

> select subtract #13

2852 atoms, 2846 bonds, 5 pseudobonds, 184 residues, 4 models selected  

> select subtract #14

2591 atoms, 2586 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> select add #15

2800 atoms, 2794 bonds, 4 pseudobonds, 182 residues, 3 models selected  

> select add #16

3041 atoms, 3034 bonds, 4 pseudobonds, 197 residues, 4 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #15,0.94186,-0.12927,-0.31014,100.37,0.09066,0.98657,-0.13589,36.411,0.32354,0.099876,0.94093,-71.321,#16,0.90175,0.093114,-0.42211,84.91,-0.11422,0.99314,-0.024926,51.081,0.41689,0.07069,0.9062,-76.368,#66,0.6573,0.7534,-0.018641,-100.21,-0.72798,0.62834,-0.2743,231.63,-0.19494,0.19387,0.96146,1.9974

> undo

> select subtract #66

450 atoms, 448 bonds, 30 residues, 2 models selected  

> view matrix models
> #15,0.9419,-0.09525,-0.32211,95.03,0.061586,0.99167,-0.11316,36.634,0.33021,0.086744,0.93991,-68.379,#16,0.89387,0.12745,-0.42983,80.14,-0.14058,0.99007,0.00123,51.773,0.42572,0.059324,0.90291,-73.732

> ui mousemode right "translate selected models"

> view matrix models
> #15,0.9419,-0.09525,-0.32211,95.767,0.061586,0.99167,-0.11316,36.288,0.33021,0.086744,0.93991,-69.238,#16,0.89387,0.12745,-0.42983,80.877,-0.14058,0.99007,0.00123,51.427,0.42572,0.059324,0.90291,-74.591

> show #!8 models

> select subtract #15

241 atoms, 240 bonds, 15 residues, 1 model selected  

> select subtract #16

Nothing selected  

> select add #57

197 atoms, 195 bonds, 1 pseudobond, 13 residues, 2 models selected  

> select subtract #57

Nothing selected  

> select add #14

261 atoms, 260 bonds, 1 pseudobond, 17 residues, 2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #14,0.80806,0.40301,0.42968,-133.08,-0.54675,0.78462,0.29229,73.016,-0.21934,-0.47111,0.85437,171.35

> ui mousemode right "translate selected models"

> view matrix models
> #14,0.80806,0.40301,0.42968,-130.93,-0.54675,0.78462,0.29229,72.08,-0.21934,-0.47111,0.85437,171.19

> view matrix models
> #14,0.80806,0.40301,0.42968,-131.25,-0.54675,0.78462,0.29229,72.436,-0.21934,-0.47111,0.85437,171.51

> view matrix models
> #14,0.80806,0.40301,0.42968,-131.09,-0.54675,0.78462,0.29229,72.451,-0.21934,-0.47111,0.85437,171.02

> view matrix models
> #14,0.80806,0.40301,0.42968,-131.67,-0.54675,0.78462,0.29229,72.718,-0.21934,-0.47111,0.85437,170.52

> view matrix models
> #14,0.80806,0.40301,0.42968,-131.87,-0.54675,0.78462,0.29229,72.615,-0.21934,-0.47111,0.85437,170.65

> select add #57

458 atoms, 455 bonds, 2 pseudobonds, 30 residues, 4 models selected  

> ui mousemode right "translate selected models"

> view matrix models
> #14,0.80806,0.40301,0.42968,-129.83,-0.54675,0.78462,0.29229,71.621,-0.21934,-0.47111,0.85437,170.37,#57,0.93395,0.29916,0.19554,-86.984,-0.32647,0.93675,0.12614,25.945,-0.14544,-0.18164,0.97255,71.049

> view matrix models
> #14,0.80806,0.40301,0.42968,-129.05,-0.54675,0.78462,0.29229,71.696,-0.21934,-0.47111,0.85437,171.02,#57,0.93395,0.29916,0.19554,-86.209,-0.32647,0.93675,0.12614,26.02,-0.14544,-0.18164,0.97255,71.703

> select clear

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> mmaker #67/9 to #64/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#64) with combination, chain 9 (#67),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> mmaker #68/9 to #65/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#65) with combination, chain 9 (#68),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> mmaker #69/9 to #66/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#66) with combination, chain 9 (#69),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> color #68 #73fa79ff

> color #67 #fffc79ff

> color #69 #ff8ad8ff

> hide #!64 models

> hide #!65 models

> hide #!66 models

> select add #67

2591 atoms, 2586 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #67,0.74837,0.66121,-0.052283,-87.793,-0.64684,0.71012,-0.27809,247.12,-0.14675,0.24193,0.95913,-19.858

> ui mousemode right "translate selected models"

> view matrix models
> #67,0.74837,0.66121,-0.052283,-87.517,-0.64684,0.71012,-0.27809,244.09,-0.14675,0.24193,0.95913,-19.969

> ui mousemode right "rotate selected models"

> view matrix models
> #67,0.76087,0.64651,-0.055712,-85.903,-0.62617,0.70896,-0.32449,249.67,-0.17029,0.28178,0.94425,-21.485

> view matrix models
> #67,0.75283,0.65626,-0.05069,-87.577,-0.637,0.70699,-0.30724,248.77,-0.16579,0.26359,0.95028,-19.411

> view matrix models
> #67,0.72135,0.68972,-0.062788,-86.629,-0.67737,0.68371,-0.2715,254.82,-0.14433,0.23837,0.96039,-19.882

> view matrix models
> #67,0.72615,0.68321,-0.077001,-83.206,-0.67539,0.68787,-0.26586,252.34,-0.12867,0.24506,0.96093,-24.603

> select add #68

5182 atoms, 5172 bonds, 8 pseudobonds, 334 residues, 4 models selected  

> select subtract #67

2591 atoms, 2586 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> ui mousemode right "translate selected models"

> view matrix models
> #68,0.69389,0.71916,-0.036435,-97.998,-0.69389,0.65427,-0.30075,199.83,-0.19245,0.23397,0.95301,-5.1577

> view matrix models
> #68,0.69389,0.71916,-0.036435,-97.902,-0.69389,0.65427,-0.30075,199.7,-0.19245,0.23397,0.95301,-5.5624

> ui mousemode right "rotate selected models"

> view matrix models
> #68,0.65821,0.75283,-0.0032772,-105.32,-0.73838,0.64471,-0.19788,189.85,-0.14685,0.13266,0.98022,3.2424

> ui mousemode right "translate selected models"

> view matrix models
> #68,0.65821,0.75283,-0.0032772,-105.5,-0.73838,0.64471,-0.19788,189.89,-0.14685,0.13266,0.98022,3.2392

> ui mousemode right "rotate selected models"

> view matrix models
> #68,0.65834,0.75272,-0.00056889,-106.05,-0.73881,0.64603,-0.19184,188.45,-0.14404,0.12672,0.98143,3.8076

> ui mousemode right "translate selected models"

> view matrix models
> #68,0.65834,0.75272,-0.00056889,-105.4,-0.73881,0.64603,-0.19184,187.25,-0.14404,0.12672,0.98143,3.6605

> ui mousemode right "rotate selected models"

> view matrix models
> #68,0.5937,0.80447,-0.018505,-100.96,-0.79416,0.58206,-0.17469,209.34,-0.12977,0.11841,0.98445,2.1527

> ui mousemode right "translate selected models"

> view matrix models
> #68,0.5937,0.80447,-0.018505,-103.27,-0.79416,0.58206,-0.17469,210.38,-0.12977,0.11841,0.98445,2.5761

> view matrix models
> #68,0.5937,0.80447,-0.018505,-100.86,-0.79416,0.58206,-0.17469,211.15,-0.12977,0.11841,0.98445,2.3055

> view matrix models
> #68,0.5937,0.80447,-0.018505,-100.84,-0.79416,0.58206,-0.17469,211.32,-0.12977,0.11841,0.98445,2.5512

> view matrix models
> #68,0.5937,0.80447,-0.018505,-100.95,-0.79416,0.58206,-0.17469,210.36,-0.12977,0.11841,0.98445,0.15105

> ui mousemode right "rotate selected models"

> view matrix models
> #68,0.59056,0.80121,-0.096483,-83.826,-0.77944,0.53533,-0.32541,248.67,-0.20907,0.26738,0.94064,-9.6201

> ui mousemode right "translate selected models"

> view matrix models
> #68,0.59056,0.80121,-0.096483,-86.695,-0.77944,0.53533,-0.32541,248.26,-0.20907,0.26738,0.94064,-9.8718

> ui mousemode right "rotate selected models"

> view matrix models
> #68,0.559,0.82892,-0.020333,-102.25,-0.79646,0.52997,-0.29116,245.92,-0.23057,0.17895,0.95646,11.462

> view matrix models
> #68,0.6127,0.79023,0.011432,-110.34,-0.75544,0.58984,-0.28531,222.92,-0.2322,0.16617,0.95837,14.332

> ui mousemode right "translate selected models"

> view matrix models
> #68,0.6127,0.79023,0.011432,-108.42,-0.75544,0.58984,-0.28531,224.18,-0.2322,0.16617,0.95837,14.305

> view matrix models
> #68,0.6127,0.79023,0.011432,-108.71,-0.75544,0.58984,-0.28531,220.84,-0.2322,0.16617,0.95837,14.061

> view matrix models
> #68,0.6127,0.79023,0.011432,-107.13,-0.75544,0.58984,-0.28531,221.24,-0.2322,0.16617,0.95837,14.782

> view matrix models
> #68,0.6127,0.79023,0.011432,-106.52,-0.75544,0.58984,-0.28531,221.81,-0.2322,0.16617,0.95837,15.438

> ui mousemode right "rotate selected models"

> view matrix models
> #68,0.61876,0.78544,0.014546,-107.24,-0.74213,0.59051,-0.31707,225.46,-0.25763,0.18539,0.94829,18.056

> view matrix models
> #68,0.61524,0.78825,-0.011454,-101.94,-0.75669,0.58641,-0.28904,223.6,-0.22112,0.1865,0.95725,8.8184

> view matrix models
> #68,0.6196,0.78483,-0.011589,-101.98,-0.75,0.58762,-0.30367,224.96,-0.23152,0.19684,0.95271,9.4032

> ui mousemode right "translate selected models"

> view matrix models
> #68,0.6196,0.78483,-0.011589,-100.38,-0.75,0.58762,-0.30367,223.86,-0.23152,0.19684,0.95271,9.7836

> select add #69

5182 atoms, 5172 bonds, 8 pseudobonds, 334 residues, 4 models selected  

> select subtract #68

2591 atoms, 2586 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> view matrix models
> #69,0.66866,0.74344,-0.013796,-102.1,-0.71095,0.63379,-0.30473,233.63,-0.2178,0.21357,0.95234,3.2339

> view matrix models
> #69,0.66866,0.74344,-0.013796,-100.87,-0.71095,0.63379,-0.30473,233.98,-0.2178,0.21357,0.95234,4.0443

> view matrix models
> #69,0.66866,0.74344,-0.013796,-101.26,-0.71095,0.63379,-0.30473,233.43,-0.2178,0.21357,0.95234,4.2404

> view matrix models
> #69,0.66866,0.74344,-0.013796,-101.13,-0.71095,0.63379,-0.30473,233.27,-0.2178,0.21357,0.95234,3.3945

> view matrix models
> #69,0.66866,0.74344,-0.013796,-101.18,-0.71095,0.63379,-0.30473,233.28,-0.2178,0.21357,0.95234,3.385

> ui mousemode right "rotate selected models"

> select add #68

5182 atoms, 5172 bonds, 8 pseudobonds, 334 residues, 4 models selected  

> select subtract #69

2591 atoms, 2586 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> view matrix models
> #68,0.60652,0.79497,-0.012182,-100.02,-0.76707,0.58107,-0.27195,222.31,-0.20912,0.17429,0.96223,8.6359

> ui mousemode right "translate selected models"

> view matrix models
> #68,0.60652,0.79497,-0.012182,-100.33,-0.76707,0.58107,-0.27195,223.64,-0.20912,0.17429,0.96223,9.613

> view matrix models
> #68,0.60652,0.79497,-0.012182,-101.27,-0.76707,0.58107,-0.27195,223.52,-0.20912,0.17429,0.96223,9.7016

> view matrix models
> #68,0.60652,0.79497,-0.012182,-101.22,-0.76707,0.58107,-0.27195,223.81,-0.20912,0.17429,0.96223,9.6805

> select add #69

5182 atoms, 5172 bonds, 8 pseudobonds, 334 residues, 4 models selected  

> view matrix models
> #68,0.60652,0.79497,-0.012182,-101.43,-0.76707,0.58107,-0.27195,224.95,-0.20912,0.17429,0.96223,9.695,#69,0.66866,0.74344,-0.013796,-101.39,-0.71095,0.63379,-0.30473,234.41,-0.2178,0.21357,0.95234,3.3994

> view matrix models
> #68,0.60652,0.79497,-0.012182,-101.32,-0.76707,0.58107,-0.27195,224.95,-0.20912,0.17429,0.96223,9.0128,#69,0.66866,0.74344,-0.013796,-101.28,-0.71095,0.63379,-0.30473,234.42,-0.2178,0.21357,0.95234,2.7172

> view matrix models
> #68,0.60652,0.79497,-0.012182,-101.31,-0.76707,0.58107,-0.27195,226.01,-0.20912,0.17429,0.96223,8.9544,#69,0.66866,0.74344,-0.013796,-101.27,-0.71095,0.63379,-0.30473,235.48,-0.2178,0.21357,0.95234,2.6588

> ui mousemode right "rotate selected models"

> view matrix models
> #68,0.57965,0.81451,-0.023904,-98.615,-0.78469,0.55004,-0.28586,239.42,-0.21969,0.18446,0.95797,9.3585,#69,0.64375,0.76478,-0.026647,-98.228,-0.73067,0.60394,-0.31841,248.97,-0.22742,0.22444,0.94758,3.2074

> view matrix models
> #68,0.59821,0.80045,-0.03773,-96.005,-0.76514,0.55657,-0.32372,241.71,-0.23812,0.22252,0.9454,6.2486,#69,0.66145,0.74894,-0.039668,-95.671,-0.70974,0.60797,-0.35587,251.5,-0.24241,0.26354,0.93369,0.48394

> undo

> view matrix models
> #68,0.57532,0.81784,-0.012108,-100.93,-0.7871,0.54954,-0.28014,238.85,-0.22245,0.1707,0.95988,12.766,#69,0.63941,0.76872,-0.015044,-100.6,-0.73324,0.60378,-0.31274,248.37,-0.23132,0.211,0.94972,6.554

> select subtract #69

2591 atoms, 2586 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> view matrix models
> #68,0.62746,0.7786,0.0081972,-106.27,-0.74992,0.60711,-0.26276,214.81,-0.20956,0.15872,0.96483,11.983

> ui mousemode right "translate selected models"

> view matrix models
> #68,0.62746,0.7786,0.0081972,-103.16,-0.74992,0.60711,-0.26276,212.51,-0.20956,0.15872,0.96483,12.87

> ui mousemode right "rotate selected models"

> view matrix models
> #68,0.6854,0.72775,0.024805,-106.23,-0.69827,0.66653,-0.26107,188.37,-0.20653,0.16162,0.965,11.574

> ui mousemode right "translate selected models"

> view matrix models
> #68,0.6854,0.72775,0.024805,-109.15,-0.69827,0.66653,-0.26107,189.24,-0.20653,0.16162,0.965,11.605

> view matrix models
> #68,0.6854,0.72775,0.024805,-108.46,-0.69827,0.66653,-0.26107,188.22,-0.20653,0.16162,0.965,11.555

> view matrix models
> #68,0.6854,0.72775,0.024805,-106.95,-0.69827,0.66653,-0.26107,186.9,-0.20653,0.16162,0.965,11.867

> ui mousemode right "rotate selected models"

> view matrix models
> #68,0.67946,0.73339,0.021658,-106.44,-0.70379,0.65981,-0.26332,189.99,-0.20741,0.16368,0.96446,11.676

> view matrix models
> #68,0.68413,0.72929,-0.010052,-100.01,-0.70752,0.66023,-0.25201,188.34,-0.17715,0.17952,0.96767,1.4435

> ui mousemode right "translate selected models"

> view matrix models
> #68,0.68413,0.72929,-0.010052,-98.057,-0.70752,0.66023,-0.25201,189.57,-0.17715,0.17952,0.96767,1.3439

> ui mousemode right "rotate selected models"

> view matrix models
> #68,0.64499,0.76292,-0.044085,-91.211,-0.74484,0.61471,-0.2595,208.87,-0.17088,0.20021,0.96474,-4.0471

> ui mousemode right "translate selected models"

> view matrix models
> #68,0.64499,0.76292,-0.044085,-92.977,-0.74484,0.61471,-0.2595,208.23,-0.17088,0.20021,0.96474,-4.1161

> view matrix models
> #68,0.64499,0.76292,-0.044085,-95.761,-0.74484,0.61471,-0.2595,209.68,-0.17088,0.20021,0.96474,-4.7238

> view matrix models
> #68,0.64499,0.76292,-0.044085,-93.521,-0.74484,0.61471,-0.2595,208.57,-0.17088,0.20021,0.96474,-4.4662

> ui mousemode right "rotate selected models"

> view matrix models
> #68,0.57274,0.8156,-0.082229,-83.713,-0.79889,0.53288,-0.27896,241.91,-0.1837,0.22546,0.95678,-6.1369

> ui mousemode right "translate selected models"

> view matrix models
> #68,0.57274,0.8156,-0.082229,-87.166,-0.79889,0.53288,-0.27896,246.2,-0.1837,0.22546,0.95678,-7.6509

> view matrix models
> #68,0.57274,0.8156,-0.082229,-88.478,-0.79889,0.53288,-0.27896,247.9,-0.1837,0.22546,0.95678,-8.2388

> ui mousemode right "rotate selected models"

> view matrix models
> #68,0.65951,0.72564,-0.19621,-61.834,-0.72473,0.54452,-0.42221,259.61,-0.19953,0.42065,0.88501,-35.448

> ui mousemode right "translate selected models"

> view matrix models
> #68,0.65951,0.72564,-0.19621,-59.447,-0.72473,0.54452,-0.42221,256.89,-0.19953,0.42065,0.88501,-34.587

> select add #69

5182 atoms, 5172 bonds, 8 pseudobonds, 334 residues, 4 models selected  

> view matrix models
> #68,0.65951,0.72564,-0.19621,-60.593,-0.72473,0.54452,-0.42221,256.16,-0.19953,0.42065,0.88501,-34.909,#69,0.63941,0.76872,-0.015044,-101.75,-0.73324,0.60378,-0.31274,247.64,-0.23132,0.211,0.94972,6.2312

> undo

[Repeated 9 time(s)]

> redo

> hide #!67-69 target m

> hide #!57 models

> hide #!9-19 target m

> hide #!8 models

> show #!9 models

> hide #!9 models

> show #!8 models

> show #!18 models

> show #!17 models

> show #!16 models

> show #!15 models

> show #!14 models

> show #!13 models

> hide #!8 models

> show #!9 models

> hide #!9 models

> show #!8 models

> hide #!13 models

> show #!13 models

> hide #!14 models

> show #!14 models

> hide #!15 models

> show #!15 models

> hide #!16 models

> show #!16 models

> select add #15

2800 atoms, 2794 bonds, 4 pseudobonds, 182 residues, 3 models selected  

> select add #16

3041 atoms, 3034 bonds, 4 pseudobonds, 197 residues, 4 models selected  

> select add #17

3298 atoms, 3293 bonds, 4 pseudobonds, 212 residues, 5 models selected  

> select subtract #17

3041 atoms, 3034 bonds, 4 pseudobonds, 197 residues, 4 models selected  

> select add #17

3298 atoms, 3293 bonds, 4 pseudobonds, 212 residues, 5 models selected  

> select add #18

4628 atoms, 4622 bonds, 5 pseudobonds, 296 residues, 7 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #15,0.94141,-0.074496,-0.32893,93.362,0.041359,0.99344,-0.10662,38.754,0.33471,0.086772,0.93832,-69.838,#17,0.67237,-0.73216,0.10895,173.73,0.72732,0.68081,0.086583,-73.881,-0.13756,0.021025,0.99027,24.719,#18,0.98014,-0.19508,-0.035582,47.621,0.19499,0.98079,-0.0058233,-9.2874,0.036034,-0.0012307,0.99935,-6.2376,#16,0.88863,0.14825,-0.434,78.824,-0.15977,0.9871,0.010049,54.21,0.4299,0.060411,0.90086,-75.255,#68,0.62977,0.77489,-0.054207,-91.981,-0.75836,0.59822,-0.25888,214.66,-0.16817,0.20414,0.96439,-5.5314

> ui mousemode right "translate selected models"

> view matrix models
> #15,0.94141,-0.074496,-0.32893,93.612,0.041359,0.99344,-0.10662,39.469,0.33471,0.086772,0.93832,-69.992,#17,0.67237,-0.73216,0.10895,173.98,0.72732,0.68081,0.086583,-73.167,-0.13756,0.021025,0.99027,24.565,#18,0.98014,-0.19508,-0.035582,47.871,0.19499,0.98079,-0.0058233,-8.5733,0.036034,-0.0012307,0.99935,-6.392,#16,0.88863,0.14825,-0.434,79.073,-0.15977,0.9871,0.010049,54.924,0.4299,0.060411,0.90086,-75.409,#68,0.62977,0.77489,-0.054207,-91.732,-0.75836,0.59822,-0.25888,215.37,-0.16817,0.20414,0.96439,-5.6858

> view matrix models
> #15,0.94141,-0.074496,-0.32893,93.158,0.041359,0.99344,-0.10662,39.735,0.33471,0.086772,0.93832,-69.948,#17,0.67237,-0.73216,0.10895,173.52,0.72732,0.68081,0.086583,-72.901,-0.13756,0.021025,0.99027,24.609,#18,0.98014,-0.19508,-0.035582,47.417,0.19499,0.98079,-0.0058233,-8.3071,0.036034,-0.0012307,0.99935,-6.3477,#16,0.88863,0.14825,-0.434,78.619,-0.15977,0.9871,0.010049,55.19,0.4299,0.060411,0.90086,-75.365,#68,0.62977,0.77489,-0.054207,-92.186,-0.75836,0.59822,-0.25888,215.64,-0.16817,0.20414,0.96439,-5.6416

> view matrix models
> #15,0.94141,-0.074496,-0.32893,93.165,0.041359,0.99344,-0.10662,39.48,0.33471,0.086772,0.93832,-69.893,#17,0.67237,-0.73216,0.10895,173.53,0.72732,0.68081,0.086583,-73.156,-0.13756,0.021025,0.99027,24.664,#18,0.98014,-0.19508,-0.035582,47.424,0.19499,0.98079,-0.0058233,-8.5617,0.036034,-0.0012307,0.99935,-6.2929,#16,0.88863,0.14825,-0.434,78.627,-0.15977,0.9871,0.010049,54.936,0.4299,0.060411,0.90086,-75.31,#68,0.62977,0.77489,-0.054207,-92.178,-0.75836,0.59822,-0.25888,215.38,-0.16817,0.20414,0.96439,-5.5868

> view matrix models
> #15,0.94141,-0.074496,-0.32893,93.458,0.041359,0.99344,-0.10662,40.06,0.33471,0.086772,0.93832,-69.973,#17,0.67237,-0.73216,0.10895,173.83,0.72732,0.68081,0.086583,-72.575,-0.13756,0.021025,0.99027,24.584,#18,0.98014,-0.19508,-0.035582,47.718,0.19499,0.98079,-0.0058233,-7.9816,0.036034,-0.0012307,0.99935,-6.3725,#16,0.88863,0.14825,-0.434,78.92,-0.15977,0.9871,0.010049,55.516,0.4299,0.060411,0.90086,-75.39,#68,0.62977,0.77489,-0.054207,-91.885,-0.75836,0.59822,-0.25888,215.96,-0.16817,0.20414,0.96439,-5.6664

> view matrix models
> #15,0.94141,-0.074496,-0.32893,93.304,0.041359,0.99344,-0.10662,39.944,0.33471,0.086772,0.93832,-69.865,#17,0.67237,-0.73216,0.10895,173.67,0.72732,0.68081,0.086583,-72.692,-0.13756,0.021025,0.99027,24.692,#18,0.98014,-0.19508,-0.035582,47.564,0.19499,0.98079,-0.0058233,-8.098,0.036034,-0.0012307,0.99935,-6.2647,#16,0.88863,0.14825,-0.434,78.766,-0.15977,0.9871,0.010049,55.4,0.4299,0.060411,0.90086,-75.282,#68,0.62977,0.77489,-0.054207,-92.039,-0.75836,0.59822,-0.25888,215.85,-0.16817,0.20414,0.96439,-5.5585

> view matrix models
> #15,0.94141,-0.074496,-0.32893,93.299,0.041359,0.99344,-0.10662,39.948,0.33471,0.086772,0.93832,-69.842,#17,0.67237,-0.73216,0.10895,173.67,0.72732,0.68081,0.086583,-72.688,-0.13756,0.021025,0.99027,24.714,#18,0.98014,-0.19508,-0.035582,47.558,0.19499,0.98079,-0.0058233,-8.094,0.036034,-0.0012307,0.99935,-6.2421,#16,0.88863,0.14825,-0.434,78.761,-0.15977,0.9871,0.010049,55.404,0.4299,0.060411,0.90086,-75.259,#68,0.62977,0.77489,-0.054207,-92.044,-0.75836,0.59822,-0.25888,215.85,-0.16817,0.20414,0.96439,-5.536

> view matrix models
> #15,0.94141,-0.074496,-0.32893,93.274,0.041359,0.99344,-0.10662,39.881,0.33471,0.086772,0.93832,-69.845,#17,0.67237,-0.73216,0.10895,173.64,0.72732,0.68081,0.086583,-72.755,-0.13756,0.021025,0.99027,24.711,#18,0.98014,-0.19508,-0.035582,47.533,0.19499,0.98079,-0.0058233,-8.161,0.036034,-0.0012307,0.99935,-6.2453,#16,0.88863,0.14825,-0.434,78.735,-0.15977,0.9871,0.010049,55.337,0.4299,0.060411,0.90086,-75.263,#68,0.62977,0.77489,-0.054207,-92.07,-0.75836,0.59822,-0.25888,215.78,-0.16817,0.20414,0.96439,-5.5392

> show #!57 models

> select clear

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> mmaker #71/9 to #67/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#67) with combination, chain 9 (#71),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> mmaker #72/9 to #68/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#68) with combination, chain 9 (#72),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> mmaker #73/9 to #69/9 pairing ss

No molecules/chains to match specified  

> mmaker #70/9 to #69/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#69) with combination, chain 9 (#70),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> color #70 #7a81ffff

> color #71 #76d6ffff

> color #72 #ff2f92ff

> select add #71

2591 atoms, 2586 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> view matrix models
> #71,0.73965,0.6697,-0.066478,-85.077,-0.66002,0.70255,-0.26608,246.86,-0.13149,0.24068,0.96166,-23.367

> view matrix models
> #71,0.73965,0.6697,-0.066478,-84.958,-0.66002,0.70255,-0.26608,247.21,-0.13149,0.24068,0.96166,-23.39

> select add #70

5182 atoms, 5172 bonds, 8 pseudobonds, 334 residues, 4 models selected  

> select subtract #71

2591 atoms, 2586 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> view matrix models
> #70,0.65408,0.75641,-0.0045745,-101.44,-0.7191,0.61992,-0.314,239.62,-0.23468,0.20867,0.94941,8.0724

> ui mousemode right "rotate selected models"

> view matrix models
> #70,0.66216,0.74936,0.000628,-102.45,-0.71161,0.62906,-0.31288,235.82,-0.23486,0.20673,0.94979,8.4773

> ui mousemode right "translate selected models"

> view matrix models
> #70,0.66216,0.74936,0.000628,-105.12,-0.71161,0.62906,-0.31288,235.31,-0.23486,0.20673,0.94979,8.2739

> ui mousemode right "rotate selected models"

> view matrix models
> #70,0.67638,0.73648,0.0098907,-106.81,-0.69798,0.64519,-0.31073,228.49,-0.23523,0.20327,0.95045,9.0126

> view matrix models
> #70,0.70632,0.7062,-0.048942,-93.82,-0.66482,0.63801,-0.38853,239.35,-0.24315,0.30696,0.92014,-7.207

> ui mousemode right "translate selected models"

> view matrix models
> #70,0.70632,0.7062,-0.048942,-92.779,-0.66482,0.63801,-0.38853,240.51,-0.24315,0.30696,0.92014,-7.2553

> ui mousemode right "rotate selected models"

> view matrix models
> #70,0.73671,0.65888,-0.15212,-67.005,-0.6529,0.63452,-0.41366,244.05,-0.17603,0.40406,0.89764,-38.231

> view matrix models
> #70,0.72072,0.67305,-0.16605,-64.324,-0.68212,0.6458,-0.34302,232.92,-0.12363,0.36049,0.92454,-43.885

> view matrix models
> #70,0.72259,0.68142,-0.11635,-76.65,-0.66895,0.64684,-0.36619,234.77,-0.17426,0.34244,0.92324,-29.547

> view matrix models
> #70,0.72227,0.683,-0.10877,-78.485,-0.67409,0.66004,-0.33159,225.76,-0.15468,0.31282,0.93713,-29.363

> ui mousemode right "translate selected models"

> view matrix models
> #70,0.72227,0.683,-0.10877,-77.937,-0.67409,0.66004,-0.33159,226.32,-0.15468,0.31282,0.93713,-29.99

> view matrix models
> #70,0.72227,0.683,-0.10877,-78.379,-0.67409,0.66004,-0.33159,226.27,-0.15468,0.31282,0.93713,-30.071

> select add #72

5182 atoms, 5172 bonds, 8 pseudobonds, 334 residues, 4 models selected  

> select subtract #70

2591 atoms, 2586 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #72,0.63006,0.77617,0.024125,-108.11,-0.73921,0.60899,-0.28756,214.1,-0.23789,0.16335,0.95746,18.963

> undo

> view matrix models
> #72,0.66869,0.74204,-0.047259,-93.402,-0.71541,0.62476,-0.31283,210.9,-0.20261,0.243,0.94863,-4.5164

> ui mousemode right "translate selected models"

> view matrix models
> #72,0.66869,0.74204,-0.047259,-97.23,-0.71541,0.62476,-0.31283,212.58,-0.20261,0.243,0.94863,-5.2719

> view matrix models
> #72,0.66869,0.74204,-0.047259,-94.574,-0.71541,0.62476,-0.31283,209.36,-0.20261,0.243,0.94863,-3.545

> ui mousemode right "rotate selected models"

> view matrix models
> #72,0.67444,0.71994,0.16377,-133.2,-0.53902,0.63169,-0.55716,222.53,-0.50457,0.2875,0.8141,72.505

> view matrix models
> #72,0.65811,0.73801,0.14909,-131.21,-0.55407,0.60879,-0.56779,232.9,-0.5098,0.29106,0.80956,73.623

> view matrix models
> #72,0.74533,0.65345,0.13223,-125.41,-0.50818,0.68522,-0.52176,197.01,-0.43155,0.32168,0.84278,44.535

> view matrix models
> #72,0.82102,0.56035,-0.10924,-70.043,-0.5281,0.67273,-0.51822,203.08,-0.21689,0.48316,0.84824,-35.813

> view matrix models
> #72,0.55527,0.8209,-0.13342,-73.134,-0.83006,0.53702,-0.1504,219.25,-0.051812,0.19426,0.97958,-28.101

> view matrix models
> #72,0.54869,0.81525,-0.18524,-60.085,-0.83586,0.53054,-0.14092,219.96,-0.016607,0.23215,0.97254,-42.304

> view matrix models
> #72,0.62419,0.75273,-0.20922,-55.631,-0.77407,0.5596,-0.29608,232.48,-0.10579,0.34676,0.93197,-43.052

> view matrix models
> #72,0.68973,0.70211,-0.17694,-63.321,-0.71802,0.63171,-0.29221,204.11,-0.093387,0.3286,0.93984,-42.885

> view matrix models
> #72,0.7084,0.68997,-0.14872,-69.877,-0.67907,0.6088,-0.41016,225.56,-0.19245,0.39154,0.89981,-29.902

> view matrix models
> #72,0.74709,0.59085,-0.30456,-23.165,-0.66434,0.64825,-0.37205,205.9,-0.022397,0.48029,0.87683,-79.017

> view matrix models
> #72,0.73353,0.61204,-0.29552,-27.215,-0.6795,0.6696,-0.29986,189.38,0.014354,0.42077,0.90705,-78.605

> view matrix models
> #72,0.77232,0.58182,-0.25497,-36.036,-0.63523,0.70956,-0.30497,172.53,0.0034793,0.39749,0.9176,-73.241

> ui mousemode right "translate selected models"

> view matrix models
> #72,0.77232,0.58182,-0.25497,-35.244,-0.63523,0.70956,-0.30497,172.28,0.0034793,0.39749,0.9176,-74.955

> view matrix models
> #72,0.77232,0.58182,-0.25497,-34.045,-0.63523,0.70956,-0.30497,173.69,0.0034793,0.39749,0.9176,-76.606

> ui mousemode right "rotate selected models"

> view matrix models
> #72,0.78466,0.55956,-0.26682,-28.943,-0.61974,0.69768,-0.35939,184.38,-0.014948,0.44736,0.89423,-79.768

> view matrix models
> #72,0.75065,0.65782,-0.061586,-86.343,-0.63614,0.69443,-0.33629,183.68,-0.17845,0.29161,0.93974,-21.048

> ui mousemode right "translate selected models"

> view matrix models
> #72,0.75065,0.65782,-0.061586,-86.699,-0.63614,0.69443,-0.33629,184.09,-0.17845,0.29161,0.93974,-19.065

> ui mousemode right "rotate selected models"

> view matrix models
> #72,0.7407,0.66968,-0.053753,-89.063,-0.65425,0.7008,-0.28432,175.68,-0.15273,0.24576,0.95722,-17.067

> view matrix models
> #72,0.726,0.68527,-0.057589,-89.003,-0.66981,0.68568,-0.28496,182.34,-0.15579,0.24545,0.95681,-16.315

> ui mousemode right "translate selected models"

> view matrix models
> #72,0.726,0.68527,-0.057589,-90.161,-0.66981,0.68568,-0.28496,180.73,-0.15579,0.24545,0.95681,-16.599

> ui mousemode right "rotate selected models"

> view matrix models
> #72,0.75042,0.62456,-0.21632,-48.918,-0.63918,0.60238,-0.47811,232.9,-0.16831,0.49705,0.85124,-50.802

> ui mousemode right "translate selected models"

> view matrix models
> #72,0.75042,0.62456,-0.21632,-46.402,-0.63918,0.60238,-0.47811,235.46,-0.16831,0.49705,0.85124,-50.291

> ui mousemode right "rotate selected models"

> view matrix models
> #72,0.75038,0.58474,-0.30825,-18.662,-0.65688,0.6076,-0.44646,231.34,-0.073765,0.5375,0.84003,-75.865

> undo

> view matrix models
> #72,0.73029,0.65271,-0.20161,-51.913,-0.66839,0.62173,-0.40829,222.63,-0.14115,0.43292,0.89031,-48.723

> view matrix models
> #72,0.7199,0.67032,-0.18008,-58.28,-0.67699,0.62091,-0.39516,221.86,-0.15307,0.40638,0.90079,-42.388

> view matrix models
> #72,0.72134,0.67005,-0.17519,-59.488,-0.68172,0.6423,-0.3503,208.8,-0.12219,0.37212,0.92011,-44.442

> view matrix models
> #72,0.72301,0.66886,-0.17287,-60.008,-0.68288,0.65407,-0.32537,201.28,-0.10456,0.35329,0.92965,-45.486

> select clear

> show #!69 models

> hide #!69 models

> show #!68 models

> hide #!68 models

> mmaker #72/9 to #68/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#68) with combination, chain 9 (#72),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> combine #13-18,57, 70,71

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  
Remapping chain ID '6' in combination #70 to '0'  
Remapping chain ID '7' in combination #70 to 'AA'  
Remapping chain ID '8' in combination #70 to 'AB'  
Remapping chain ID '9' in combination #70 to 'AC'  
Remapping chain ID 'o' in combination #70 to 'r'  
Remapping chain ID 'p' in combination #70 to 's'  
Remapping chain ID 'q' in combination #70 to 't'  
Remapping chain ID 'x' in combination #70 to 'y'  
Remapping chain ID '6' in combination #71 to 'AD'  
Remapping chain ID '7' in combination #71 to 'AE'  
Remapping chain ID '8' in combination #71 to 'AF'  
Remapping chain ID '9' in combination #71 to 'AG'  
Remapping chain ID 'o' in combination #71 to 'u'  
Remapping chain ID 'p' in combination #71 to 'v'  
Remapping chain ID 'q' in combination #71 to 'w'  
Remapping chain ID 'x' in combination #71 to 'z'  

> select add #73

7773 atoms, 7758 bonds, 12 pseudobonds, 501 residues, 2 models selected  

> hide #!72 models

> hide #!71 models

> hide #!70 models

> show #!72 models

> hide #!72 models

> hide #!73 models

> select up

7773 atoms, 7758 bonds, 12 pseudobonds, 501 residues, 2 models selected  

> select up

173444 atoms, 173307 bonds, 12 pseudobonds, 11148 residues, 81 models selected  

> select up

173444 atoms, 173307 bonds, 12 pseudobonds, 11148 residues, 81 models selected  

> select down

7773 atoms, 7758 bonds, 12 pseudobonds, 501 residues, 2 models selected  

> mmaker #73/AG to #18/6 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker copy of copy of copy of pointy-1pf.pdb, chain 6 (#18) with
combination, chain AG (#73), sequence alignment score = 670.7  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> show #!73 models

> show #!72 models

> hide #!72 models

> show #!71 models

> hide #!71 models

> show #!70 models

> hide #!73 models

> show #!73 models

> hide #!73 models

> show #!73 models

> hide #!73 models

> mmaker #73/AG to #70/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#70) with combination, chain AG (#73),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> show #!73 models

> select clear

> hide #!70 models

> hide #!57 models

> show #!57 models

> hide #!73 models

> show #!73 models

> hide #!73 models

> show #!73 models

> hide #!73 models

> show #!73 models

> hide #!73 models

> show #!72 models

> show #!71 models

> show #!70 models

> select add #72

2591 atoms, 2586 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> view matrix models
> #72,0.67507,0.73603,-0.050421,-92.629,-0.68899,0.60455,-0.39977,227.94,-0.26376,0.30461,0.91523,0.008559

> view matrix models
> #72,0.64366,0.76451,-0.035005,-96.15,-0.7364,0.60625,-0.30029,216.75,-0.20835,0.21906,0.95321,1.1998

> select clear

> select add #70

2591 atoms, 2586 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #70,0.68908,0.71891,-0.091369,-83.66,-0.70039,0.62829,-0.33868,240.16,-0.18607,0.29737,0.93646,-20.227

> view matrix models
> #70,0.68822,0.71998,-0.089318,-84.155,-0.70262,0.63077,-0.32933,238.14,-0.18077,0.28941,0.93998,-20.143

> select add #71

5182 atoms, 5172 bonds, 8 pseudobonds, 334 residues, 4 models selected  

> select subtract #70

2591 atoms, 2586 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> view matrix models
> #71,0.74084,0.668,-0.070293,-84.028,-0.65839,0.70147,-0.2729,248.52,-0.13299,0.24845,0.95947,-24.446

> ui mousemode right "translate selected models"

> view matrix models
> #71,0.74084,0.668,-0.070293,-83.981,-0.65839,0.70147,-0.2729,248.75,-0.13299,0.24845,0.95947,-24.418

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Fit14-14.cxs"

> combine #13-18,57, 70,71

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  
Remapping chain ID '6' in combination #70 to '0'  
Remapping chain ID '7' in combination #70 to 'AA'  
Remapping chain ID '8' in combination #70 to 'AB'  
Remapping chain ID '9' in combination #70 to 'AC'  
Remapping chain ID 'o' in combination #70 to 'r'  
Remapping chain ID 'p' in combination #70 to 's'  
Remapping chain ID 'q' in combination #70 to 't'  
Remapping chain ID 'x' in combination #70 to 'y'  
Remapping chain ID '6' in combination #71 to 'AD'  
Remapping chain ID '7' in combination #71 to 'AE'  
Remapping chain ID '8' in combination #71 to 'AF'  
Remapping chain ID '9' in combination #71 to 'AG'  
Remapping chain ID 'o' in combination #71 to 'u'  
Remapping chain ID 'p' in combination #71 to 'v'  
Remapping chain ID 'q' in combination #71 to 'w'  
Remapping chain ID 'x' in combination #71 to 'z'  

> close #74

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> select add #74

5182 atoms, 5172 bonds, 8 pseudobonds, 334 residues, 4 models selected  

> select subtract #71

2591 atoms, 2586 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> ui mousemode right "translate selected models"

> view matrix models
> #74,0.72714,0.68586,-0.029519,-91.483,-0.66467,0.69261,-0.28017,277.39,-0.17171,0.22334,0.9595,-13.253

> view matrix models
> #74,0.72714,0.68586,-0.029519,-92.01,-0.66467,0.69261,-0.28017,278.05,-0.17171,0.22334,0.9595,-11.071

> view matrix models
> #74,0.72714,0.68586,-0.029519,-91.514,-0.66467,0.69261,-0.28017,278.23,-0.17171,0.22334,0.9595,-12.055

> ui mousemode right "rotate selected models"

> view matrix models
> #74,0.75915,0.63699,-0.13392,-65.455,-0.64465,0.70727,-0.29017,272.94,-0.09012,0.30661,0.94756,-44.81

> view matrix models
> #74,0.75087,0.65489,-0.085554,-77.717,-0.6439,0.69705,-0.31546,280.26,-0.14696,0.29196,0.94507,-29.8

> ui mousemode right "translate selected models"

> view matrix models
> #74,0.75087,0.65489,-0.085554,-78.619,-0.6439,0.69705,-0.31546,280.82,-0.14696,0.29196,0.94507,-28.282

> view matrix models
> #74,0.75087,0.65489,-0.085554,-78.439,-0.6439,0.69705,-0.31546,280.94,-0.14696,0.29196,0.94507,-28.723

> ui mousemode right "translate selected models"

> ui mousemode right "rotate selected models"

> view matrix models
> #74,0.7948,0.59523,-0.11826,-66.699,-0.60045,0.74308,-0.29546,257.79,-0.087987,0.30584,0.94801,-44.065

> view matrix models
> #74,0.80729,0.57849,-0.11676,-65.592,-0.57881,0.73752,-0.34791,265.42,-0.11515,0.34845,0.93023,-44.971

> view matrix models
> #74,0.79897,0.59725,-0.070257,-77.67,-0.57818,0.73077,-0.36287,269.87,-0.16538,0.33054,0.92919,-30.797

> view matrix models
> #74,0.80385,0.58392,-0.11342,-66.842,-0.57947,0.72567,-0.37098,272.94,-0.13432,0.36394,0.92169,-43.061

> view matrix models
> #74,0.80031,0.59481,-0.075562,-76.298,-0.57421,0.72406,-0.38211,274.52,-0.17257,0.3492,0.92102,-32.038

> view matrix models
> #74,0.83009,0.55132,-0.08365,-70.48,-0.52254,0.71669,-0.46186,282.2,-0.19468,0.4271,0.883,-37.98

> view matrix models
> #74,0.82771,0.55698,-0.06834,-74.409,-0.52006,0.71562,-0.46628,282.85,-0.21081,0.42149,0.88199,-33.326

> ui mousemode right "translate selected models"

> view matrix models
> #74,0.82771,0.55698,-0.06834,-74.708,-0.52006,0.71562,-0.46628,282.83,-0.21081,0.42149,0.88199,-32.308

> view matrix models
> #74,0.82771,0.55698,-0.06834,-73.739,-0.52006,0.71562,-0.46628,282.7,-0.21081,0.42149,0.88199,-34.033

> ui mousemode right "rotate selected models"

> view matrix models
> #74,0.7457,0.65023,-0.14537,-63.61,-0.63039,0.6179,-0.46991,327.55,-0.21572,0.44205,0.87066,-35.521

> view matrix models
> #74,0.75513,0.64106,-0.13721,-64.991,-0.6193,0.62889,-0.47007,322.88,-0.21505,0.43994,0.8719,-35.415

> view matrix models
> #74,0.75883,0.63736,-0.13396,-65.52,-0.61485,0.63322,-0.4701,321.02,-0.21479,0.43909,0.87239,-35.369

> select add #72

5182 atoms, 5172 bonds, 8 pseudobonds, 334 residues, 4 models selected  

> select subtract #74

2591 atoms, 2586 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #72,0.68121,0.73198,-0.012598,-100.53,-0.69942,0.64563,-0.30655,201.7,-0.21625,0.21763,0.95177,3.3657

> color #74 #fffc79ff

> select add #74

5182 atoms, 5172 bonds, 8 pseudobonds, 334 residues, 4 models selected  

> select subtract #72

2591 atoms, 2586 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> ui mousemode right "translate selected models"

> view matrix models
> #74,0.75883,0.63736,-0.13396,-66.224,-0.61485,0.63322,-0.4701,321.05,-0.21479,0.43909,0.87239,-32.922

> view matrix models
> #74,0.75883,0.63736,-0.13396,-66.1,-0.61485,0.63322,-0.4701,321.05,-0.21479,0.43909,0.87239,-33.296

> view matrix models
> #74,0.75883,0.63736,-0.13396,-66.075,-0.61485,0.63322,-0.4701,321.38,-0.21479,0.43909,0.87239,-33.284

> ui mousemode right "rotate selected models"

> view matrix models
> #74,0.81385,0.5728,-0.097706,-69.296,-0.55023,0.70562,-0.44648,287.28,-0.1868,0.41713,0.88944,-37.149

> ui mousemode right "translate selected models"

> view matrix models
> #74,0.81385,0.5728,-0.097706,-71.327,-0.55023,0.70562,-0.44648,285.25,-0.1868,0.41713,0.88944,-38.156

> select add #70

5182 atoms, 5172 bonds, 8 pseudobonds, 334 residues, 4 models selected  

> select subtract #74

2591 atoms, 2586 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> view matrix models
> #70,0.68822,0.71998,-0.089318,-82.412,-0.70262,0.63077,-0.32933,235.55,-0.18077,0.28941,0.93998,-19.822

> view matrix models
> #70,0.68822,0.71998,-0.089318,-82.958,-0.70262,0.63077,-0.32933,235.51,-0.18077,0.28941,0.93998,-19.875

> ui mousemode right "rotate selected models"

> view matrix models
> #70,0.64313,0.76067,-0.088141,-83.736,-0.74163,0.59006,-0.31908,250.47,-0.19071,0.27058,0.94362,-14.326

> select add #72

5182 atoms, 5172 bonds, 8 pseudobonds, 334 residues, 4 models selected  

> select subtract #70

2591 atoms, 2586 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> view matrix models
> #72,0.70016,0.71159,-0.05842,-90.299,-0.6914,0.65532,-0.30417,197.41,-0.17816,0.25336,0.95082,-12.135

> view matrix models
> #72,0.69809,0.71355,-0.059234,-90.181,-0.69605,0.6569,-0.28982,195.06,-0.16789,0.24355,0.95525,-12.779

> select add #70

5182 atoms, 5172 bonds, 8 pseudobonds, 334 residues, 4 models selected  

> select subtract #72

2591 atoms, 2586 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> view matrix models
> #70,0.64808,0.7514,-0.12406,-75.322,-0.7362,0.57641,-0.35463,259.72,-0.19496,0.32116,0.92674,-21.738

> undo

> view matrix models
> #70,0.67049,0.73737,-0.082054,-84.956,-0.71853,0.61782,-0.3194,239.61,-0.18482,0.27311,0.94406,-16.152

> select add #74

5182 atoms, 5172 bonds, 8 pseudobonds, 334 residues, 4 models selected  

> view matrix models
> #70,0.65465,0.75053,-0.090174,-84.053,-0.73246,0.60031,-0.32114,246.75,-0.1869,0.27628,0.94273,-16.349,#74,0.8017,0.58778,-0.10857,-69.394,-0.56737,0.69117,-0.44763,292.16,-0.18807,0.42046,0.8876,-38.162

> undo

> select subtract #70

2591 atoms, 2586 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> ui mousemode right "translate selected models"

> view matrix models
> #74,0.81385,0.5728,-0.097706,-69.674,-0.55023,0.70562,-0.44648,285.6,-0.1868,0.41713,0.88944,-37.885

> view matrix models
> #74,0.81385,0.5728,-0.097706,-69.173,-0.55023,0.70562,-0.44648,285.37,-0.1868,0.41713,0.88944,-37.724

> view matrix models
> #74,0.81385,0.5728,-0.097706,-69.208,-0.55023,0.70562,-0.44648,285.68,-0.1868,0.41713,0.88944,-37.467

> ui mousemode right "rotate selected models"

> view matrix models
> #74,0.80811,0.58494,-0.069333,-76.607,-0.5483,0.70398,-0.45143,286.68,-0.21525,0.40282,0.88961,-28.631

> view matrix models
> #74,0.80671,0.58758,-0.06302,-78.215,-0.54784,0.70362,-0.45253,286.89,-0.22155,0.39959,0.88952,-26.633

> view matrix models
> #74,0.78436,0.61494,-0.081382,-76.435,-0.57954,0.67971,-0.44958,298.01,-0.22115,0.39979,0.88953,-26.763

> view matrix models
> #74,0.7698,0.63174,-0.091207,-75.469,-0.59748,0.66292,-0.45116,305.72,-0.22455,0.4018,0.88777,-26.203

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Fit14-15.cxs"

> select add #72

5182 atoms, 5172 bonds, 8 pseudobonds, 334 residues, 4 models selected  

> select subtract #74

2591 atoms, 2586 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> hide #!70-74 target m

> hide #!57 models

> hide #!12-20 target m

> show #!9 models

> hide #!9 models

> hide #!8 models

> hide #!13-18 target m

[Repeated 1 time(s)]

> show #!13-18 target m

> show #!55 models

> select subtract #72

Nothing selected  

> hide #!55 models

> show #!55 models

> hide #!55 models

> show #!57 models

> show #!8 models

> show #!7 models

> show #!72 models

> show #!73 models

> show #!74 models

> show #!71 models

> hide #!73 models

> show #!73 models

> hide #!72 models

> show #!72 models

> hide #!74 models

> show #!74 models

> hide #!71 models

> show #!71 models

> hide #!57 models

> show #!57 models

> hide #!73 models

> show #!73 models

> hide #!73 models

> show #!70 models

> close #73

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Fit14-15.cxs"

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> hide #!57 models

> hide #!12-19 target m

> select clear

> hide #!7 models

> hide #!8 models

Drag select of 820 residues, 5 pseudobonds  

> ui tool show "Color Zone"

> color zone #5 near sel distance 9.04

> show #!7 models

> color zone #7 near sel distance 9.04

> color zone #7 near sel distance 10.19

> color zone #7 near sel distance 2.76

> volume #7 level 0.01496

> volume #7 level 0.01358

> volume #7 level 0.009636

> hide #!7 models

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/1-2.pdb" models #72 format pdb

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/2-2.pdb" models #70 format pdb

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/3-2.pdb" models #73 format pdb

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/4-2.pdb" models #71 format pdb

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/5-2.pdb" models #74 format pdb

> show #!9 models

> hide #!9 models

> show #!8 models

> select add #8

12850 atoms, 5 pseudobonds, 820 residues, 12 models selected  

> select subtract #8

12850 atoms, 5 pseudobonds, 820 residues, 10 models selected  

> select add #70

12871 atoms, 2586 bonds, 8 pseudobonds, 823 residues, 10 models selected  

> select subtract #70

10280 atoms, 4 pseudobonds, 656 residues, 8 models selected  

> select add #71

10301 atoms, 2586 bonds, 7 pseudobonds, 659 residues, 8 models selected  

> select subtract #71

7710 atoms, 3 pseudobonds, 492 residues, 6 models selected  

> select add #72

7731 atoms, 2586 bonds, 6 pseudobonds, 495 residues, 6 models selected  

> select subtract #72

5140 atoms, 2 pseudobonds, 328 residues, 4 models selected  

> select add #73

5161 atoms, 2586 bonds, 5 pseudobonds, 331 residues, 4 models selected  

> select clear

> select add #70

2591 atoms, 2586 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> view matrix models
> #70,0.69873,0.71215,-0.067899,-87.536,-0.69198,0.64874,-0.31671,226.74,-0.1815,0.26828,0.94609,-16.099

> ui mousemode right "translate selected models"

> view matrix models
> #70,0.69873,0.71215,-0.067899,-86.971,-0.69198,0.64874,-0.31671,227.29,-0.1815,0.26828,0.94609,-15.892

> view matrix models
> #70,0.69873,0.71215,-0.067899,-88.07,-0.69198,0.64874,-0.31671,227.82,-0.1815,0.26828,0.94609,-16.022

> view matrix models
> #70,0.69873,0.71215,-0.067899,-87.812,-0.69198,0.64874,-0.31671,227.8,-0.1815,0.26828,0.94609,-16.304

> view matrix models
> #70,0.69873,0.71215,-0.067899,-87.788,-0.69198,0.64874,-0.31671,228.07,-0.1815,0.26828,0.94609,-16.308

> select add #74

5182 atoms, 5172 bonds, 8 pseudobonds, 334 residues, 4 models selected  

> select subtract #70

2591 atoms, 2586 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> view matrix models
> #74,0.7698,0.63174,-0.091207,-76.808,-0.59748,0.66292,-0.45116,307.25,-0.22455,0.4018,0.88777,-26.683

> ui mousemode right "rotate selected models"

> view matrix models
> #74,0.76993,0.63181,-0.08962,-77.17,-0.59647,0.6626,-0.45297,307.49,-0.22681,0.40221,0.88701,-26.182

> view matrix models
> #74,0.80652,0.57012,-0.1565,-56.625,-0.54148,0.60608,-0.58263,335.91,-0.23732,0.55465,0.79752,-41.181

> view matrix models
> #74,0.69961,0.71412,-0.02414,-95.576,-0.58566,0.55374,-0.59192,358.49,-0.40934,0.42825,0.80563,19.996

> view matrix models
> #74,0.69116,0.72261,-0.011268,-98.477,-0.5992,0.56427,-0.56794,353.88,-0.40404,0.39929,0.82299,22.127

> view matrix models
> #74,0.74989,0.62636,-0.21292,-47.103,-0.66138,0.7173,-0.21924,260.42,0.015402,0.30523,0.95215,-64.431

> view matrix models
> #74,0.74421,0.59088,-0.31146,-17.927,-0.66793,0.66124,-0.34151,299.3,0.0041565,0.46219,0.88677,-85.193

> view matrix models
> #74,0.69238,0.69071,-0.20865,-51.523,-0.70932,0.59859,-0.37222,328.04,-0.1322,0.40572,0.90439,-49.03

> ui mousemode right "translate selected models"

> view matrix models
> #74,0.69238,0.69071,-0.20865,-50.641,-0.70932,0.59859,-0.37222,326.15,-0.1322,0.40572,0.90439,-49.316

> view matrix models
> #74,0.69238,0.69071,-0.20865,-50.302,-0.70932,0.59859,-0.37222,325.96,-0.1322,0.40572,0.90439,-49.335

> ui mousemode right "rotate selected models"

> view matrix models
> #74,0.77665,0.61015,-0.15665,-58.744,-0.61419,0.67818,-0.40355,295.31,-0.13999,0.40963,0.90145,-48.117

> show #!7 models

> hide #!7 models

> hide #!8 models

> show #!8 models

> show #!11 models

> hide #!11 models

> show #!12 models

> hide #!12 models

> show #!9 models

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Fit14-16.cxs"

> select add #13

2687 atoms, 2681 bonds, 5 pseudobonds, 175 residues, 4 models selected  

> select subtract #13

2591 atoms, 2586 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> show #!13-18 target m

> show #!57 models

> hide #!73 models

> select subtract #74

Nothing selected  

> select add #16

241 atoms, 240 bonds, 15 residues, 1 model selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #16,0.92051,-0.13436,-0.3669,121.02,0.049784,0.97169,-0.23094,66.092,0.38754,0.19432,0.90114,-96.408

> ui mousemode right "translate selected models"

> view matrix models
> #16,0.92051,-0.13436,-0.3669,118.19,0.049784,0.97169,-0.23094,66.25,0.38754,0.19432,0.90114,-95.105

> view matrix models
> #16,0.92051,-0.13436,-0.3669,118.21,0.049784,0.97169,-0.23094,66.455,0.38754,0.19432,0.90114,-94.334

> view matrix models
> #16,0.92051,-0.13436,-0.3669,118.04,0.049784,0.97169,-0.23094,66.567,0.38754,0.19432,0.90114,-94.232

> view matrix models
> #16,0.92051,-0.13436,-0.3669,117.35,0.049784,0.97169,-0.23094,66.386,0.38754,0.19432,0.90114,-94.688

> view matrix models
> #16,0.92051,-0.13436,-0.3669,117.56,0.049784,0.97169,-0.23094,66.41,0.38754,0.19432,0.90114,-94.664

> view matrix models
> #16,0.92051,-0.13436,-0.3669,117.52,0.049784,0.97169,-0.23094,66.727,0.38754,0.19432,0.90114,-94.349

> view matrix models
> #16,0.92051,-0.13436,-0.3669,117.25,0.049784,0.97169,-0.23094,66.666,0.38754,0.19432,0.90114,-94.66

> select subtract #16

Nothing selected  

> select add #15

209 atoms, 208 bonds, 15 residues, 1 model selected  

> select subtract #15

Nothing selected  

> select add #14

261 atoms, 260 bonds, 1 pseudobond, 17 residues, 2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #14,0.94805,0.15621,0.27711,-76.192,-0.2304,0.93784,0.25957,-15.14,-0.21934,-0.30993,0.92511,124.25

> ui mousemode right "translate selected models"

> view matrix models
> #14,0.94805,0.15621,0.27711,-72.912,-0.2304,0.93784,0.25957,-17.07,-0.21934,-0.30993,0.92511,122.14

> view matrix models
> #14,0.94805,0.15621,0.27711,-73.415,-0.2304,0.93784,0.25957,-17.152,-0.21934,-0.30993,0.92511,122.28

> view matrix models
> #14,0.94805,0.15621,0.27711,-73.642,-0.2304,0.93784,0.25957,-17.242,-0.21934,-0.30993,0.92511,123.11

> ui mousemode right "rotate selected models"

> view matrix models
> #14,0.9503,0.16371,0.26483,-73.298,-0.23482,0.93539,0.26439,-16.791,-0.20444,-0.31344,0.92734,120.53

> view matrix models
> #14,0.9534,0.17517,0.24567,-72.632,-0.22949,0.9496,0.21351,-11.11,-0.19589,-0.25994,0.94555,104.35

> ui mousemode right "translate selected models"

> view matrix models
> #14,0.9534,0.17517,0.24567,-72.771,-0.22949,0.9496,0.21351,-10.817,-0.19589,-0.25994,0.94555,103.34

> view matrix models
> #14,0.9534,0.17517,0.24567,-73.025,-0.22949,0.9496,0.21351,-11.017,-0.19589,-0.25994,0.94555,103.19

> view matrix models
> #14,0.9534,0.17517,0.24567,-73.274,-0.22949,0.9496,0.21351,-11.237,-0.19589,-0.25994,0.94555,103.47

> view matrix models
> #14,0.9534,0.17517,0.24567,-73.158,-0.22949,0.9496,0.21351,-11.232,-0.19589,-0.25994,0.94555,103.68

> view matrix models
> #14,0.9534,0.17517,0.24567,-73.015,-0.22949,0.9496,0.21351,-11.257,-0.19589,-0.25994,0.94555,104.12

> view matrix models
> #14,0.9534,0.17517,0.24567,-72.914,-0.22949,0.9496,0.21351,-11.32,-0.19589,-0.25994,0.94555,103.84

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> hide #!9 models

> select up

261 atoms, 260 bonds, 1 pseudobond, 17 residues, 2 models selected  

> select up

181217 atoms, 181065 bonds, 1 pseudobond, 11649 residues, 86 models selected  

> select up

181217 atoms, 181065 bonds, 1 pseudobond, 11649 residues, 86 models selected  

> select up

181217 atoms, 181065 bonds, 1 pseudobond, 11649 residues, 86 models selected  

> select down

261 atoms, 260 bonds, 1 pseudobond, 17 residues, 2 models selected  

> hide #!74 models

> show #!74 models

> mmaker #75/9 to #70/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#70) with combination, chain 9 (#75),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> mmaker #76/9 to #71/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#71) with combination, chain 9 (#76),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> mmaker #77/9 to #72/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#72) with combination, chain 9 (#77),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> mmaker #78/9 to #74/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#74) with combination, chain 9 (#78),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> color #75 #d4fb79ff

> color #76 #0433ffff

> color #77 #d783ffff

> color #78 #73fdffff

> hide #!75 models

> show #!75 models

> hide #!74 models

> hide #!72 models

> hide #!71 models

> hide #!70 models

> hide #!75-78 target m

> show #!75-78 target m

> hide #!75-78 target m

> select subtract #14

Nothing selected  

> select add #18

1330 atoms, 1329 bonds, 1 pseudobond, 84 residues, 2 models selected  

> select subtract #18

Nothing selected  

> select add #17

257 atoms, 259 bonds, 15 residues, 1 model selected  

> select subtract #17

Nothing selected  

> select add #16

241 atoms, 240 bonds, 15 residues, 1 model selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #16,0.91919,-0.064102,-0.38857,106.47,-0.0059604,0.98429,-0.17648,63.832,0.39378,0.16453,0.90436,-89.995

> ui mousemode right "translate selected models"

> view matrix models
> #16,0.91919,-0.064102,-0.38857,108.15,-0.0059604,0.98429,-0.17648,63.276,0.39378,0.16453,0.90436,-90.619

> view sel

> view matrix models
> #16,0.91919,-0.064102,-0.38857,108.2,-0.0059604,0.98429,-0.17648,63.437,0.39378,0.16453,0.90436,-90.095

> view matrix models
> #16,0.91919,-0.064102,-0.38857,108.08,-0.0059604,0.98429,-0.17648,63.668,0.39378,0.16453,0.90436,-89.847

> view matrix models
> #16,0.91919,-0.064102,-0.38857,108.19,-0.0059604,0.98429,-0.17648,63.571,0.39378,0.16453,0.90436,-89.88

> view matrix models
> #16,0.91919,-0.064102,-0.38857,108.19,-0.0059604,0.98429,-0.17648,63.713,0.39378,0.16453,0.90436,-89.951

> view matrix models
> #16,0.91919,-0.064102,-0.38857,108.23,-0.0059604,0.98429,-0.17648,63.498,0.39378,0.16453,0.90436,-89.929

> select add #17

498 atoms, 499 bonds, 30 residues, 2 models selected  

> select subtract #17

241 atoms, 240 bonds, 15 residues, 1 model selected  

> select subtract #16

Nothing selected  

> select add #18

1330 atoms, 1329 bonds, 1 pseudobond, 84 residues, 2 models selected  

> select subtract #18

Nothing selected  

> select add #14

261 atoms, 260 bonds, 1 pseudobond, 17 residues, 2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #14,0.92276,0.29202,0.25145,-92.244,-0.34211,0.92112,0.18573,21.689,-0.17738,-0.25741,0.94988,98.906

> ui mousemode right "translate selected models"

> view matrix models
> #14,0.92276,0.29202,0.25145,-93.574,-0.34211,0.92112,0.18573,22.675,-0.17738,-0.25741,0.94988,98.771

> ui mousemode right "rotate selected models"

> view matrix models
> #14,0.9037,0.31564,0.2893,-101.95,-0.38476,0.89509,0.22531,28.817,-0.18783,-0.31492,0.93035,116.4

> ui mousemode right "translate selected models"

> view matrix models
> #14,0.9037,0.31564,0.2893,-102.15,-0.38476,0.89509,0.22531,29.227,-0.18783,-0.31492,0.93035,117.07

> ui mousemode right "rotate selected models"

> view matrix models
> #14,0.89961,0.32523,0.29142,-103.75,-0.39457,0.89132,0.2233,32.29,-0.18713,-0.31587,0.93017,117.16

> view matrix models
> #14,0.89571,0.31842,0.31035,-105.17,-0.39731,0.88651,0.23714,31.19,-0.19962,-0.33571,0.92057,125.51

> ui mousemode right "translate selected models"

> view matrix models
> #14,0.89571,0.31842,0.31035,-105.47,-0.39731,0.88651,0.23714,30.743,-0.19962,-0.33571,0.92057,125.52

> view matrix models
> #14,0.89571,0.31842,0.31035,-105.53,-0.39731,0.88651,0.23714,30.872,-0.19962,-0.33571,0.92057,125.97

> view matrix models
> #14,0.89571,0.31842,0.31035,-105.29,-0.39731,0.88651,0.23714,30.712,-0.19962,-0.33571,0.92057,125.93

> view matrix models
> #14,0.89571,0.31842,0.31035,-105.24,-0.39731,0.88651,0.23714,30.582,-0.19962,-0.33571,0.92057,125.72

> select add #16

502 atoms, 500 bonds, 1 pseudobond, 32 residues, 3 models selected  

> select subtract #16

261 atoms, 260 bonds, 1 pseudobond, 17 residues, 2 models selected  

> select add #13

357 atoms, 355 bonds, 2 pseudobonds, 25 residues, 4 models selected  

> select subtract #14

96 atoms, 95 bonds, 1 pseudobond, 8 residues, 2 models selected  

> view matrix models
> #13,0.72714,0.68586,-0.029519,-94.684,-0.66467,0.69261,-0.28017,229.61,-0.17171,0.22334,0.9595,-10.915

> view matrix models
> #13,0.72714,0.68586,-0.029519,-94.998,-0.66467,0.69261,-0.28017,229.91,-0.17171,0.22334,0.9595,-10.71

> view matrix models
> #13,0.72714,0.68586,-0.029519,-94.393,-0.66467,0.69261,-0.28017,230.33,-0.17171,0.22334,0.9595,-10.995

> view matrix models
> #13,0.72714,0.68586,-0.029519,-94.991,-0.66467,0.69261,-0.28017,230.07,-0.17171,0.22334,0.9595,-11.212

> show #!75 models

> hide #!75 models

> show #!74 models

> hide #!74 models

> show #!78 models

> hide #!78 models

> close #75-78

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> mmaker #75/9 to #70/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#70) with combination, chain 9 (#75),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> mmaker #76/9 to #71/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#71) with combination, chain 9 (#76),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> mmaker #77/9 to #72/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#72) with combination, chain 9 (#77),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> mmaker #78/9 to #74/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#74) with combination, chain 9 (#78),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> color #75 #ffd479ff

> color #76 #76d6ffff

> color #77 #ff85ffff

> color #78 #00fdffff

> color #78 #ff2f92ff

> select subtract #13

Nothing selected  

> select add #14

261 atoms, 260 bonds, 1 pseudobond, 17 residues, 2 models selected  

> select subtract #14

Nothing selected  

> select add #15

209 atoms, 208 bonds, 15 residues, 1 model selected  

> select subtract #15

Nothing selected  

> select add #16

241 atoms, 240 bonds, 15 residues, 1 model selected  

> select subtract #16

Nothing selected  

> select add #16

241 atoms, 240 bonds, 15 residues, 1 model selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #16,0.92035,-0.062307,-0.3861,107.15,-0.0051429,0.98521,-0.17125,62.13,0.39106,0.15959,0.90642,-88.749

> select add #15

450 atoms, 448 bonds, 30 residues, 2 models selected  

> view matrix models
> #15,0.93879,-0.021204,-0.34384,85.704,0.013532,0.9996,-0.024696,27.8,0.34423,0.018532,0.9387,-57.644,#16,0.91465,-0.010228,-0.40412,100.96,-0.027829,0.99572,-0.088186,47.935,0.40329,0.091906,0.91045,-77.811

> ui mousemode right "translate selected models"

> view matrix models
> #15,0.93879,-0.021204,-0.34384,85.944,0.013532,0.9996,-0.024696,27.863,0.34423,0.018532,0.9387,-57.991,#16,0.91465,-0.010228,-0.40412,101.2,-0.027829,0.99572,-0.088186,47.998,0.40329,0.091906,0.91045,-78.157

> view matrix models
> #15,0.93879,-0.021204,-0.34384,86.118,0.013532,0.9996,-0.024696,27.959,0.34423,0.018532,0.9387,-58.068,#16,0.91465,-0.010228,-0.40412,101.37,-0.027829,0.99572,-0.088186,48.094,0.40329,0.091906,0.91045,-78.235

> view matrix models
> #15,0.93879,-0.021204,-0.34384,86.222,0.013532,0.9996,-0.024696,28.061,0.34423,0.018532,0.9387,-58.378,#16,0.91465,-0.010228,-0.40412,101.48,-0.027829,0.99572,-0.088186,48.195,0.40329,0.091906,0.91045,-78.544

> view matrix models
> #15,0.93879,-0.021204,-0.34384,86.575,0.013532,0.9996,-0.024696,28.168,0.34423,0.018532,0.9387,-58.273,#16,0.91465,-0.010228,-0.40412,101.83,-0.027829,0.99572,-0.088186,48.302,0.40329,0.091906,0.91045,-78.439

> view matrix models
> #15,0.93879,-0.021204,-0.34384,86.478,0.013532,0.9996,-0.024696,28.24,0.34423,0.018532,0.9387,-58.407,#16,0.91465,-0.010228,-0.40412,101.73,-0.027829,0.99572,-0.088186,48.374,0.40329,0.091906,0.91045,-78.574

> view matrix models
> #15,0.93879,-0.021204,-0.34384,86.534,0.013532,0.9996,-0.024696,28.275,0.34423,0.018532,0.9387,-58.394,#16,0.91465,-0.010228,-0.40412,101.79,-0.027829,0.99572,-0.088186,48.409,0.40329,0.091906,0.91045,-78.561

> close #75-78

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> mmaker #75/9 to #70/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#70) with combination, chain 9 (#75),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> mmaker #76/9 to #71/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#71) with combination, chain 9 (#76),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> mmaker #77/9 to #72/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#72) with combination, chain 9 (#77),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> mmaker #78/9 to #74/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#74) with combination, chain 9 (#78),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> color #75 #fffc79ff

> color #76 #73fcd6ff

> color #77 #ff85ffff

> color #78 #0096ffff

> select add #77

3041 atoms, 3034 bonds, 4 pseudobonds, 197 residues, 4 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #15,0.94195,-0.014904,-0.33543,83.252,0.012659,0.99988,-0.0088774,25.178,0.33553,0.0041157,0.94202,-55.196,#16,0.91809,-0.0032846,-0.39635,98.447,-0.027686,0.99699,-0.072393,44.921,0.3954,0.077437,0.91524,-75.791,#77,0.69225,0.71976,-0.052316,-92.829,-0.70278,0.6559,-0.27551,194.3,-0.16399,0.22749,0.95987,-10.746

> view matrix models
> #15,0.90469,0.032148,-0.42486,101.92,0.021286,0.99249,0.12043,-2.0058,0.42554,-0.11799,0.89722,-45.31,#16,0.87328,0.036485,-0.48584,119.95,-0.010418,0.99836,0.056247,14.469,0.4871,-0.044059,0.87223,-66.484,#77,0.67078,0.72469,-0.15773,-69.421,-0.74162,0.65344,-0.15168,177.42,-0.006852,0.21872,0.97576,-39.702

> undo

[Repeated 1 time(s)]

> select subtract #16

2800 atoms, 2794 bonds, 4 pseudobonds, 182 residues, 3 models selected  

> select subtract #15

2591 atoms, 2586 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> view matrix models
> #77,0.68081,0.70397,-0.20231,-56.432,-0.73131,0.66877,-0.1339,168.25,0.041037,0.23911,0.97012,-56.002

> view matrix models
> #77,0.64426,0.73439,-0.21355,-53.979,-0.76348,0.63402,-0.12298,180.32,0.04508,0.24228,0.96916,-57.324

> ui mousemode right "translate selected models"

> view matrix models
> #77,0.64426,0.73439,-0.21355,-56.401,-0.76348,0.63402,-0.12298,180.52,0.04508,0.24228,0.96916,-57.304

> ui mousemode right "rotate selected models"

> view matrix models
> #77,0.67901,0.70573,-0.20223,-58.922,-0.73306,0.63693,-0.23861,197.32,-0.039589,0.31027,0.94982,-52.413

> view matrix models
> #77,0.68087,0.72591,-0.09727,-85.179,-0.725,0.6492,-0.23002,191.18,-0.10383,0.22714,0.96831,-24.496

> ui mousemode right "translate selected models"

> view matrix models
> #77,0.68087,0.72591,-0.09727,-83.282,-0.725,0.6492,-0.23002,191.3,-0.10383,0.22714,0.96831,-26.342

> view matrix models
> #77,0.68087,0.72591,-0.09727,-84.76,-0.725,0.6492,-0.23002,192.31,-0.10383,0.22714,0.96831,-26.371

> select add #76

5182 atoms, 5172 bonds, 8 pseudobonds, 334 residues, 4 models selected  

> select subtract #77

2591 atoms, 2586 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> view matrix models
> #76,0.74084,0.668,-0.070293,-83.685,-0.65839,0.70147,-0.2729,249.29,-0.13299,0.24845,0.95947,-24.514

> ui mousemode right "rotate selected models"

> view matrix models
> #76,0.76995,0.63516,-0.061148,-83.704,-0.60914,0.70308,-0.36691,258.32,-0.19006,0.31975,0.92824,-23.378

> select add #75

5182 atoms, 5172 bonds, 8 pseudobonds, 334 residues, 4 models selected  

> select subtract #76

2591 atoms, 2586 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> view matrix models
> #75,0.70976,0.70287,-0.046979,-92.866,-0.686,0.67449,-0.2729,212.71,-0.16013,0.22592,0.96089,-14.072

> view matrix models
> #75,0.71623,0.69641,-0.045142,-93.02,-0.67608,0.67637,-0.29231,214.27,-0.17304,0.23988,0.95526,-13.606

> select add #77

5182 atoms, 5172 bonds, 8 pseudobonds, 334 residues, 4 models selected  

> select subtract #75

2591 atoms, 2586 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> view matrix models
> #77,0.69347,0.71531,-0.08625,-87.024,-0.69965,0.63999,-0.31765,207.21,-0.17202,0.28063,0.94428,-20.426

> view matrix models
> #77,0.68134,0.73158,-0.024023,-100.99,-0.69692,0.63832,-0.32688,208.92,-0.2238,0.23946,0.94476,-0.93372

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Fit14-17.cxs"

> select subtract #77

Nothing selected  

> select add #16

241 atoms, 240 bonds, 15 residues, 1 model selected  

> select subtract #16

Nothing selected  

> select add #15

209 atoms, 208 bonds, 15 residues, 1 model selected  

> select subtract #15

Nothing selected  

> select add #14

261 atoms, 260 bonds, 1 pseudobond, 17 residues, 2 models selected  

> view matrix models
> #14,0.91746,0.26143,0.29987,-95.685,-0.29679,0.95173,0.078302,27.744,-0.26493,-0.16084,0.95076,96.485

> ui mousemode right "translate selected models"

> view matrix models
> #14,0.91746,0.26143,0.29987,-94.481,-0.29679,0.95173,0.078302,27.065,-0.26493,-0.16084,0.95076,94.627

> view matrix models
> #14,0.91746,0.26143,0.29987,-94.981,-0.29679,0.95173,0.078302,27.329,-0.26493,-0.16084,0.95076,94.457

> view matrix models
> #14,0.91746,0.26143,0.29987,-95.157,-0.29679,0.95173,0.078302,27.052,-0.26493,-0.16084,0.95076,94.416

> view matrix models
> #14,0.91746,0.26143,0.29987,-94.951,-0.29679,0.95173,0.078302,27.433,-0.26493,-0.16084,0.95076,94.395

> view matrix models
> #14,0.91746,0.26143,0.29987,-95.035,-0.29679,0.95173,0.078302,27.345,-0.26493,-0.16084,0.95076,94.681

> view matrix models
> #14,0.91746,0.26143,0.29987,-95.032,-0.29679,0.95173,0.078302,27.31,-0.26493,-0.16084,0.95076,94.638

> select subtract #14

Nothing selected  

> close #75-78

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> mmaker #75/9 to #70/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#70) with combination, chain 9 (#75),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> mmaker #76/9 to #71/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#71) with combination, chain 9 (#76),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> mmaker #77/9 to #72/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#72) with combination, chain 9 (#77),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> mmaker #78/9 to #74/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#74) with combination, chain 9 (#78),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> color #75 #ffd479ff

> color #75 #73fcd6ff

> color #76 #fffc79ff

> color #77 #76d6ffff

> color #77 #ff8ad8ff

> color #78 #0433ffff

> color #78 #212121ff

> color #78 #9437ffff

> select add #77

2591 atoms, 2586 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> select subtract #77

Nothing selected  

> select add #78

2591 atoms, 2586 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> view matrix models
> #78,0.77665,0.61015,-0.15665,-59.388,-0.61419,0.67818,-0.40355,295.8,-0.13999,0.40963,0.90145,-48.542

> undo

> ui mousemode right "rotate selected models"

> view matrix models
> #78,0.66291,0.72659,-0.18058,-59.12,-0.74095,0.60207,-0.2975,316.65,-0.10744,0.33102,0.93749,-44.142

> view matrix models
> #78,0.73168,0.65696,-0.18177,-56.395,-0.67881,0.67792,-0.28221,284,-0.062171,0.32987,0.94198,-53.653

> ui mousemode right "translate selected models"

> view matrix models
> #78,0.73168,0.65696,-0.18177,-55.96,-0.67881,0.67792,-0.28221,285.28,-0.062171,0.32987,0.94198,-53.64

> view matrix models
> #78,0.73168,0.65696,-0.18177,-56.279,-0.67881,0.67792,-0.28221,285.38,-0.062171,0.32987,0.94198,-54.341

> ui mousemode right "rotate selected models"

> view matrix models
> #78,0.72671,0.67855,-0.10708,-75.378,-0.67443,0.67514,-0.29889,288.54,-0.13051,0.28942,0.94826,-32.963

> select subtract #78

Nothing selected  

> select add #77

2591 atoms, 2586 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> ui mousemode right "translate selected models"

> view matrix models
> #77,0.69809,0.71355,-0.059234,-91.354,-0.69605,0.6569,-0.28982,195.64,-0.16789,0.24355,0.95525,-14.098

> view matrix models
> #77,0.69809,0.71355,-0.059234,-91.888,-0.69605,0.6569,-0.28982,195.59,-0.16789,0.24355,0.95525,-14.178

> ui mousemode right "rotate selected models"

> view matrix models
> #77,0.70261,0.70896,-0.060905,-91.383,-0.68785,0.65478,-0.31323,199.22,-0.18219,0.26198,0.94772,-14.074

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Fit14-17.cxs"

> select add #15

2800 atoms, 2794 bonds, 4 pseudobonds, 182 residues, 3 models selected  

> select add #16

3041 atoms, 3034 bonds, 4 pseudobonds, 197 residues, 4 models selected  

> view sel

> select subtract #77

450 atoms, 448 bonds, 30 residues, 2 models selected  

> view sel

> ui mousemode right "move picked models"

> ui mousemode right "rotate selected models"

> view matrix models
> #15,0.94067,-0.036096,-0.33739,87.981,0.0054805,0.99581,-0.091257,43.723,0.33927,0.083994,0.93693,-70.629,#16,0.91754,-0.024591,-0.39689,102.8,-0.040017,0.98731,-0.15369,65.364,0.39563,0.1569,0.90491,-89.518

> ui mousemode right "translate selected models"

> view matrix models
> #15,0.94067,-0.036096,-0.33739,87.98,0.0054805,0.99581,-0.091257,43.751,0.33927,0.083994,0.93693,-70.461,#16,0.91754,-0.024591,-0.39689,102.8,-0.040017,0.98731,-0.15369,65.393,0.39563,0.1569,0.90491,-89.349

> view matrix models
> #15,0.94067,-0.036096,-0.33739,87.935,0.0054805,0.99581,-0.091257,43.833,0.33927,0.083994,0.93693,-70.474,#16,0.91754,-0.024591,-0.39689,102.76,-0.040017,0.98731,-0.15369,65.474,0.39563,0.1569,0.90491,-89.363

> select subtract #16

209 atoms, 208 bonds, 15 residues, 1 model selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #15,0.94086,-0.058237,-0.33375,91.52,0.026539,0.99476,-0.098762,41.46,0.33776,0.084064,0.93747,-70.302

> select add #14

470 atoms, 468 bonds, 1 pseudobond, 32 residues, 3 models selected  

> select subtract #14

209 atoms, 208 bonds, 15 residues, 1 model selected  

> select add #16

450 atoms, 448 bonds, 30 residues, 2 models selected  

> ui mousemode right "translate selected models"

> view matrix models
> #15,0.94086,-0.058237,-0.33375,91.616,0.026539,0.99476,-0.098762,41.198,0.33776,0.084064,0.93747,-70.208,#16,0.91754,-0.024591,-0.39689,102.85,-0.040017,0.98731,-0.15369,65.213,0.39563,0.1569,0.90491,-89.269

> undo

> select subtract #16

209 atoms, 208 bonds, 15 residues, 1 model selected  

> view matrix models
> #15,0.94086,-0.058237,-0.33375,91.613,0.026539,0.99476,-0.098762,41.264,0.33776,0.084064,0.93747,-70.23

> select add #14

470 atoms, 468 bonds, 1 pseudobond, 32 residues, 3 models selected  

> select subtract #14

209 atoms, 208 bonds, 15 residues, 1 model selected  

> select add #16

450 atoms, 448 bonds, 30 residues, 2 models selected  

> ui mousemode right "translate selected models"

> view matrix models
> #15,0.94086,-0.058237,-0.33375,91.482,0.026539,0.99476,-0.098762,41.422,0.33776,0.084064,0.93747,-70.078,#16,0.91754,-0.024591,-0.39689,102.62,-0.040017,0.98731,-0.15369,65.632,0.39563,0.1569,0.90491,-89.211

> view matrix models
> #15,0.94086,-0.058237,-0.33375,91.572,0.026539,0.99476,-0.098762,41.244,0.33776,0.084064,0.93747,-70.008,#16,0.91754,-0.024591,-0.39689,102.71,-0.040017,0.98731,-0.15369,65.454,0.39563,0.1569,0.90491,-89.141

> select clear

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> mmaker #79/9 to #75/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#75) with combination, chain 9 (#79),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> mmaker #80/9 to #76/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#76) with combination, chain 9 (#80),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> mmaker #81/9 to #77/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#77) with combination, chain 9 (#81),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> mmaker #82/9 to #78/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#78) with combination, chain 9 (#82),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> hide #!74-78 target m

> hide #!79 models

> show #!79 models

> color #79 #fffc79ff

> color #80 #73fdffff

> color #80 #ff85ffff

> color #81 #73fdffff

> color #82 #ff40ffff

> color #82 #0096ffff

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Fit14-17.cxs"

> show #!9 models

> hide #!9 models

> show #!9 models

> hide #!8 models

> hide #!9 models

> select add #18

1330 atoms, 1329 bonds, 1 pseudobond, 84 residues, 2 models selected  

> select subtract #18

Nothing selected  

> select add #17

257 atoms, 259 bonds, 15 residues, 1 model selected  

> select subtract #17

Nothing selected  

> select add #16

241 atoms, 240 bonds, 15 residues, 1 model selected  

> select subtract #16

Nothing selected  

> select add #15

209 atoms, 208 bonds, 15 residues, 1 model selected  

> select subtract #15

Nothing selected  

> select add #14

261 atoms, 260 bonds, 1 pseudobond, 17 residues, 2 models selected  

> select subtract #14

Nothing selected  

> select add #13

96 atoms, 95 bonds, 1 pseudobond, 8 residues, 2 models selected  

> ui mousemode right "rotate selected models"

> show #!8 models

> view matrix models
> #13,0.97528,0.21916,0.028197,-43.358,-0.21548,0.97156,-0.098212,37.587,-0.048919,0.089708,0.99477,-10.423

> view matrix models
> #13,0.94795,0.31651,0.034769,-62.635,-0.31108,0.94388,-0.111,65.871,-0.067949,0.094403,0.99321,-7.4456

> show #!9 models

> hide #!9 models

> show #!9 models

> hide #!9 models

> select add #14

357 atoms, 355 bonds, 2 pseudobonds, 25 residues, 4 models selected  

> select subtract #13

261 atoms, 260 bonds, 1 pseudobond, 17 residues, 2 models selected  

> view matrix models
> #14,0.92116,0.259,0.29048,-93.465,-0.28985,0.95465,0.067974,27.32,-0.2597,-0.14681,0.95447,90.019

> view matrix models
> #14,0.93877,0.24441,0.24283,-84.818,-0.25536,0.96674,0.014204,28.337,-0.23128,-0.075344,0.96997,66.783

> ui mousemode right "translate selected models"

> view matrix models
> #14,0.93877,0.24441,0.24283,-84.697,-0.25536,0.96674,0.014204,27.975,-0.23128,-0.075344,0.96997,66.035

> view matrix models
> #14,0.93877,0.24441,0.24283,-84.667,-0.25536,0.96674,0.014204,28.485,-0.23128,-0.075344,0.96997,65.903

> view matrix models
> #14,0.93877,0.24441,0.24283,-84.489,-0.25536,0.96674,0.014204,28.385,-0.23128,-0.075344,0.96997,65.899

> select add #15

470 atoms, 468 bonds, 1 pseudobond, 32 residues, 3 models selected  

> select subtract #14

209 atoms, 208 bonds, 15 residues, 1 model selected  

> select subtract #15

Nothing selected  

> select add #17

257 atoms, 259 bonds, 15 residues, 1 model selected  

> select subtract #17

Nothing selected  

> select add #18

1330 atoms, 1329 bonds, 1 pseudobond, 84 residues, 2 models selected  

> select subtract #18

Nothing selected  

> select add #13

96 atoms, 95 bonds, 1 pseudobond, 8 residues, 2 models selected  

> select subtract #13

Nothing selected  

> select add #14

261 atoms, 260 bonds, 1 pseudobond, 17 residues, 2 models selected  

> select subtract #14

Nothing selected  

> select add #15

209 atoms, 208 bonds, 15 residues, 1 model selected  

> select subtract #15

Nothing selected  

> select add #16

241 atoms, 240 bonds, 15 residues, 1 model selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #16,0.91914,-0.053509,-0.39028,107.4,0.012797,0.99426,-0.10618,44.83,0.39373,0.0926,0.91455,-76.713

> ui mousemode right "translate selected models"

> view matrix models
> #16,0.91914,-0.053509,-0.39028,107.06,0.012797,0.99426,-0.10618,44.802,0.39373,0.0926,0.91455,-76.699

> view matrix models
> #16,0.91914,-0.053509,-0.39028,106.97,0.012797,0.99426,-0.10618,44.668,0.39373,0.0926,0.91455,-77.001

> view matrix models
> #16,0.91914,-0.053509,-0.39028,107.12,0.012797,0.99426,-0.10618,44.624,0.39373,0.0926,0.91455,-77.031

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> hide #!79-82 target m

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> mmaker #83/9 to #79/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#79) with combination, chain 9 (#83),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> mmaker #84/9 to #80/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#80) with combination, chain 9 (#84),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> mmaker #85/9 to #81/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#81) with combination, chain 9 (#85),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> mmaker #86/9 to #82/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#82) with combination, chain 9 (#86),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> color #83 #fffc79ff

> color #84 #d4fb79ff

> color #84 #73fcd6ff

> color #85 #7a81ffff

> color #86 #ff85ffff

> select add #83

2832 atoms, 2826 bonds, 4 pseudobonds, 182 residues, 3 models selected  

> select subtract #16

2591 atoms, 2586 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> view matrix models
> #83,0.93343,0.35874,0.0035085,-64.237,-0.35405,0.92273,-0.15237,61.994,-0.057899,0.14099,0.98832,-18.755

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Fit14-18.cxs"

> select add #15

2800 atoms, 2794 bonds, 4 pseudobonds, 182 residues, 3 models selected  

> select subtract #15

2591 atoms, 2586 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> select add #16

2832 atoms, 2826 bonds, 4 pseudobonds, 182 residues, 3 models selected  

> view matrix models
> #16,0.91914,-0.053509,-0.39028,107.11,0.012797,0.99426,-0.10618,44.602,0.39373,0.0926,0.91455,-77.046,#83,0.93343,0.35874,0.0035085,-64.25,-0.35405,0.92273,-0.15237,61.972,-0.057899,0.14099,0.98832,-18.77

> undo

> select subtract #83

241 atoms, 240 bonds, 15 residues, 1 model selected  

> view matrix models
> #16,0.91914,-0.053509,-0.39028,106.61,0.012797,0.99426,-0.10618,44.678,0.39373,0.0926,0.91455,-77.629

> view matrix models
> #16,0.91914,-0.053509,-0.39028,106.66,0.012797,0.99426,-0.10618,44.497,0.39373,0.0926,0.91455,-77.56

> view matrix models
> #16,0.91914,-0.053509,-0.39028,106.78,0.012797,0.99426,-0.10618,44.474,0.39373,0.0926,0.91455,-77.592

> close #83-86

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> mmaker #83/9 to #79/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#79) with combination, chain 9 (#83),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> mmaker #84/9 to #80/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#80) with combination, chain 9 (#84),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> mmaker #85/9 to #81/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#81) with combination, chain 9 (#85),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> mmaker #86/9 to #82/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#82) with combination, chain 9 (#86),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> color #83 #fffc79ff

> color #84 #7a81ffff

> color #85 #ff8ad8ff

> color #85 #942193ff

> color #86 #fffc79ff

> color #86 #4f8f00ff

> color #86 #ff2600ff

> color #86 #73fdffff

> show #!56 models

> hide #!56 models

> select subtract #16

Nothing selected  

> select add #16

241 atoms, 240 bonds, 15 residues, 1 model selected  

> select subtract #16

Nothing selected  

> select add #83

2591 atoms, 2586 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> ui mousemode right "translate selected models"

> view matrix models
> #83,0.93343,0.35874,0.0035085,-64.329,-0.35405,0.92273,-0.15237,63.256,-0.057899,0.14099,0.98832,-18.301

> ui mousemode right "rotate selected models"

> view matrix models
> #83,0.92912,0.36978,-0.0020438,-64.965,-0.36643,0.91991,-0.13962,63.745,-0.049748,0.13047,0.9902,-17.793

> view matrix models
> #83,0.92801,0.37253,-0.0047038,-64.855,-0.37004,0.92018,-0.12783,61.981,-0.043292,0.12037,0.99179,-16.989

> show #!9 models

> hide #!8 models

> show #!8 models

> hide #!9 models

> hide #!83 models

> hide #!84 models

> hide #!85 models

> hide #!86 models

> select add #14

2852 atoms, 2846 bonds, 5 pseudobonds, 184 residues, 4 models selected  

> select subtract #14

2591 atoms, 2586 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> select add #15

2800 atoms, 2794 bonds, 4 pseudobonds, 182 residues, 3 models selected  

> select subtract #15

2591 atoms, 2586 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> select add #16

2832 atoms, 2826 bonds, 4 pseudobonds, 182 residues, 3 models selected  

> select subtract #16

2591 atoms, 2586 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> select add #16

2832 atoms, 2826 bonds, 4 pseudobonds, 182 residues, 3 models selected  

> view matrix models
> #16,0.92468,-0.13179,-0.35721,116.3,0.10406,0.98994,-0.095853,26.291,0.36625,0.051462,0.92909,-66.338,#83,0.95363,0.29943,0.030676,-54.609,-0.2961,0.95154,-0.083057,32.705,-0.054059,0.070122,0.99607,-1.6331

> view sel

> undo

[Repeated 2 time(s)]

> redo

[Repeated 1 time(s)]

> undo

> select subtract #83

241 atoms, 240 bonds, 15 residues, 1 model selected  

> view sel

> view matrix models
> #16,0.9227,-0.21273,-0.3215,127.29,0.20216,0.9771,-0.066307,4.9445,0.32825,-0.0038149,0.94458,-50.228

> undo

> view matrix models
> #16,0.91972,-0.053989,-0.38883,106.49,0.014115,0.99441,-0.10468,43.906,0.39231,0.090792,0.91534,-77.088

> view matrix models
> #16,0.92145,-0.075878,-0.38101,109.39,0.043112,0.99466,-0.09382,36.307,0.3861,0.070024,0.9198,-72.283

> select add #13

337 atoms, 335 bonds, 1 pseudobond, 23 residues, 3 models selected  

> select subtract #13

241 atoms, 240 bonds, 15 residues, 1 model selected  

> select add #14

502 atoms, 500 bonds, 1 pseudobond, 32 residues, 3 models selected  

> select subtract #14

241 atoms, 240 bonds, 15 residues, 1 model selected  

> select add #15

450 atoms, 448 bonds, 30 residues, 2 models selected  

> view matrix models
> #15,0.94246,-0.085928,-0.3231,94.884,0.058945,0.99398,-0.092407,33.941,0.32909,0.068044,0.94184,-65.901,#16,0.92298,-0.10367,-0.37062,112.82,0.075772,0.99314,-0.089108,29.475,0.37731,0.054162,0.9245,-68.247

> ui mousemode right "translate selected models"

> view matrix models
> #15,0.94246,-0.085928,-0.3231,94.138,0.058945,0.99398,-0.092407,33.872,0.32909,0.068044,0.94184,-65.547,#16,0.92298,-0.10367,-0.37062,112.08,0.075772,0.99314,-0.089108,29.405,0.37731,0.054162,0.9245,-67.894

> view matrix models
> #15,0.94246,-0.085928,-0.3231,93.711,0.058945,0.99398,-0.092407,33.628,0.32909,0.068044,0.94184,-66.207,#16,0.92298,-0.10367,-0.37062,111.65,0.075772,0.99314,-0.089108,29.162,0.37731,0.054162,0.9245,-68.554

> view matrix models
> #15,0.94246,-0.085928,-0.3231,93.882,0.058945,0.99398,-0.092407,33.753,0.32909,0.068044,0.94184,-66.193,#16,0.92298,-0.10367,-0.37062,111.82,0.075772,0.99314,-0.089108,29.287,0.37731,0.054162,0.9245,-68.54

> view matrix models
> #15,0.94246,-0.085928,-0.3231,93.679,0.058945,0.99398,-0.092407,33.917,0.32909,0.068044,0.94184,-66.028,#16,0.92298,-0.10367,-0.37062,111.62,0.075772,0.99314,-0.089108,29.451,0.37731,0.054162,0.9245,-68.375

> view matrix models
> #15,0.94246,-0.085928,-0.3231,93.773,0.058945,0.99398,-0.092407,33.804,0.32909,0.068044,0.94184,-65.957,#16,0.92298,-0.10367,-0.37062,111.71,0.075772,0.99314,-0.089108,29.337,0.37731,0.054162,0.9245,-68.304

> select clear

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> mmaker #87/9 to #83/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#83) with combination, chain 9 (#87),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> mmaker #88/9 to #84/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#84) with combination, chain 9 (#88),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> mmaker #89/9 to #85/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#85) with combination, chain 9 (#89),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> mmaker #90/9 to #86/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#86) with combination, chain 9 (#90),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> select add #18

1330 atoms, 1329 bonds, 1 pseudobond, 84 residues, 2 models selected  

> select subtract #18

Nothing selected  

> select add #17

257 atoms, 259 bonds, 15 residues, 1 model selected  

> select subtract #17

Nothing selected  

> select add #16

241 atoms, 240 bonds, 15 residues, 1 model selected  

> select subtract #16

Nothing selected  

> select add #15

209 atoms, 208 bonds, 15 residues, 1 model selected  

> select subtract #15

Nothing selected  

> select add #14

261 atoms, 260 bonds, 1 pseudobond, 17 residues, 2 models selected  

> select subtract #14

Nothing selected  

> select add #13

96 atoms, 95 bonds, 1 pseudobond, 8 residues, 2 models selected  

> select subtract #13

Nothing selected  

> select add #57

197 atoms, 195 bonds, 1 pseudobond, 13 residues, 2 models selected  

> select add #18

1527 atoms, 1524 bonds, 2 pseudobonds, 97 residues, 4 models selected  

> select subtract #18

197 atoms, 195 bonds, 1 pseudobond, 13 residues, 2 models selected  

> select subtract #57

Nothing selected  

> select add #16

241 atoms, 240 bonds, 15 residues, 1 model selected  

> select subtract #16

Nothing selected  

> select add #15

209 atoms, 208 bonds, 15 residues, 1 model selected  

> select subtract #15

Nothing selected  

> select add #14

261 atoms, 260 bonds, 1 pseudobond, 17 residues, 2 models selected  

> select add #57

458 atoms, 455 bonds, 2 pseudobonds, 30 residues, 4 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #14,0.92073,0.28252,0.26915,-94.155,-0.29821,0.95432,0.018395,38.622,-0.25166,-0.097199,0.96292,75.912,#57,0.91524,0.3331,0.22667,-95.816,-0.36776,0.92047,0.13225,36.42,-0.16459,-0.2044,0.96495,81.796

> ui mousemode right "translate selected models"

> view matrix models
> #14,0.92073,0.28252,0.26915,-95.276,-0.29821,0.95432,0.018395,38.611,-0.25166,-0.097199,0.96292,76.318,#57,0.91524,0.3331,0.22667,-96.937,-0.36776,0.92047,0.13225,36.409,-0.16459,-0.2044,0.96495,82.202

> view matrix models
> #14,0.92073,0.28252,0.26915,-95.176,-0.29821,0.95432,0.018395,39.227,-0.25166,-0.097199,0.96292,76.642,#57,0.91524,0.3331,0.22667,-96.836,-0.36776,0.92047,0.13225,37.024,-0.16459,-0.2044,0.96495,82.526

> select subtract #57

261 atoms, 260 bonds, 1 pseudobond, 17 residues, 2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #14,0.91109,0.30069,0.28194,-99.494,-0.32105,0.94665,0.027846,43.449,-0.25853,-0.11589,0.95903,82.578

> ui mousemode right "translate selected models"

> view matrix models
> #14,0.91109,0.30069,0.28194,-99.736,-0.32105,0.94665,0.027846,43.062,-0.25853,-0.11589,0.95903,82.514

> view matrix models
> #14,0.91109,0.30069,0.28194,-99.786,-0.32105,0.94665,0.027846,43.029,-0.25853,-0.11589,0.95903,82.902

> view matrix models
> #14,0.91109,0.30069,0.28194,-99.662,-0.32105,0.94665,0.027846,43,-0.25853,-0.11589,0.95903,83.12

> ui mousemode right "rotate selected models"

> view matrix models
> #14,0.87811,0.33794,0.33869,-111.74,-0.38086,0.92218,0.067292,52.175,-0.2896,-0.18808,0.93849,107.98

> ui mousemode right "translate selected models"

> view matrix models
> #14,0.87811,0.33794,0.33869,-112.09,-0.38086,0.92218,0.067292,52.497,-0.2896,-0.18808,0.93849,108.76

> view matrix models
> #14,0.87811,0.33794,0.33869,-112.16,-0.38086,0.92218,0.067292,52.877,-0.2896,-0.18808,0.93849,108.82

> view matrix models
> #14,0.87811,0.33794,0.33869,-112.16,-0.38086,0.92218,0.067292,52.995,-0.2896,-0.18808,0.93849,108.83

> view matrix models
> #14,0.87811,0.33794,0.33869,-112.13,-0.38086,0.92218,0.067292,52.762,-0.2896,-0.18808,0.93849,108.56

> view matrix models
> #14,0.87811,0.33794,0.33869,-112.25,-0.38086,0.92218,0.067292,52.747,-0.2896,-0.18808,0.93849,108.59

> view matrix models
> #14,0.87811,0.33794,0.33869,-112.27,-0.38086,0.92218,0.067292,52.701,-0.2896,-0.18808,0.93849,108.63

> view matrix models
> #14,0.87811,0.33794,0.33869,-112.1,-0.38086,0.92218,0.067292,52.772,-0.2896,-0.18808,0.93849,108.89

> view matrix models
> #14,0.87811,0.33794,0.33869,-111.96,-0.38086,0.92218,0.067292,53.177,-0.2896,-0.18808,0.93849,108.74

> view matrix models
> #14,0.87811,0.33794,0.33869,-112.07,-0.38086,0.92218,0.067292,52.973,-0.2896,-0.18808,0.93849,108.83

> view matrix models
> #14,0.87811,0.33794,0.33869,-111.99,-0.38086,0.92218,0.067292,52.904,-0.2896,-0.18808,0.93849,108.64

> view matrix models
> #14,0.87811,0.33794,0.33869,-111.91,-0.38086,0.92218,0.067292,52.879,-0.2896,-0.18808,0.93849,108.47

> view matrix models
> #14,0.87811,0.33794,0.33869,-111.95,-0.38086,0.92218,0.067292,52.913,-0.2896,-0.18808,0.93849,108.57

> view matrix models
> #14,0.87811,0.33794,0.33869,-112.12,-0.38086,0.92218,0.067292,53.012,-0.2896,-0.18808,0.93849,108.52

> view matrix models
> #14,0.87811,0.33794,0.33869,-112.16,-0.38086,0.92218,0.067292,52.96,-0.2896,-0.18808,0.93849,108.54

> select subtract #14

Nothing selected  

> select add #15

209 atoms, 208 bonds, 15 residues, 1 model selected  

> select subtract #15

Nothing selected  

> select add #16

241 atoms, 240 bonds, 15 residues, 1 model selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #16,0.9253,-0.11479,-0.36144,111.9,0.074412,0.98952,-0.12376,37.094,0.37185,0.087617,0.92415,-74.465

> undo

> view matrix models
> #16,0.92414,-0.10409,-0.36761,111,0.070346,0.99208,-0.10406,33.483,0.37553,0.070308,0.92414,-71.399

> undo

> view matrix models
> #16,0.82095,0.26002,-0.50836,78.694,0.56601,-0.48795,0.66448,112.42,-0.075278,-0.83324,-0.54776,494.42

> undo

> view matrix models
> #16,0.92524,-0.097734,-0.36658,109.22,0.049623,0.98912,-0.13846,44.681,0.37613,0.10992,0.92003,-79.303

> undo

> view matrix models
> #16,0.92578,-0.10266,-0.36385,109.65,0.051395,0.98766,-0.14791,46.495,0.37455,0.11823,0.91964,-80.734

> view sel

> ui mousemode right "translate selected models"

> view matrix models
> #16,0.92578,-0.10266,-0.36385,109.69,0.051395,0.98766,-0.14791,46.285,0.37455,0.11823,0.91964,-80.673

> view matrix models
> #16,0.92578,-0.10266,-0.36385,109.67,0.051395,0.98766,-0.14791,46.271,0.37455,0.11823,0.91964,-80.713

> view matrix models
> #16,0.92578,-0.10266,-0.36385,109.21,0.051395,0.98766,-0.14791,46.827,0.37455,0.11823,0.91964,-80.209

> view matrix models
> #16,0.92578,-0.10266,-0.36385,109.14,0.051395,0.98766,-0.14791,46.795,0.37455,0.11823,0.91964,-80.257

> view matrix models
> #16,0.92578,-0.10266,-0.36385,109.11,0.051395,0.98766,-0.14791,46.976,0.37455,0.11823,0.91964,-80.33

> view matrix models
> #16,0.92578,-0.10266,-0.36385,109.1,0.051395,0.98766,-0.14791,47.018,0.37455,0.11823,0.91964,-80.306

> view matrix models
> #16,0.92578,-0.10266,-0.36385,109.05,0.051395,0.98766,-0.14791,46.982,0.37455,0.11823,0.91964,-80.361

> view matrix models
> #16,0.92578,-0.10266,-0.36385,109.02,0.051395,0.98766,-0.14791,47.083,0.37455,0.11823,0.91964,-80.38

> close #87-90

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> mmaker #87/9 to #83/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#83) with combination, chain 9 (#87),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> mmaker #88/9 to #84/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#84) with combination, chain 9 (#88),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> mmaker #89/9 to #85/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#85) with combination, chain 9 (#89),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> mmaker #90/9 to #86/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#86) with combination, chain 9 (#90),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> view matrix models
> #16,0.92578,-0.10266,-0.36385,108.81,0.051395,0.98766,-0.14791,47.014,0.37455,0.11823,0.91964,-80.343

> undo

> view matrix models
> #16,0.92578,-0.10266,-0.36385,109.14,0.051395,0.98766,-0.14791,47.088,0.37455,0.11823,0.91964,-80.475

> view matrix models
> #16,0.92578,-0.10266,-0.36385,109.11,0.051395,0.98766,-0.14791,47.166,0.37455,0.11823,0.91964,-80.492

> view matrix models
> #16,0.92578,-0.10266,-0.36385,109.1,0.051395,0.98766,-0.14791,47.358,0.37455,0.11823,0.91964,-80.52

> view matrix models
> #16,0.92578,-0.10266,-0.36385,108.88,0.051395,0.98766,-0.14791,47.291,0.37455,0.11823,0.91964,-80.791

> view matrix models
> #16,0.92578,-0.10266,-0.36385,108.88,0.051395,0.98766,-0.14791,47.22,0.37455,0.11823,0.91964,-80.767

> view matrix models
> #16,0.92578,-0.10266,-0.36385,108.89,0.051395,0.98766,-0.14791,47.167,0.37455,0.11823,0.91964,-80.746

> select add #17

498 atoms, 499 bonds, 30 residues, 2 models selected  

> select subtract #16

257 atoms, 259 bonds, 15 residues, 1 model selected  

> select add #18

1587 atoms, 1588 bonds, 1 pseudobond, 99 residues, 3 models selected  

> select subtract #17

1330 atoms, 1329 bonds, 1 pseudobond, 84 residues, 2 models selected  

> select subtract #18

Nothing selected  

> select add #13

96 atoms, 95 bonds, 1 pseudobond, 8 residues, 2 models selected  

> select subtract #13

Nothing selected  

> select add #14

261 atoms, 260 bonds, 1 pseudobond, 17 residues, 2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #14,0.82945,0.39739,0.39256,-125.24,-0.48324,0.86298,0.14744,69.85,-0.28018,-0.31199,0.90783,138.17

> view matrix models
> #14,0.83517,0.16493,0.52468,-103.34,-0.34678,0.89837,0.2696,12.88,-0.42689,-0.40711,0.80748,205.34

> view matrix models
> #14,0.83187,0.18904,0.52179,-107.14,-0.35821,0.90102,0.24466,19.283,-0.42389,-0.39043,0.81724,199.46

> ui mousemode right "translate selected models"

> view matrix models
> #14,0.83187,0.18904,0.52179,-105.98,-0.35821,0.90102,0.24466,19.067,-0.42389,-0.39043,0.81724,200.42

> view matrix models
> #14,0.83187,0.18904,0.52179,-106.1,-0.35821,0.90102,0.24466,19.478,-0.42389,-0.39043,0.81724,200.79

> view matrix models
> #14,0.83187,0.18904,0.52179,-106.25,-0.35821,0.90102,0.24466,19.413,-0.42389,-0.39043,0.81724,200.89

> view matrix models
> #14,0.83187,0.18904,0.52179,-105.83,-0.35821,0.90102,0.24466,19.391,-0.42389,-0.39043,0.81724,200.79

> view matrix models
> #14,0.83187,0.18904,0.52179,-105.83,-0.35821,0.90102,0.24466,19.38,-0.42389,-0.39043,0.81724,200.79

> view matrix models
> #14,0.83187,0.18904,0.52179,-106.05,-0.35821,0.90102,0.24466,19.182,-0.42389,-0.39043,0.81724,200.86

> ui mousemode right "rotate selected models"

> view matrix models
> #14,0.84585,0.21179,0.48957,-107.35,-0.35344,0.90994,0.21699,21.66,-0.39953,-0.35658,0.84453,183.96

> ui mousemode right "translate selected models"

> view matrix models
> #14,0.84585,0.21179,0.48957,-107.24,-0.35344,0.90994,0.21699,21.758,-0.39953,-0.35658,0.84453,183.85

> view matrix models
> #14,0.84585,0.21179,0.48957,-107.42,-0.35344,0.90994,0.21699,21.671,-0.39953,-0.35658,0.84453,184.15

> view matrix models
> #14,0.84585,0.21179,0.48957,-107.61,-0.35344,0.90994,0.21699,21.459,-0.39953,-0.35658,0.84453,184.2

> view matrix models
> #14,0.84585,0.21179,0.48957,-107.65,-0.35344,0.90994,0.21699,21.454,-0.39953,-0.35658,0.84453,184.53

> view matrix models
> #14,0.84585,0.21179,0.48957,-107.44,-0.35344,0.90994,0.21699,21.697,-0.39953,-0.35658,0.84453,184.42

> view matrix models
> #14,0.84585,0.21179,0.48957,-107.31,-0.35344,0.90994,0.21699,21.709,-0.39953,-0.35658,0.84453,184.81

> select clear

> close #87-90

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> mmaker #87/9 to #83/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#83) with combination, chain 9 (#87),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> mmaker #88/9 to #84/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#84) with combination, chain 9 (#88),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> mmaker #89/9 to #85/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#85) with combination, chain 9 (#89),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> mmaker #90/9 to #86/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#86) with combination, chain 9 (#90),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> select add #89

2591 atoms, 2586 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> select subtract #89

Nothing selected  

> select add #88

2591 atoms, 2586 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> select subtract #88

Nothing selected  

> select add #87

2591 atoms, 2586 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> select subtract #87

Nothing selected  

> select add #90

2591 atoms, 2586 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> select subtract #90

Nothing selected  

> select add #18

1330 atoms, 1329 bonds, 1 pseudobond, 84 residues, 2 models selected  

> select subtract #18

Nothing selected  

> select add #17

257 atoms, 259 bonds, 15 residues, 1 model selected  

> select subtract #17

Nothing selected  

> select add #16

241 atoms, 240 bonds, 15 residues, 1 model selected  

> select subtract #16

Nothing selected  

> select add #15

209 atoms, 208 bonds, 15 residues, 1 model selected  

> select subtract #15

Nothing selected  

> select add #15

209 atoms, 208 bonds, 15 residues, 1 model selected  

> select subtract #15

Nothing selected  

> select add #14

261 atoms, 260 bonds, 1 pseudobond, 17 residues, 2 models selected  

> select add #13

357 atoms, 355 bonds, 2 pseudobonds, 25 residues, 4 models selected  

> select subtract #13

261 atoms, 260 bonds, 1 pseudobond, 17 residues, 2 models selected  

> select add #15

470 atoms, 468 bonds, 1 pseudobond, 32 residues, 3 models selected  

> select subtract #15

261 atoms, 260 bonds, 1 pseudobond, 17 residues, 2 models selected  

> select add #16

502 atoms, 500 bonds, 1 pseudobond, 32 residues, 3 models selected  

> select subtract #16

261 atoms, 260 bonds, 1 pseudobond, 17 residues, 2 models selected  

> select add #17

518 atoms, 519 bonds, 1 pseudobond, 32 residues, 3 models selected  

> select subtract #17

261 atoms, 260 bonds, 1 pseudobond, 17 residues, 2 models selected  

> select add #18

1591 atoms, 1589 bonds, 2 pseudobonds, 101 residues, 4 models selected  

> select subtract #18

261 atoms, 260 bonds, 1 pseudobond, 17 residues, 2 models selected  

> select add #57

458 atoms, 455 bonds, 2 pseudobonds, 30 residues, 4 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #14,0.87128,0.181,0.4562,-99.255,-0.29975,0.93226,0.2026,9.2561,-0.38862,-0.31326,0.86651,169.2,#57,0.93478,0.29751,0.19411,-86.678,-0.32082,0.94167,0.10168,29.246,-0.15254,-0.15732,0.9757,67.969

> view matrix models
> #14,0.90918,-0.011606,0.41625,-57.833,-0.33912,0.55947,0.7563,-10.109,-0.24166,-0.82877,0.50472,320.23,#57,0.97819,0.10241,0.1807,-50.599,-0.20144,0.67977,0.70522,-54.634,-0.050617,-0.72624,0.68558,226.57

> undo

> close #87-90

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> mmaker #87/9 to #83/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#83) with combination, chain 9 (#87),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> mmaker #88/9 to #84/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#84) with combination, chain 9 (#88),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> mmaker #89/9 to #85/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#85) with combination, chain 9 (#89),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> mmaker #90/9 to #86/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#86) with combination, chain 9 (#90),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> ui mousemode right "translate selected models"

> view matrix models
> #14,0.87128,0.181,0.4562,-98.853,-0.29975,0.93226,0.2026,9.3011,-0.38862,-0.31326,0.86651,168.07,#57,0.93478,0.29751,0.19411,-86.276,-0.32082,0.94167,0.10168,29.291,-0.15254,-0.15732,0.9757,66.832

> select subtract #57

261 atoms, 260 bonds, 1 pseudobond, 17 residues, 2 models selected  

> view matrix models
> #14,0.87128,0.181,0.4562,-98.52,-0.29975,0.93226,0.2026,9.08,-0.38862,-0.31326,0.86651,167.59

> show #!9 models

> hide #!9 models

> select add #57

458 atoms, 455 bonds, 2 pseudobonds, 30 residues, 4 models selected  

> view matrix models
> #14,0.87128,0.181,0.4562,-97.721,-0.29975,0.93226,0.2026,8.5745,-0.38862,-0.31326,0.86651,167.22,#57,0.93478,0.29751,0.19411,-85.478,-0.32082,0.94167,0.10168,28.786,-0.15254,-0.15732,0.9757,66.464

> view matrix models
> #14,0.87128,0.181,0.4562,-97.232,-0.29975,0.93226,0.2026,8.4033,-0.38862,-0.31326,0.86651,167.24,#57,0.93478,0.29751,0.19411,-84.988,-0.32082,0.94167,0.10168,28.615,-0.15254,-0.15732,0.9757,66.482

> ui mousemode right "rotate selected models"

> view matrix models
> #14,0.86401,0.20928,0.45791,-102.19,-0.32479,0.92664,0.18933,17.037,-0.3847,-0.31231,0.8686,165.87,#57,0.9258,0.32531,0.19252,-88.908,-0.34769,0.93268,0.096021,36.887,-0.14833,-0.15583,0.97658,65.171

> view matrix models
> #14,0.84659,0.2241,0.48278,-106.75,-0.3629,0.90655,0.21558,23.69,-0.38935,-0.3577,0.8488,180.29,#57,0.91339,0.3439,0.21785,-95.383,-0.37698,0.91651,0.13377,38.777,-0.15365,-0.20431,0.96677,78.531

> ui mousemode right "translate selected models"

> view matrix models
> #14,0.84659,0.2241,0.48278,-107.03,-0.3629,0.90655,0.21558,23.599,-0.38935,-0.3577,0.8488,180.61,#57,0.91339,0.3439,0.21785,-95.662,-0.37698,0.91651,0.13377,38.686,-0.15365,-0.20431,0.96677,78.857

> view matrix models
> #14,0.84659,0.2241,0.48278,-107.32,-0.3629,0.90655,0.21558,23.377,-0.38935,-0.3577,0.8488,180.89,#57,0.91339,0.3439,0.21785,-95.955,-0.37698,0.91651,0.13377,38.464,-0.15365,-0.20431,0.96677,79.132

> view matrix models
> #14,0.84659,0.2241,0.48278,-107.32,-0.3629,0.90655,0.21558,23.392,-0.38935,-0.3577,0.8488,180.89,#57,0.91339,0.3439,0.21785,-95.95,-0.37698,0.91651,0.13377,38.479,-0.15365,-0.20431,0.96677,79.132

> ui mousemode right "rotate selected models"

> view matrix models
> #14,0.8421,0.26168,0.47159,-112.31,-0.39165,0.89785,0.20116,33.625,-0.37078,-0.3541,0.85857,174.62,#57,0.90338,0.37847,0.20164,-98.288,-0.40746,0.90414,0.12846,48.115,-0.13369,-0.19821,0.971,73.105

> view matrix models
> #14,0.85007,0.24951,0.46382,-109.76,-0.37346,0.90653,0.19679,29.072,-0.37137,-0.3405,0.8638,170.82,#57,0.91033,0.36536,0.19444,-95.434,-0.39153,0.91252,0.11838,45.155,-0.13418,-0.1839,0.97374,69.593

> ui mousemode right "translate selected models"

> view matrix models
> #14,0.85007,0.24951,0.46382,-109.9,-0.37346,0.90653,0.19679,29.596,-0.37137,-0.3405,0.8638,170.6,#57,0.91033,0.36536,0.19444,-95.57,-0.39153,0.91252,0.11838,45.679,-0.13418,-0.1839,0.97374,69.372

> view matrix models
> #14,0.85007,0.24951,0.46382,-110.12,-0.37346,0.90653,0.19679,29.468,-0.37137,-0.3405,0.8638,170.84,#57,0.91033,0.36536,0.19444,-95.786,-0.39153,0.91252,0.11838,45.551,-0.13418,-0.1839,0.97374,69.615

> select clear

> close #87-90

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> mmaker #87/9 to #83/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#83) with combination, chain 9 (#87),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> mmaker #88/9 to #84/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#84) with combination, chain 9 (#88),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> mmaker #89/9 to #85/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#85) with combination, chain 9 (#89),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> mmaker #90/9 to #86/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#86) with combination, chain 9 (#90),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> select add #33

2584 atoms, 2582 bonds, 3 pseudobonds, 166 residues, 2 models selected  

> select subtract #33

Nothing selected  

> select add #16

241 atoms, 240 bonds, 15 residues, 1 model selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #16,0.92288,-0.13427,-0.36093,115.72,0.048239,0.97017,-0.23756,68.932,0.38207,0.20183,0.90183,-96.829

> ui mousemode right "translate selected models"

> view matrix models
> #16,0.92288,-0.13427,-0.36093,115.3,0.048239,0.97017,-0.23756,69.121,0.38207,0.20183,0.90183,-95.672

> view matrix models
> #16,0.92288,-0.13427,-0.36093,115.82,0.048239,0.97017,-0.23756,68.78,0.38207,0.20183,0.90183,-95.87

> view matrix models
> #16,0.92288,-0.13427,-0.36093,115.64,0.048239,0.97017,-0.23756,69.018,0.38207,0.20183,0.90183,-95.446

> select add #15

450 atoms, 448 bonds, 30 residues, 2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #15,0.94204,-0.095512,-0.32162,95.547,0.060553,0.99128,-0.11702,38.909,0.33,0.090761,0.93961,-70.394,#16,0.92259,-0.14354,-0.35808,117.05,0.048451,0.96396,-0.26158,74.998,0.38272,0.22399,0.8963,-99.079

> ui mousemode right "translate selected models"

> view matrix models
> #15,0.94204,-0.095512,-0.32162,95.462,0.060553,0.99128,-0.11702,38.988,0.33,0.090761,0.93961,-70.169,#16,0.92259,-0.14354,-0.35808,116.97,0.048451,0.96396,-0.26158,75.077,0.38272,0.22399,0.8963,-98.854

> view matrix models
> #15,0.94204,-0.095512,-0.32162,95.409,0.060553,0.99128,-0.11702,39.214,0.33,0.090761,0.93961,-70.237,#16,0.92259,-0.14354,-0.35808,116.91,0.048451,0.96396,-0.26158,75.303,0.38272,0.22399,0.8963,-98.922

> view matrix models
> #15,0.94204,-0.095512,-0.32162,95.549,0.060553,0.99128,-0.11702,39.245,0.33,0.090761,0.93961,-70.207,#16,0.92259,-0.14354,-0.35808,117.05,0.048451,0.96396,-0.26158,75.334,0.38272,0.22399,0.8963,-98.892

> view matrix models
> #15,0.94204,-0.095512,-0.32162,95.426,0.060553,0.99128,-0.11702,39.204,0.33,0.090761,0.93961,-70.173,#16,0.92259,-0.14354,-0.35808,116.93,0.048451,0.96396,-0.26158,75.293,0.38272,0.22399,0.8963,-98.858

> view matrix models
> #15,0.94204,-0.095512,-0.32162,95.405,0.060553,0.99128,-0.11702,39.246,0.33,0.090761,0.93961,-70.195,#16,0.92259,-0.14354,-0.35808,116.91,0.048451,0.96396,-0.26158,75.335,0.38272,0.22399,0.8963,-98.88

> select subtract #16

209 atoms, 208 bonds, 15 residues, 1 model selected  

> select subtract #15

Nothing selected  

> close #87-90

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> mmaker #87/9 to #83/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#83) with combination, chain 9 (#87),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> mmaker #88/9 to #84/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#84) with combination, chain 9 (#88),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> mmaker #89/9 to #85/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#85) with combination, chain 9 (#89),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> mmaker #90/9 to #86/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#86) with combination, chain 9 (#90),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> select add #87

2591 atoms, 2586 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> color #87 #fffc79ff

> color #88 #76d6ffff

> color #89 #ff8ad8ff

> color #90 #d4fb79ff

> color #90 #73fa79ff

> color #90 #531b93ff

> select clear

> select add #87

2591 atoms, 2586 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #87,0.92576,0.37803,-0.0072894,-65.192,-0.37722,0.92212,-0.086067,54.356,-0.025815,0.082428,0.99626,-12.32

> show #!9 models

> hide #!9 models

> select add #57

2788 atoms, 2781 bonds, 5 pseudobonds, 180 residues, 4 models selected  

> select add #15

2997 atoms, 2989 bonds, 5 pseudobonds, 195 residues, 5 models selected  

> select subtract #15

2788 atoms, 2781 bonds, 5 pseudobonds, 180 residues, 4 models selected  

> select add #14

3049 atoms, 3041 bonds, 6 pseudobonds, 197 residues, 6 models selected  

> view matrix models
> #14,0.84928,0.28755,0.44276,-113.38,-0.37287,0.92042,0.11744,42.929,-0.37376,-0.26484,0.88891,150.65,#57,0.90161,0.39865,0.16785,-95.448,-0.41029,0.91108,0.040056,65.927,-0.13696,-0.10498,0.985,51.352,#87,0.91413,0.40338,-0.04065,-62.086,-0.4045,0.90065,-0.15876,79.721,-0.027429,0.16157,0.98648,-28.796

> undo

> select subtract #87

458 atoms, 455 bonds, 2 pseudobonds, 30 residues, 4 models selected  

> view matrix models
> #14,0.84805,0.25851,0.46258,-111.4,-0.37838,0.90655,0.18708,32.295,-0.37099,-0.33368,0.86662,168.77,#57,0.90735,0.37388,0.19216,-96.594,-0.39853,0.9105,0.11029,48.917,-0.13373,-0.17666,0.97515,67.7

> view matrix models
> #14,0.86415,0.37462,0.336,-115.03,-0.4251,0.90076,0.089018,61.505,-0.26931,-0.21976,0.93765,110.96,#57,0.88441,0.46432,0.047055,-83.577,-0.46585,0.88439,0.02894,83.389,-0.028177,-0.047515,0.99847,14.823

> view matrix models
> #14,0.85544,0.39162,0.33892,-117.52,-0.44147,0.89354,0.081804,67.622,-0.2708,-0.2196,0.93725,111.3,#57,0.87523,0.48122,0.048953,-85.781,-0.48279,0.87531,0.027258,88.971,-0.029732,-0.047491,0.99843,15.129

> ui mousemode right "translate selected models"

[Repeated 1 time(s)]

> view matrix models
> #14,0.85544,0.39162,0.33892,-119.84,-0.44147,0.89354,0.081804,68.815,-0.2708,-0.2196,0.93725,110.52,#57,0.87523,0.48122,0.048953,-88.098,-0.48279,0.87531,0.027258,90.164,-0.029732,-0.047491,0.99843,14.351

> view matrix models
> #14,0.85544,0.39162,0.33892,-120.19,-0.44147,0.89354,0.081804,68.103,-0.2708,-0.2196,0.93725,110.9,#57,0.87523,0.48122,0.048953,-88.449,-0.48279,0.87531,0.027258,89.451,-0.029732,-0.047491,0.99843,14.732

> select subtract #57

261 atoms, 260 bonds, 1 pseudobond, 17 residues, 2 models selected  

> select subtract #14

Nothing selected  

> select add #13

96 atoms, 95 bonds, 1 pseudobond, 8 residues, 2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #13,0.97468,0.22279,0.019089,-42.342,-0.22009,0.97094,-0.094031,37.846,-0.039484,0.087449,0.99539,-11.887

> view matrix models
> #13,0.97535,0.16934,-0.14146,1.6225,-0.16444,0.98533,0.04577,-3.9376,0.14714,-0.02138,0.98888,-21.726

> view matrix models
> #13,0.97672,0.16272,-0.13982,2.6253,-0.16376,0.98649,0.0041316,3.7416,0.1386,0.018861,0.99017,-29.968

> select clear

> select add #14

261 atoms, 260 bonds, 1 pseudobond, 17 residues, 2 models selected  

> select subtract #14

Nothing selected  

> select add #16

241 atoms, 240 bonds, 15 residues, 1 model selected  

> select subtract #16

Nothing selected  

> select add #17

257 atoms, 259 bonds, 15 residues, 1 model selected  

> select subtract #17

Nothing selected  

> select add #18

1330 atoms, 1329 bonds, 1 pseudobond, 84 residues, 2 models selected  

> select subtract #18

Nothing selected  

> select add #13

96 atoms, 95 bonds, 1 pseudobond, 8 residues, 2 models selected  

> view matrix models
> #13,0.94349,0.30778,-0.12289,-28.985,-0.31161,0.95012,-0.012794,45.38,0.11282,0.050366,0.99234,-32.827

> ui mousemode right "translate selected models"

> view matrix models
> #13,0.94349,0.30778,-0.12289,-28.087,-0.31161,0.95012,-0.012794,44.861,0.11282,0.050366,0.99234,-32.667

> ui mousemode right "rotate selected models"

> view matrix models
> #13,0.93901,0.30442,-0.15995,-19.178,-0.28039,0.94706,0.15639,6.46,0.19909,-0.102,0.97466,-9.758

> select clear

> hide #!87 models

> hide #!88 models

> hide #!89 models

> hide #!90 models

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> mmaker #91/9 to #87/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#87) with combination, chain 9 (#91),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> mmaker #92/9 to #88/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#88) with combination, chain 9 (#92),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> mmaker #93/9 to #89/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#89) with combination, chain 9 (#93),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> mmaker #94/9 to #90/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#90) with combination, chain 9 (#94),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> color #91 #fffc79ff

> color #92 #7a81ffff

> color #93 #73fdffff

> color #94 #011993ff

> select add #91

2591 atoms, 2586 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> view matrix models
> #91,0.93402,0.29446,-0.20222,-8.0654,-0.25784,0.94755,0.18887,-29.565,0.24723,-0.12426,0.96096,-10.065

> select add #93

5182 atoms, 5172 bonds, 8 pseudobonds, 334 residues, 4 models selected  

> select subtract #91

2591 atoms, 2586 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> view matrix models
> #93,0.94425,0.2767,-0.17843,-11.989,-0.258,0.95852,0.12112,-44.893,0.20454,-0.068336,0.97647,-17.278

> select add #91

5182 atoms, 5172 bonds, 8 pseudobonds, 334 residues, 4 models selected  

> select subtract #93

2591 atoms, 2586 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> view matrix models
> #91,0.95014,0.24836,-0.18854,-3.0685,-0.2138,0.95903,0.18591,-40.508,0.22698,-0.13633,0.96431,-3.8181

> undo

> ui mousemode right "translate selected models"

> view matrix models
> #91,0.93402,0.29446,-0.20222,-7.5434,-0.25784,0.94755,0.18887,-28.876,0.24723,-0.12426,0.96096,-10.494

> view matrix models
> #91,0.93402,0.29446,-0.20222,-7.7595,-0.25784,0.94755,0.18887,-29.602,0.24723,-0.12426,0.96096,-10.746

> view matrix models
> #91,0.93402,0.29446,-0.20222,-8.8758,-0.25784,0.94755,0.18887,-29.546,0.24723,-0.12426,0.96096,-10.903

> view matrix models
> #91,0.93402,0.29446,-0.20222,-8.5998,-0.25784,0.94755,0.18887,-28.973,0.24723,-0.12426,0.96096,-10.908

> ui mousemode right "rotate selected models"

> view matrix models
> #91,0.94909,0.23455,-0.21026,4.2539,-0.19767,0.96318,0.18222,-43.39,0.24526,-0.13138,0.96051,-8.7327

> select add #93

5182 atoms, 5172 bonds, 8 pseudobonds, 334 residues, 4 models selected  

> select subtract #91

2591 atoms, 2586 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> view matrix models
> #93,0.95174,0.24128,-0.18966,-2.8066,-0.21456,0.96498,0.15091,-61.092,0.21943,-0.10293,0.97018,-10.763

> view matrix models
> #93,0.96296,0.18609,-0.19515,9.1817,-0.15233,0.97258,0.17575,-80.329,0.22251,-0.13952,0.9649,-1.6145

> view matrix models
> #93,0.95991,0.2034,-0.19289,5.2202,-0.17191,0.97068,0.16803,-74.412,0.22141,-0.12814,0.96673,-4.4687

> select add #92

5182 atoms, 5172 bonds, 8 pseudobonds, 334 residues, 4 models selected  

> select subtract #93

2591 atoms, 2586 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> view matrix models
> #92,0.91923,0.33547,-0.2061,-12.937,-0.31031,0.93948,0.14518,40.554,0.24233,-0.069497,0.9677,-24.539

> select add #94

5182 atoms, 5172 bonds, 8 pseudobonds, 334 residues, 4 models selected  

> select subtract #92

2591 atoms, 2586 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> view matrix models
> #94,0.90305,0.37943,-0.20132,-19.381,-0.35538,0.92326,0.14594,77.768,0.24124,-0.060248,0.96859,-26.83

> view matrix models
> #94,0.87227,0.46549,-0.14986,-44.029,-0.44474,0.88255,0.1527,103.96,0.20334,-0.066553,0.97684,-19.407

> undo

> select add #92

5182 atoms, 5172 bonds, 8 pseudobonds, 334 residues, 4 models selected  

> select subtract #94

2591 atoms, 2586 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> view matrix models
> #92,0.91701,0.34441,-0.2012,-15.6,-0.31495,0.93473,0.16457,38.721,0.24475,-0.087541,0.96563,-20.314

> undo

> view matrix models
> #92,0.91847,0.33478,-0.21056,-11.725,-0.308,0.93946,0.15019,39.094,0.24809,-0.073087,0.96598,-24.491

> select add #94

5182 atoms, 5172 bonds, 8 pseudobonds, 334 residues, 4 models selected  

> select subtract #92

2591 atoms, 2586 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> view matrix models
> #94,0.89877,0.38012,-0.21846,-15.248,-0.35538,0.92345,0.14472,77.967,0.25675,-0.052435,0.96505,-31.08

> view matrix models
> #94,0.91354,0.33805,-0.22623,-6.6327,-0.31104,0.93895,0.14703,64.95,0.26212,-0.063949,0.96291,-28.985

> view matrix models
> #94,0.92943,0.32935,-0.16639,-19.751,-0.31093,0.94185,0.12745,68.168,0.19869,-0.066721,0.97779,-18.628

> view matrix models
> #94,0.92699,0.3218,-0.19271,-12.186,-0.30179,0.94497,0.12629,65.831,0.22274,-0.058909,0.9731,-24.353

> select add #93

5182 atoms, 5172 bonds, 8 pseudobonds, 334 residues, 4 models selected  

> select subtract #94

2591 atoms, 2586 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> view matrix models
> #93,0.95173,0.24625,-0.1832,-5.2853,-0.21639,0.96166,0.16846,-63.459,0.21766,-0.12069,0.96853,-5.8543

> view matrix models
> #93,0.94137,0.27361,-0.19736,-6.8804,-0.24665,0.95731,0.15071,-52.813,0.23017,-0.0932,0.96868,-14.924

> view matrix models
> #93,0.95232,0.24886,-0.17651,-7.365,-0.22546,0.96379,0.14238,-56.917,0.20555,-0.095791,0.97395,-10.441

> select add #91

5182 atoms, 5172 bonds, 8 pseudobonds, 334 residues, 4 models selected  

> select subtract #93

2591 atoms, 2586 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> view matrix models
> #91,0.94128,0.26743,-0.20612,-2.8357,-0.23012,0.95484,0.18796,-36.067,0.24707,-0.12949,0.96031,-9.5035

> ui mousemode right "translate selected models"

> view matrix models
> #91,0.94128,0.26743,-0.20612,-3.8227,-0.23012,0.95484,0.18796,-37.172,0.24707,-0.12949,0.96031,-9.4586

> view matrix models
> #91,0.94128,0.26743,-0.20612,-3.2183,-0.23012,0.95484,0.18796,-36.485,0.24707,-0.12949,0.96031,-9.9114

> select add #94

5182 atoms, 5172 bonds, 8 pseudobonds, 334 residues, 4 models selected  

> select subtract #91

2591 atoms, 2586 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> view matrix models
> #94,0.92699,0.3218,-0.19271,-12.118,-0.30179,0.94497,0.12629,66.542,0.22274,-0.058909,0.9731,-24.384

> view matrix models
> #94,0.92699,0.3218,-0.19271,-12.581,-0.30179,0.94497,0.12629,66.212,0.22274,-0.058909,0.9731,-22.601

> ui mousemode right "rotate selected models"

> view matrix models
> #94,0.91755,0.33597,-0.21265,-10.061,-0.31223,0.93996,0.1378,67.183,0.24618,-0.060039,0.96736,-25.869

> undo

> ui mousemode right "translate selected models"

> view matrix models
> #94,0.92699,0.3218,-0.19271,-11.851,-0.30179,0.94497,0.12629,66.321,0.22274,-0.058909,0.9731,-24.95

> ui mousemode right "rotate selected models"

> view matrix models
> #94,0.92238,0.31704,-0.22069,-4.1806,-0.29883,0.94766,0.11242,67.873,0.24478,-0.037746,0.96884,-33.538

> ui mousemode right "translate selected models"

> view matrix models
> #94,0.92238,0.31704,-0.22069,-4.599,-0.29883,0.94766,0.11242,67.759,0.24478,-0.037746,0.96884,-32.113

> select add #91

5182 atoms, 5172 bonds, 8 pseudobonds, 334 residues, 4 models selected  

> select subtract #94

2591 atoms, 2586 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> view matrix models
> #91,0.94128,0.26743,-0.20612,-3.0211,-0.23012,0.95484,0.18796,-36.351,0.24707,-0.12949,0.96031,-9.5153

> undo

> ui mousemode right "rotate selected models"

> view matrix models
> #91,0.94097,0.27134,-0.20234,-4.8476,-0.23887,0.95588,0.17096,-31.571,0.2398,-0.11254,0.96428,-13.286

> select add #94

5182 atoms, 5172 bonds, 8 pseudobonds, 334 residues, 4 models selected  

> select clear

> select add #94

2591 atoms, 2586 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> view matrix models
> #94,0.93529,0.27337,-0.22472,4.0154,-0.25644,0.96117,0.10196,58.169,0.24386,-0.037734,0.96908,-31.978

> undo

> ui mousemode right "translate selected models"

> view matrix models
> #94,0.92238,0.31704,-0.22069,-5.3357,-0.29883,0.94766,0.11242,68.29,0.24478,-0.037746,0.96884,-32.119

> select add #91

5182 atoms, 5172 bonds, 8 pseudobonds, 334 residues, 4 models selected  

> select subtract #94

2591 atoms, 2586 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> view matrix models
> #91,0.94097,0.27134,-0.20234,-4.9627,-0.23887,0.95588,0.17096,-31.585,0.2398,-0.11254,0.96428,-12.991

> undo

> ui mousemode right "rotate selected models"

> view matrix models
> #91,0.94232,0.26581,-0.20341,-3.5865,-0.23697,0.959,0.15544,-29.579,0.23639,-0.098267,0.96668,-16.481

> select clear

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Fit14-20.cxs"

> select add #91

2591 atoms, 2586 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> view matrix models
> #91,0.94407,0.25831,-0.20497,-1.8383,-0.2346,0.96295,0.13302,-26.493,0.23174,-0.077497,0.96969,-21.096

> ui mousemode right "translate selected models"

> view matrix models
> #91,0.94407,0.25831,-0.20497,-2.1126,-0.2346,0.96295,0.13302,-26.404,0.23174,-0.077497,0.96969,-20.34

> view matrix models
> #91,0.94407,0.25831,-0.20497,-1.5449,-0.2346,0.96295,0.13302,-26.516,0.23174,-0.077497,0.96969,-20.193

> view matrix models
> #91,0.94407,0.25831,-0.20497,-1.5476,-0.2346,0.96295,0.13302,-26.631,0.23174,-0.077497,0.96969,-20.182

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Fit14-20.cxs"

> select add #94

5182 atoms, 5172 bonds, 8 pseudobonds, 334 residues, 4 models selected  

> select subtract #91

2591 atoms, 2586 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #94,0.91922,0.32661,-0.21992,-7.1349,-0.30857,0.94448,0.1129,70.898,0.24458,-0.035921,0.96896,-32.537

> hide #!8 models

> select clear

> ui windowfill toggle

> ui mousemode right "translate selected models"

> ui windowfill toggle

> select add #94

2591 atoms, 2586 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> ui windowfill toggle

> view matrix models
> #94,0.91922,0.32661,-0.21992,-6.8999,-0.30857,0.94448,0.1129,70.724,0.24458,-0.035921,0.96896,-32.45

> view matrix models
> #94,0.91922,0.32661,-0.21992,-6.9092,-0.30857,0.94448,0.1129,71.134,0.24458,-0.035921,0.96896,-32.47

> ui windowfill toggle

> show #!8 models

> select add #13

2687 atoms, 2681 bonds, 5 pseudobonds, 175 residues, 4 models selected  

> select subtract #13

2591 atoms, 2586 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> select add #14

2852 atoms, 2846 bonds, 5 pseudobonds, 184 residues, 4 models selected  

> select add #15

3061 atoms, 3054 bonds, 5 pseudobonds, 199 residues, 5 models selected  

> select subtract #15

2852 atoms, 2846 bonds, 5 pseudobonds, 184 residues, 4 models selected  

> select add #15

3061 atoms, 3054 bonds, 5 pseudobonds, 199 residues, 5 models selected  

> select subtract #15

2852 atoms, 2846 bonds, 5 pseudobonds, 184 residues, 4 models selected  

> select add #16

3093 atoms, 3086 bonds, 5 pseudobonds, 199 residues, 5 models selected  

> select subtract #16

2852 atoms, 2846 bonds, 5 pseudobonds, 184 residues, 4 models selected  

> select add #17

3109 atoms, 3105 bonds, 5 pseudobonds, 199 residues, 5 models selected  

> select subtract #17

2852 atoms, 2846 bonds, 5 pseudobonds, 184 residues, 4 models selected  

> select add #18

4182 atoms, 4175 bonds, 6 pseudobonds, 268 residues, 6 models selected  

> select subtract #18

2852 atoms, 2846 bonds, 5 pseudobonds, 184 residues, 4 models selected  

> select add #57

3049 atoms, 3041 bonds, 6 pseudobonds, 197 residues, 6 models selected  

> select subtract #94

458 atoms, 455 bonds, 2 pseudobonds, 30 residues, 4 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #14,0.82373,0.41545,0.38584,-128.1,-0.48613,0.86773,0.10352,78.158,-0.2918,-0.27284,0.91674,130.3,#57,0.85328,0.51232,0.097177,-100.14,-0.51901,0.85243,0.063266,94.508,-0.050425,-0.10442,0.99325,32.006

> ui mousemode right "rotate selected models"

> view matrix models
> #14,0.81467,0.43167,0.38728,-130.07,-0.50234,0.85895,0.099316,84.004,-0.28978,-0.27545,0.9166,130.49,#57,0.84349,0.52815,0.097882,-101.76,-0.53497,0.84239,0.064697,99.508,-0.048285,-0.10694,0.99309,32.16

> ui mousemode right "translate selected models"

> view matrix models
> #14,0.81467,0.43167,0.38728,-130.46,-0.50234,0.85895,0.099316,84.016,-0.28978,-0.27545,0.9166,130.71,#57,0.84349,0.52815,0.097882,-102.16,-0.53497,0.84239,0.064697,99.52,-0.048285,-0.10694,0.99309,32.381

> ui mousemode right "rotate selected models"

> view matrix models
> #14,0.84042,0.47172,0.2668,-120.89,-0.52454,0.83178,0.18166,78.327,-0.13622,-0.29262,0.94648,98.698,#57,0.83755,0.54551,-0.030359,-79.998,-0.53539,0.83055,0.15341,85.038,0.1089,-0.11224,0.9877,3.8629

> view matrix models
> #14,0.82137,0.43392,0.37022,-129.01,-0.48192,0.87513,0.04349,87.326,-0.30512,-0.21414,0.92793,118.44,#57,0.8459,0.52738,0.079592,-98.967,-0.5293,0.84843,0.0036487,108.91,-0.065604,-0.045214,0.99682,21.778

> undo

[Repeated 3 time(s)]

> redo

> select #8

4 models selected  

> select clear

> select add #57

197 atoms, 195 bonds, 1 pseudobond, 13 residues, 2 models selected  

> select subtract #57

Nothing selected  

> select add #17

257 atoms, 259 bonds, 15 residues, 1 model selected  

> select subtract #17

Nothing selected  

> select add #16

241 atoms, 240 bonds, 15 residues, 1 model selected  

> select subtract #16

Nothing selected  

> select add #15

209 atoms, 208 bonds, 15 residues, 1 model selected  

> select subtract #15

Nothing selected  

> select add #14

261 atoms, 260 bonds, 1 pseudobond, 17 residues, 2 models selected  

> ui mousemode right "translate selected models"

> view matrix models
> #14,0.81467,0.43167,0.38728,-130.04,-0.50234,0.85895,0.099316,84.282,-0.28978,-0.27545,0.9166,130.41

> view matrix models
> #14,0.81467,0.43167,0.38728,-130.1,-0.50234,0.85895,0.099316,84.075,-0.28978,-0.27545,0.9166,130.32

> select clear

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> mmaker #95/9 to #91/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#91) with combination, chain 9 (#95),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> mmaker #96/9 to #92/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#92) with combination, chain 9 (#96),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> mmaker #97/9 to #93/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#93) with combination, chain 9 (#97),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> mmaker #98/9 to #94/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#94) with combination, chain 9 (#98),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> hide #!90-94 target m

> color #95 #fffc79ff

> color #96 #73fdffff

> color #97 #ff85ffff

> color #98 #941751ff

> color #98 #531b93ff

> select clear

> select add #98

2591 atoms, 2586 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #98,0.91348,0.32667,-0.24256,-1.2377,-0.30738,0.94465,0.11466,70.501,0.26659,-0.030183,0.96334,-37.108

> select clear

> select add #95

2591 atoms, 2586 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> ui mousemode right "translate selected models"

[Repeated 1 time(s)]

> view matrix models
> #95,0.94407,0.25831,-0.20497,-1.3927,-0.2346,0.96295,0.13302,-26.642,0.23174,-0.077497,0.96969,-20.165

Drag select of 8 postprocess_masked330_onepf.mrc , 43 residues  

> select clear

> select add #95

2591 atoms, 2586 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> view matrix models
> #95,0.94407,0.25831,-0.20497,-1.2069,-0.2346,0.96295,0.13302,-26.654,0.23174,-0.077497,0.96969,-20.145

> select clear

[Repeated 1 time(s)]

> select add #95

2591 atoms, 2586 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> view matrix models
> #95,0.94407,0.25831,-0.20497,-1.0561,-0.2346,0.96295,0.13302,-26.728,0.23174,-0.077497,0.96969,-20.13

Drag select of 8 postprocess_masked330_onepf.mrc , 12 residues  

> select clear

> select add #98

2591 atoms, 2586 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> view matrix models
> #98,0.91348,0.32667,-0.24256,-0.961,-0.30738,0.94465,0.11466,70.45,0.26659,-0.030183,0.96334,-37.079

> view matrix models
> #98,0.91348,0.32667,-0.24256,-0.57952,-0.30738,0.94465,0.11466,70.44,0.26659,-0.030183,0.96334,-36.919

> undo

> ui mousemode right "rotate selected models"

> view matrix models
> #98,0.91743,0.32652,-0.22738,-4.7594,-0.30788,0.94455,0.11417,70.673,0.25205,-0.034742,0.96709,-33.839

> ui mousemode right "translate selected models"

> view matrix models
> #98,0.91743,0.32652,-0.22738,-4.9377,-0.30788,0.94455,0.11417,70.674,0.25205,-0.034742,0.96709,-34.096

> select clear

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Fit14-20.cxs"

> select add #95

2591 atoms, 2586 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #95,0.9546,0.25747,-0.1498,-14.029,-0.23884,0.9621,0.13161,-25.393,0.17801,-0.089857,0.97992,-8.4947

> ui mousemode right "translate selected models"

> view matrix models
> #95,0.9546,0.25747,-0.1498,-14.364,-0.23884,0.9621,0.13161,-25.373,0.17801,-0.089857,0.97992,-8.3977

> select clear

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Fit14-20.cxs"

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Fit14-20-1.pdb" #97 format pdb

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Fit14-20-2.pdb" #95 format pdb

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Fit14-20-3.pdb" #99 format pdb

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Fit14-20-4.pdb" #96 format pdb

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Fit14-20-5.pdb" #98 format pdb

> hide #!8-99 target m

> show #!9 models

> ui tool show "Show Sequence Viewer"

> sequence chain #9/r

Alignment identifier is 9/r  
Drag select of 1 residues  

> open "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Fit14-20-stitched-refined-rechained-ss.pdb"

Summary of feedback from opening /Users/chaaban/Library/CloudStorage/OneDrive-
MRCLaboratoryofMolecularBiology/Documents/Carter
Lab/Diorge/Membranes/Fit14-20-stitched-refined-rechained-ss.pdb  
---  
warning | PDB SEQRES record for chain b is incomplete. Ignoring input sequence
records as basis for sequence.  
  
Chain information for Fit14-20-stitched-refined-rechained-ss.pdb #100  
---  
Chain | Description  
A | No description available  
B C N | No description available  
G | No description available  
O W Y | No description available  
b | No description available  
  

> hide sel atoms

> hide sel cartoons

> hide sel atoms

> select clear

> hide #!9,100 atoms

> show #!9,100 cartoons

> ui mousemode right zoom

> hide #!9 models

> show #!8 models

> select add #100

12796 atoms, 12821 bonds, 5 pseudobonds, 820 residues, 2 models selected  

> color sel bychain

> show #!7 models

> hide #!8 models

> color zone #7 near sel distance 2.43

> color zone #7 near sel distance 7.73

[Repeated 1 time(s)]

> color zone #7 near sel distance 7.59

> color zone #7 near sel distance 1.99

> show #!8 models

> hide #!7 models

> show #!99 models

> show #!98 models

> show #!97 models

> show #!96 models

> show #!95 models

> hide #!95-100 target m

> show #!100 models

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Fit14-20.cxs"

——— End of log from Wed Jan 10 14:43:33 2024 ———

opened ChimeraX session  

> hide #!100 models

> select add #57

12993 atoms, 13016 bonds, 6 pseudobonds, 833 residues, 4 models selected  

> show #!57 models

> select subtract #57

12796 atoms, 12821 bonds, 5 pseudobonds, 820 residues, 2 models selected  

> show #!13-18 target m

> select add #15

13005 atoms, 13029 bonds, 5 pseudobonds, 835 residues, 3 models selected  

> select add #16

13246 atoms, 13269 bonds, 5 pseudobonds, 850 residues, 4 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #15,0.9284,-0.065012,-0.36585,100.42,0.074433,0.99716,0.01169,9.9801,0.36405,-0.038085,0.9306,-48.231,#16,0.90629,-0.11968,-0.40537,124.38,0.06964,0.98825,-0.13607,41.529,0.41689,0.095085,0.90397,-80.14,#100,0.99846,0.034584,-0.043285,0.7636,-0.028882,0.9916,0.12605,-17.333,0.047281,-0.12461,0.99108,21.718

> view matrix models
> #15,0.93408,-0.078145,-0.34841,98.61,0.068219,0.99684,-0.040687,21.576,0.35048,0.014237,0.93646,-57.639,#16,0.91302,-0.13018,-0.38658,121.57,0.060441,0.98042,-0.18741,55.03,0.4034,0.14774,0.90302,-88.319,#100,0.99946,0.019868,-0.026215,0.63687,-0.017859,0.99704,0.074756,-10.602,0.027623,-0.074247,0.99686,12.614

> ui mousemode right "translate selected models"

> view matrix models
> #15,0.93408,-0.078145,-0.34841,98.914,0.068219,0.99684,-0.040687,21.572,0.35048,0.014237,0.93646,-58.833,#16,0.91302,-0.13018,-0.38658,121.87,0.060441,0.98042,-0.18741,55.026,0.4034,0.14774,0.90302,-89.514,#100,0.99946,0.019868,-0.026215,0.9406,-0.017859,0.99704,0.074756,-10.606,0.027623,-0.074247,0.99686,11.42

> ui mousemode right "rotate selected models"

> view matrix models
> #15,0.92461,-0.034563,-0.37933,97.794,0.042229,0.99904,0.011903,15.704,0.37856,-0.027025,0.92518,-53.42,#16,0.90157,-0.091473,-0.42285,123.17,0.037491,0.99023,-0.13428,46.886,0.431,0.10521,0.8962,-84.591,#100,0.99633,0.066116,-0.054441,-3.6766,-0.059468,0.99149,0.11579,-9.4057,0.061634,-0.11213,0.99178,14.718

> ui mousemode right "translate selected models"

> view matrix models
> #15,0.92461,-0.034563,-0.37933,98.13,0.042229,0.99904,0.011903,15.47,0.37856,-0.027025,0.92518,-54.759,#16,0.90157,-0.091473,-0.42285,123.5,0.037491,0.99023,-0.13428,46.652,0.431,0.10521,0.8962,-85.93,#100,0.99633,0.066116,-0.054441,-3.3409,-0.059468,0.99149,0.11579,-9.64,0.061634,-0.11213,0.99178,13.38

> view matrix models
> #15,0.92461,-0.034563,-0.37933,99.153,0.042229,0.99904,0.011903,14.928,0.37856,-0.027025,0.92518,-54.181,#16,0.90157,-0.091473,-0.42285,124.52,0.037491,0.99023,-0.13428,46.109,0.431,0.10521,0.8962,-85.352,#100,0.99633,0.066116,-0.054441,-2.3178,-0.059468,0.99149,0.11579,-10.182,0.061634,-0.11213,0.99178,13.957

> view matrix models
> #15,0.92461,-0.034563,-0.37933,99.101,0.042229,0.99904,0.011903,14.676,0.37856,-0.027025,0.92518,-54.124,#16,0.90157,-0.091473,-0.42285,124.47,0.037491,0.99023,-0.13428,45.858,0.431,0.10521,0.8962,-85.294,#100,0.99633,0.066116,-0.054441,-2.3697,-0.059468,0.99149,0.11579,-10.434,0.061634,-0.11213,0.99178,14.015

> select subtract #15

13037 atoms, 13061 bonds, 5 pseudobonds, 835 residues, 3 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #16,0.90102,-0.068914,-0.42827,120.73,0.020249,0.99291,-0.11717,45.196,0.4333,0.096901,0.89602,-83.891,#100,0.99452,0.089253,-0.054453,-7.641,-0.081884,0.98876,0.12513,-7.346,0.065009,-0.11998,0.99065,15.503

> ui mousemode right "translate selected models"

> view matrix models
> #16,0.90102,-0.068914,-0.42827,121.61,0.020249,0.99291,-0.11717,44.838,0.4333,0.096901,0.89602,-84.158,#100,0.99452,0.089253,-0.054453,-6.7627,-0.081884,0.98876,0.12513,-7.7045,0.065009,-0.11998,0.99065,15.236

> ui mousemode right "rotate selected models"

> view matrix models
> #16,0.9009,-0.066965,-0.42884,121.32,0.026887,0.99474,-0.098848,39.643,0.4332,0.077521,0.89796,-80.312,#100,0.99433,0.091275,-0.054577,-7.1933,-0.082584,0.98605,0.1445,-10.698,0.067005,-0.13917,0.988,20.033

> ui mousemode right "translate selected models"

> view matrix models
> #16,0.9009,-0.066965,-0.42884,121,0.026887,0.99474,-0.098848,40.13,0.4332,0.077521,0.89796,-79.945,#100,0.99433,0.091275,-0.054577,-7.5149,-0.082584,0.98605,0.1445,-10.211,0.067005,-0.13917,0.988,20.4

> view matrix models
> #16,0.9009,-0.066965,-0.42884,120.99,0.026887,0.99474,-0.098848,40.112,0.4332,0.077521,0.89796,-79.991,#100,0.99433,0.091275,-0.054577,-7.5305,-0.082584,0.98605,0.1445,-10.229,0.067005,-0.13917,0.988,20.354

> select subtract #16

12796 atoms, 12821 bonds, 5 pseudobonds, 820 residues, 2 models selected  

> select add #14

13057 atoms, 13081 bonds, 6 pseudobonds, 837 residues, 4 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #14,0.75211,0.47096,0.461,-140.09,-0.4796,0.87091,-0.10726,116.4,-0.45201,-0.14043,0.88089,140.63,#100,0.98794,0.15184,0.030179,-33.26,-0.15014,0.98728,-0.052397,39.146,-0.037752,0.047234,0.99817,4.1434

> ui mousemode right "translate selected models"

> view matrix models
> #14,0.75211,0.47096,0.461,-140.32,-0.4796,0.87091,-0.10726,115.9,-0.45201,-0.14043,0.88089,139.89,#100,0.98794,0.15184,0.030179,-33.488,-0.15014,0.98728,-0.052397,38.643,-0.037752,0.047234,0.99817,3.4021

> ui mousemode right "rotate selected models"

> view matrix models
> #14,0.72945,0.45856,0.50757,-142.2,-0.43269,0.88403,-0.17683,117.29,-0.52979,-0.090634,0.84327,151.82,#100,0.98528,0.14926,0.083302,-42.37,-0.13713,0.98116,-0.1361,52.825,-0.10205,0.12267,0.98719,3.8651

> ui mousemode right "translate selected models"

> view matrix models
> #14,0.72945,0.45856,0.50757,-142.42,-0.43269,0.88403,-0.17683,118.26,-0.52979,-0.090634,0.84327,151.76,#100,0.98528,0.14926,0.083302,-42.592,-0.13713,0.98116,-0.1361,53.795,-0.10205,0.12267,0.98719,3.8113

> view matrix models
> #14,0.72945,0.45856,0.50757,-142.64,-0.43269,0.88403,-0.17683,118.06,-0.52979,-0.090634,0.84327,151.79,#100,0.98528,0.14926,0.083302,-42.815,-0.13713,0.98116,-0.1361,53.594,-0.10205,0.12267,0.98719,3.8386

> view matrix models
> #14,0.72945,0.45856,0.50757,-142.72,-0.43269,0.88403,-0.17683,117.36,-0.52979,-0.090634,0.84327,151.45,#100,0.98528,0.14926,0.083302,-42.891,-0.13713,0.98116,-0.1361,52.9,-0.10205,0.12267,0.98719,3.4994

> view matrix models
> #14,0.72945,0.45856,0.50757,-142.76,-0.43269,0.88403,-0.17683,117.4,-0.52979,-0.090634,0.84327,151.62,#100,0.98528,0.14926,0.083302,-42.937,-0.13713,0.98116,-0.1361,52.937,-0.10205,0.12267,0.98719,3.6721

> ui mousemode right "translate selected models"

> ui mousemode right "rotate selected models"

> view matrix models
> #14,0.70213,0.46739,0.53719,-144.91,-0.41747,0.88136,-0.22118,123.42,-0.57683,-0.068963,0.81395,161.83,#100,0.97853,0.168,0.11943,-51.817,-0.14482,0.97264,-0.18165,64.458,-0.14668,0.16045,0.97608,7.3395

> view matrix models
> #14,0.69015,0.51625,0.50713,-146.99,-0.45472,0.85452,-0.25106,141.87,-0.56296,-0.057337,0.8245,154.73,#100,0.97199,0.21757,0.088858,-54.05,-0.19803,0.96183,-0.18887,78.047,-0.12656,0.16598,0.97797,2.0908

> ui mousemode right "translate selected models"

> view matrix models
> #14,0.69015,0.51625,0.50713,-147.42,-0.45472,0.85452,-0.25106,142.26,-0.56296,-0.057337,0.8245,154.46,#100,0.97199,0.21757,0.088858,-54.476,-0.19803,0.96183,-0.18887,78.444,-0.12656,0.16598,0.97797,1.8146

> view matrix models
> #14,0.69015,0.51625,0.50713,-147.29,-0.45472,0.85452,-0.25106,142.89,-0.56296,-0.057337,0.8245,154.38,#100,0.97199,0.21757,0.088858,-54.349,-0.19803,0.96183,-0.18887,79.074,-0.12656,0.16598,0.97797,1.7366

> view matrix models
> #14,0.69015,0.51625,0.50713,-147.47,-0.45472,0.85452,-0.25106,142.74,-0.56296,-0.057337,0.8245,154.36,#100,0.97199,0.21757,0.088858,-54.521,-0.19803,0.96183,-0.18887,78.92,-0.12656,0.16598,0.97797,1.7169

> view matrix models
> #14,0.69015,0.51625,0.50713,-147.37,-0.45472,0.85452,-0.25106,142.58,-0.56296,-0.057337,0.8245,154.75,#100,0.97199,0.21757,0.088858,-54.429,-0.19803,0.96183,-0.18887,78.758,-0.12656,0.16598,0.97797,2.1073

> select add #15

13266 atoms, 13289 bonds, 6 pseudobonds, 852 residues, 5 models selected  

> select add #13

13362 atoms, 13384 bonds, 7 pseudobonds, 860 residues, 7 models selected  

> select subtract #15

13153 atoms, 13176 bonds, 7 pseudobonds, 845 residues, 6 models selected  

> select subtract #13

13057 atoms, 13081 bonds, 6 pseudobonds, 837 residues, 4 models selected  

> select add #57

13254 atoms, 13276 bonds, 7 pseudobonds, 850 residues, 6 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #14,0.7342,0.4816,0.47855,-143.11,-0.40092,0.87638,-0.26687,130.43,-0.54792,0.0040788,0.83652,136.4,#57,0.86678,0.4963,0.048887,-90.077,-0.49778,0.86697,0.024257,94.747,-0.030345,-0.04536,0.99851,14.428,#100,0.98435,0.1686,0.051349,-40.562,-0.15276,0.96148,-0.22854,77.286,-0.087902,0.21712,0.97218,-14.166

> view matrix models
> #14,0.80659,0.31562,0.4998,-125.8,-0.24884,0.94825,-0.19723,72.154,-0.53619,0.034709,0.84339,126.26,#57,0.94273,0.33289,0.021177,-64.472,-0.33311,0.94286,0.0078994,49.609,-0.017338,-0.014501,0.99974,5.0448,#100,0.99749,-0.012312,0.069734,-11.989,0.028729,0.97044,-0.23961,42.039,-0.064723,0.24101,0.96836,-22.568

> ui mousemode right "translate selected models"

> view matrix models
> #14,0.80659,0.31562,0.4998,-123.68,-0.24884,0.94825,-0.19723,69.369,-0.53619,0.034709,0.84339,125.61,#57,0.94273,0.33289,0.021177,-62.345,-0.33311,0.94286,0.0078994,46.824,-0.017338,-0.014501,0.99974,4.3974,#100,0.99749,-0.012312,0.069734,-9.8632,0.028729,0.97044,-0.23961,39.254,-0.064723,0.24101,0.96836,-23.216

> select subtract #57

13057 atoms, 13081 bonds, 6 pseudobonds, 837 residues, 4 models selected  

> view matrix models
> #14,0.80659,0.31562,0.4998,-123.46,-0.24884,0.94825,-0.19723,69.164,-0.53619,0.034709,0.84339,124.97,#100,0.99749,-0.012312,0.069734,-9.647,0.028729,0.97044,-0.23961,39.049,-0.064723,0.24101,0.96836,-23.855

> ui mousemode right "rotate selected models"

> view matrix models
> #14,0.82485,0.29672,0.48123,-119.57,-0.21788,0.95229,-0.21372,65.452,-0.52168,0.071436,0.85014,113.28,#100,0.99812,-0.03685,0.048918,-1.3598,0.048643,0.9623,-0.26761,41.926,-0.037212,0.26949,0.96228,-33.293

> ui mousemode right "translate selected models"

> view matrix models
> #14,0.82485,0.29672,0.48123,-119.39,-0.21788,0.95229,-0.21372,65.324,-0.52168,0.071436,0.85014,112.81,#100,0.99812,-0.03685,0.048918,-1.182,0.048643,0.9623,-0.26761,41.797,-0.037212,0.26949,0.96228,-33.768

> view matrix models
> #14,0.82485,0.29672,0.48123,-119.37,-0.21788,0.95229,-0.21372,65.485,-0.52168,0.071436,0.85014,112.84,#100,0.99812,-0.03685,0.048918,-1.1641,0.048643,0.9623,-0.26761,41.958,-0.037212,0.26949,0.96228,-33.732

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> mmaker #101/9 to #95/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#95) with combination, chain 9 (#101),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> mmaker #102/9 to #96/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#96) with combination, chain 9 (#102),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> mmaker #103/9 to #97/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#97) with combination, chain 9 (#103),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> mmaker #104/9 to #98/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#98) with combination, chain 9 (#104),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> select clear

> volume #8 level 0.008765

> volume #8 level 0.009517

> select add #102

2591 atoms, 2586 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> select subtract #102

Nothing selected  

> select add #103

2591 atoms, 2586 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> select subtract #103

Nothing selected  

> select add #104

2591 atoms, 2586 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> select subtract #104

Nothing selected  

> select add #101

2591 atoms, 2586 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #101,0.94457,0.29471,-0.14465,-22.201,-0.27902,0.95284,0.11933,-12.712,0.173,-0.072358,0.98226,-12.007

> ui mousemode right "translate selected models"

> view matrix models
> #101,0.94457,0.29471,-0.14465,-21.661,-0.27902,0.95284,0.11933,-12.547,0.173,-0.072358,0.98226,-11.751

Drag select of 19 residues  
Drag select of 60 residues, 1 pseudobonds  

> fitmap sel inMap #8

Fit molecule combination (#101) to map postprocess_masked330_onepf.mrc (#8)
using 953 atoms  
average map value = 0.01539, steps = 92  
shifted from previous position = 3.2  
rotated from previous position = 18 degrees  
atoms outside contour = 378, contour level = 0.0095166  
  
Position of combination (#101) relative to postprocess_masked330_onepf.mrc
(#8) coordinates:  
Matrix rotation and translation  
0.90544793 0.24036188 -0.34984313 39.58122198  
-0.29493223 0.94901331 -0.11130461 41.36310621  
0.30525240 0.20396054 0.93017260 -92.88922098  
Axis 0.34920086 -0.72561119 -0.59291413  
Axis point 231.46865987 -0.00000000 11.76868988  
Rotation angle (degrees) 26.83415065  
Shift along axis 38.88359560  
  

> select add #101

2591 atoms, 2586 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> undo

[Repeated 2 time(s)]

> mmaker #101/9 to #95/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#95) with combination, chain 9 (#101),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> select clear

> combine #9

> select add #105

15238 atoms, 15247 bonds, 7 pseudobonds, 978 residues, 2 models selected  

> show sel atoms

> select clear

> select H

145528 atoms, 18567 residues, 98 models selected  

> delete atoms (#!13-18,57,101-105 & sel)

> delete bonds (#!13-18,57,101-105 & sel)

> select clear

> hide #!105 models

> show #!105 models

> hide #!105 models

> mmaker #105/f to #18/6

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker copy of copy of copy of pointy-1pf.pdb, chain 6 (#18) with copy of
pointy-1pf.pdb, chain f (#105), sequence alignment score = 607.5  
RMSD between 66 pruned atom pairs is 0.001 angstroms; (across all 66 pairs:
0.001)  
  

> show #!105 models

> select clear

> hide #!13-18,57,101-105 atoms

> hide #!105 models

> volume #8 level 0.01008

> show #!105 models

> hide #!105 models

> select add #103

1287 atoms, 1282 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> select add #102

2574 atoms, 2564 bonds, 8 pseudobonds, 334 residues, 4 models selected  

> select subtract #102

1287 atoms, 1282 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> select subtract #103

Nothing selected  

> select add #101

1287 atoms, 1282 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> select subtract #101

Nothing selected  

> select add #104

1287 atoms, 1282 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> ui mousemode right "translate selected models"

> view matrix models
> #104,0.91743,0.32652,-0.22738,-3.0444,-0.30788,0.94455,0.11417,68.995,0.25205,-0.034742,0.96709,-33.797

> view matrix models
> #104,0.91743,0.32652,-0.22738,-3.1125,-0.30788,0.94455,0.11417,68.697,0.25205,-0.034742,0.96709,-33.854

> view matrix models
> #104,0.91743,0.32652,-0.22738,-3.2763,-0.30788,0.94455,0.11417,68.648,0.25205,-0.034742,0.96709,-33.596

> select add #103

2574 atoms, 2564 bonds, 8 pseudobonds, 334 residues, 4 models selected  

> select subtract #103

1287 atoms, 1282 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> select add #102

2574 atoms, 2564 bonds, 8 pseudobonds, 334 residues, 4 models selected  

> select subtract #104

1287 atoms, 1282 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> select add #101

2574 atoms, 2564 bonds, 8 pseudobonds, 334 residues, 4 models selected  

> select subtract #102

1287 atoms, 1282 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #101,0.95019,0.27401,-0.14852,-17.653,-0.2526,0.95618,0.14804,-24.48,0.18257,-0.10316,0.97777,-5.7327

> ui mousemode right "translate selected models"

[Repeated 1 time(s)]

> view matrix models
> #101,0.95019,0.27401,-0.14852,-17.213,-0.2526,0.95618,0.14804,-26.38,0.18257,-0.10316,0.97777,-5.972

> view matrix models
> #101,0.95019,0.27401,-0.14852,-17.386,-0.2526,0.95618,0.14804,-26.918,0.18257,-0.10316,0.97777,-5.9945

> view matrix models
> #101,0.95019,0.27401,-0.14852,-17.831,-0.2526,0.95618,0.14804,-26.606,0.18257,-0.10316,0.97777,-5.8438

> view matrix models
> #101,0.95019,0.27401,-0.14852,-17.837,-0.2526,0.95618,0.14804,-26.662,0.18257,-0.10316,0.97777,-5.8431

> view matrix models
> #101,0.95019,0.27401,-0.14852,-17.702,-0.2526,0.95618,0.14804,-26.726,0.18257,-0.10316,0.97777,-6.13

> hide #!101-105 target m

> volume #8 level 0.01534

> volume #8 level 0.004252

> volume #8 level 0.01534

> show #!101 models

> select subtract #101

Nothing selected  

> hide #!101 models

> show #!102 models

> show #!103 models

> hide #!103 models

> show #!104 models

> hide #!104 models

> show #!105 models

> hide #!105 models

> show #!103 models

> show #!104 models

> show #!101 models

> close #101-104

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> mmaker #101/9 to #95/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#95) with combination, chain 9 (#101),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> mmaker #102/9 to #96/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#96) with combination, chain 9 (#102),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> mmaker #103/9 to #97/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#97) with combination, chain 9 (#103),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> mmaker #104/9 to #98/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#98) with combination, chain 9 (#104),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> volume #8 level 0.00538

> volume #8 level 0.0144

> volume #8 level 0.009517

> volume #8 level 0.01328

> select add #101

1287 atoms, 1282 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> select add #102

2574 atoms, 2564 bonds, 8 pseudobonds, 334 residues, 4 models selected  

> select subtract #102

1287 atoms, 1282 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> select subtract #101

Nothing selected  

> select add #57

100 atoms, 98 bonds, 1 pseudobond, 13 residues, 2 models selected  

> select add #14

233 atoms, 230 bonds, 2 pseudobonds, 30 residues, 4 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #14,0.7464,0.37875,0.5472,-134.19,-0.32723,0.92486,-0.19379,88.874,-0.57949,-0.034411,0.81426,153.59,#57,0.90581,0.405,0.12448,-90.327,-0.41584,0.90609,0.077974,57.464,-0.081211,-0.12239,0.98915,42.01

> ui mousemode right "translate selected models"

> view matrix models
> #14,0.7464,0.37875,0.5472,-135.2,-0.32723,0.92486,-0.19379,88.926,-0.57949,-0.034411,0.81426,155.41,#57,0.90581,0.405,0.12448,-91.336,-0.41584,0.90609,0.077974,57.516,-0.081211,-0.12239,0.98915,43.83

> view matrix models
> #14,0.7464,0.37875,0.5472,-135.25,-0.32723,0.92486,-0.19379,89.441,-0.57949,-0.034411,0.81426,155.37,#57,0.90581,0.405,0.12448,-91.38,-0.41584,0.90609,0.077974,58.031,-0.081211,-0.12239,0.98915,43.794

> close #101-104

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> mmaker #101/9 to #95/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#95) with combination, chain 9 (#101),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> mmaker #102/9 to #96/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#96) with combination, chain 9 (#102),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> mmaker #103/9 to #97/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#97) with combination, chain 9 (#103),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> mmaker #104/9 to #98/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#98) with combination, chain 9 (#104),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> ui mousemode right "rotate selected models"

> view matrix models
> #14,0.61216,0.38966,0.68806,-138.28,-0.2302,0.92028,-0.31637,94.884,-0.75648,0.035278,0.65306,205.73,#57,0.86189,0.39801,0.31422,-117.52,-0.39482,0.91555,-0.076714,81.409,-0.31822,-0.057942,0.94624,84.291

> undo

> view matrix models
> #14,0.78772,0.34302,0.51169,-128.89,-0.25867,0.93803,-0.23062,80.277,-0.55909,0.049301,0.82764,130.94,#57,0.92458,0.3745,0.070051,-78.11,-0.37623,0.92644,0.012813,58.373,-0.060099,-0.038202,0.99746,20.021

> ui mousemode right "translate selected models"

> view matrix models
> #14,0.78772,0.34302,0.51169,-128.95,-0.25867,0.93803,-0.23062,80.429,-0.55909,0.049301,0.82764,131.64,#57,0.92458,0.3745,0.070051,-78.169,-0.37623,0.92644,0.012813,58.526,-0.060099,-0.038202,0.99746,20.726

> ui mousemode right "rotate selected models"

> view matrix models
> #14,0.79835,0.34989,0.49012,-128.39,-0.27132,0.93559,-0.22595,82.531,-0.53761,0.047407,0.84186,125.15,#57,0.92244,0.38331,0.046746,-75.21,-0.38462,0.92279,0.023007,59.003,-0.034318,-0.039202,0.99864,15.702

> view matrix models
> #14,0.78198,0.3762,0.49697,-132.12,-0.29984,0.92604,-0.22921,90.754,-0.54645,0.030228,0.83695,131.48,#57,0.91085,0.40788,0.063149,-81.354,-0.41042,0.91127,0.033817,64.435,-0.043752,-0.05672,0.99743,21.528

> close #101-104

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> mmaker #101/9 to #95/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#95) with combination, chain 9 (#101),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> mmaker #102/9 to #96/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#96) with combination, chain 9 (#102),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> mmaker #103/9 to #97/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#97) with combination, chain 9 (#103),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> mmaker #104/9 to #98/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#98) with combination, chain 9 (#104),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> select add #13

285 atoms, 281 bonds, 3 pseudobonds, 38 residues, 6 models selected  

> select subtract #14

152 atoms, 149 bonds, 2 pseudobonds, 21 residues, 4 models selected  

> select subtract #57

52 atoms, 51 bonds, 1 pseudobond, 8 residues, 2 models selected  

> view matrix models
> #13,0.80327,0.58597,-0.10675,-70.231,-0.55691,0.80246,0.21423,85.392,0.2112,-0.11264,0.97093,-8.8942

> ui mousemode right "translate selected models"

> view matrix models
> #13,0.80327,0.58597,-0.10675,-70.77,-0.55691,0.80246,0.21423,84.895,0.2112,-0.11264,0.97093,-8.8583

> view matrix models
> #13,0.80327,0.58597,-0.10675,-70.756,-0.55691,0.80246,0.21423,84.872,0.2112,-0.11264,0.97093,-8.4649

> view matrix models
> #13,0.80327,0.58597,-0.10675,-70.81,-0.55691,0.80246,0.21423,84.906,0.2112,-0.11264,0.97093,-8.0302

> view matrix models
> #13,0.80327,0.58597,-0.10675,-70.998,-0.55691,0.80246,0.21423,84.902,0.2112,-0.11264,0.97093,-7.6138

> select add #57

152 atoms, 149 bonds, 2 pseudobonds, 21 residues, 4 models selected  

> select subtract #13

100 atoms, 98 bonds, 1 pseudobond, 13 residues, 2 models selected  

> select add #14

233 atoms, 230 bonds, 2 pseudobonds, 30 residues, 4 models selected  

> ui mousemode right "rotate selected models"

> ui mousemode right "translate selected models"

> view matrix models
> #14,0.78198,0.3762,0.49697,-131.93,-0.29984,0.92604,-0.22921,90.7,-0.54645,0.030228,0.83695,131.27,#57,0.91085,0.40788,0.063149,-81.163,-0.41042,0.91127,0.033817,64.382,-0.043752,-0.05672,0.99743,21.32

> view matrix models
> #14,0.78198,0.3762,0.49697,-132.33,-0.29984,0.92604,-0.22921,90.882,-0.54645,0.030228,0.83695,131.16,#57,0.91085,0.40788,0.063149,-81.558,-0.41042,0.91127,0.033817,64.564,-0.043752,-0.05672,0.99743,21.206

> view matrix models
> #14,0.78198,0.3762,0.49697,-132.44,-0.29984,0.92604,-0.22921,90.554,-0.54645,0.030228,0.83695,131.15,#57,0.91085,0.40788,0.063149,-81.666,-0.41042,0.91127,0.033817,64.236,-0.043752,-0.05672,0.99743,21.197

> close #101-104

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> mmaker #101/9 to #95/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#95) with combination, chain 9 (#101),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> mmaker #102/9 to #96/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#96) with combination, chain 9 (#102),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> mmaker #103/9 to #97/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#97) with combination, chain 9 (#103),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> mmaker #104/9 to #98/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#98) with combination, chain 9 (#104),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> view matrix models
> #14,0.78198,0.3762,0.49697,-131.41,-0.29984,0.92604,-0.22921,89.83,-0.54645,0.030228,0.83695,131.14,#57,0.91085,0.40788,0.063149,-80.64,-0.41042,0.91127,0.033817,63.512,-0.043752,-0.05672,0.99743,21.181

> view matrix models
> #14,0.78198,0.3762,0.49697,-131.22,-0.29984,0.92604,-0.22921,90.031,-0.54645,0.030228,0.83695,130.89,#57,0.91085,0.40788,0.063149,-80.451,-0.41042,0.91127,0.033817,63.713,-0.043752,-0.05672,0.99743,20.939

> view matrix models
> #14,0.78198,0.3762,0.49697,-131.83,-0.29984,0.92604,-0.22921,90.173,-0.54645,0.030228,0.83695,131.39,#57,0.91085,0.40788,0.063149,-81.064,-0.41042,0.91127,0.033817,63.855,-0.043752,-0.05672,0.99743,21.439

> close #101-104

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> mmaker #101/9 to #95/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#95) with combination, chain 9 (#101),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> mmaker #102/9 to #96/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#96) with combination, chain 9 (#102),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> mmaker #103/9 to #97/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#97) with combination, chain 9 (#103),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> mmaker #104/9 to #98/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#98) with combination, chain 9 (#104),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> select subtract #14

100 atoms, 98 bonds, 1 pseudobond, 13 residues, 2 models selected  

> select subtract #57

Nothing selected  

> select add #15

105 atoms, 104 bonds, 15 residues, 1 model selected  

> select subtract #15

Nothing selected  

> select add #14

133 atoms, 132 bonds, 1 pseudobond, 17 residues, 2 models selected  

> view matrix models
> #14,0.78198,0.3762,0.49697,-131.84,-0.29984,0.92604,-0.22921,90.531,-0.54645,0.030228,0.83695,131.4

> view matrix models
> #14,0.78198,0.3762,0.49697,-131.95,-0.29984,0.92604,-0.22921,90.45,-0.54645,0.030228,0.83695,131.42

> select subtract #14

Nothing selected  

> select add #16

112 atoms, 111 bonds, 15 residues, 1 model selected  

> select subtract #16

Nothing selected  

> select add #17

127 atoms, 129 bonds, 15 residues, 1 model selected  

> select subtract #17

Nothing selected  

> select add #18

658 atoms, 657 bonds, 1 pseudobond, 84 residues, 2 models selected  

> select subtract #18

Nothing selected  

> select add #13

52 atoms, 51 bonds, 1 pseudobond, 8 residues, 2 models selected  

> select subtract #13

Nothing selected  

> select add #13

52 atoms, 51 bonds, 1 pseudobond, 8 residues, 2 models selected  

> select subtract #13

Nothing selected  

> select add #14

133 atoms, 132 bonds, 1 pseudobond, 17 residues, 2 models selected  

> select subtract #14

Nothing selected  

> select add #15

105 atoms, 104 bonds, 15 residues, 1 model selected  

> select subtract #15

Nothing selected  

> select add #15

105 atoms, 104 bonds, 15 residues, 1 model selected  

> select add #17

232 atoms, 233 bonds, 30 residues, 2 models selected  

> select subtract #17

105 atoms, 104 bonds, 15 residues, 1 model selected  

> select subtract #15

Nothing selected  

> select add #15

105 atoms, 104 bonds, 15 residues, 1 model selected  

> select subtract #15

Nothing selected  

> select add #16

112 atoms, 111 bonds, 15 residues, 1 model selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #16,0.89852,-0.12472,-0.42084,132.4,0.042685,0.97907,-0.19902,59.968,0.43685,0.16086,0.88503,-96.24

> ui mousemode right "translate selected models"

> view matrix models
> #16,0.89852,-0.12472,-0.42084,131.74,0.042685,0.97907,-0.19902,60.111,0.43685,0.16086,0.88503,-95.209

> ui mousemode right "rotate selected models"

> view matrix models
> #16,0.89882,-0.14394,-0.41402,134.52,0.078653,0.98218,-0.17071,47.2,0.43121,0.12087,0.89412,-87.241

> ui mousemode right "translate selected models"

> view matrix models
> #16,0.89882,-0.14394,-0.41402,134.02,0.078653,0.98218,-0.17071,47.053,0.43121,0.12087,0.89412,-87.54

> view matrix models
> #16,0.89882,-0.14394,-0.41402,134.16,0.078653,0.98218,-0.17071,46.883,0.43121,0.12087,0.89412,-87.64

> view matrix models
> #16,0.89882,-0.14394,-0.41402,134.19,0.078653,0.98218,-0.17071,46.271,0.43121,0.12087,0.89412,-87.53

> view matrix models
> #16,0.89882,-0.14394,-0.41402,134.23,0.078653,0.98218,-0.17071,46.565,0.43121,0.12087,0.89412,-87.617

> select add #15

217 atoms, 215 bonds, 30 residues, 2 models selected  

> view matrix models
> #15,0.92461,-0.034563,-0.37933,99.117,0.042229,0.99904,0.011903,14.362,0.37856,-0.027025,0.92518,-54.058,#16,0.89882,-0.14394,-0.41402,134.25,0.078653,0.98218,-0.17071,46.252,0.43121,0.12087,0.89412,-87.552

> view matrix models
> #15,0.92461,-0.034563,-0.37933,99.228,0.042229,0.99904,0.011903,14.312,0.37856,-0.027025,0.92518,-54.126,#16,0.89882,-0.14394,-0.41402,134.36,0.078653,0.98218,-0.17071,46.201,0.43121,0.12087,0.89412,-87.62

> select add #14

350 atoms, 347 bonds, 1 pseudobond, 47 residues, 4 models selected  

> select subtract #14

217 atoms, 215 bonds, 30 residues, 2 models selected  

> select add #13

269 atoms, 266 bonds, 1 pseudobond, 38 residues, 4 models selected  

> select subtract #13

217 atoms, 215 bonds, 30 residues, 2 models selected  

> select add #17

344 atoms, 344 bonds, 45 residues, 3 models selected  

> select subtract #17

217 atoms, 215 bonds, 30 residues, 2 models selected  

> select add #18

875 atoms, 872 bonds, 1 pseudobond, 114 residues, 4 models selected  

> select subtract #15

770 atoms, 768 bonds, 1 pseudobond, 99 residues, 3 models selected  

> select subtract #16

658 atoms, 657 bonds, 1 pseudobond, 84 residues, 2 models selected  

> view matrix models
> #18,0.98014,-0.19508,-0.035582,47.805,0.19499,0.98079,-0.0058233,-8.6239,0.036034,-0.0012307,0.99935,-6.1662

> ui tool show "Fit in Map"

> fitmap #18 inMap #8

Fit molecule copy of copy of copy of pointy-1pf.pdb (#18) to map
postprocess_masked330_onepf.mrc (#8) using 658 atoms  
average map value = 0.01805, steps = 48  
shifted from previous position = 1.95  
rotated from previous position = 0.98 degrees  
atoms outside contour = 279, contour level = 0.013277  
  
Position of copy of copy of copy of pointy-1pf.pdb (#18) relative to
postprocess_masked330_onepf.mrc (#8) coordinates:  
Matrix rotation and translation  
0.97997231 -0.19614523 -0.03437031 46.27061492  
0.19662453 0.98041562 0.01113618 -11.38765170  
0.03151288 -0.01767119 0.99934712 -2.80786472  
Axis -0.07214511 -0.16499775 0.98365178  
Axis point 83.94589668 225.77573013 0.00000000  
Rotation angle (degrees) 11.51642155  
Shift along axis -4.22122289  
  

> view matrix models
> #18,0.97999,-0.19619,-0.03353,46.62,0.19666,0.98041,0.01107,-12.018,0.030701,-0.017443,0.99938,-2.5408

> view matrix models
> #18,0.97999,-0.19619,-0.03353,46.499,0.19666,0.98041,0.01107,-11.939,0.030701,-0.017443,0.99938,-2.1649

> view matrix models
> #18,0.97999,-0.19619,-0.03353,46.521,0.19666,0.98041,0.01107,-11.926,0.030701,-0.017443,0.99938,-2.1525

> close #101-104

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> mmaker #101/9 to #95/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#95) with combination, chain 9 (#101),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> mmaker #102/9 to #96/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#96) with combination, chain 9 (#102),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> mmaker #103/9 to #97/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#97) with combination, chain 9 (#103),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> mmaker #104/9 to #98/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#98) with combination, chain 9 (#104),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> select add #101

1945 atoms, 1939 bonds, 5 pseudobonds, 251 residues, 4 models selected  

> select subtract #101

658 atoms, 657 bonds, 1 pseudobond, 84 residues, 2 models selected  

> select add #102

1945 atoms, 1939 bonds, 5 pseudobonds, 251 residues, 4 models selected  

> select subtract #102

658 atoms, 657 bonds, 1 pseudobond, 84 residues, 2 models selected  

> select add #103

1945 atoms, 1939 bonds, 5 pseudobonds, 251 residues, 4 models selected  

> select subtract #103

658 atoms, 657 bonds, 1 pseudobond, 84 residues, 2 models selected  

> select add #104

1945 atoms, 1939 bonds, 5 pseudobonds, 251 residues, 4 models selected  

> select subtract #104

658 atoms, 657 bonds, 1 pseudobond, 84 residues, 2 models selected  

> select add #101

1945 atoms, 1939 bonds, 5 pseudobonds, 251 residues, 4 models selected  

> select subtract #18

1287 atoms, 1282 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #101,0.80844,0.58116,-0.093133,-73.736,-0.5623,0.80937,0.16952,68.201,0.1739,-0.084674,0.98112,-7.758

> ui mousemode right "translate selected models"

> view matrix models
> #101,0.80844,0.58116,-0.093133,-75.56,-0.5623,0.80937,0.16952,68.667,0.1739,-0.084674,0.98112,-8.4534

> ui mousemode right "rotate selected models"

> view matrix models
> #101,0.79497,0.59565,-0.11499,-71.917,-0.57272,0.7994,0.1815,70.678,0.20003,-0.078427,0.97665,-14.213

> ui mousemode right "translate selected models"

> view matrix models
> #101,0.79497,0.59565,-0.11499,-70.386,-0.57272,0.7994,0.1815,69.574,0.20003,-0.078427,0.97665,-13.835

> view matrix models
> #101,0.79497,0.59565,-0.11499,-70.49,-0.57272,0.7994,0.1815,69.585,0.20003,-0.078427,0.97665,-13.864

> view matrix models
> #101,0.79497,0.59565,-0.11499,-70.484,-0.57272,0.7994,0.1815,68.86,0.20003,-0.078427,0.97665,-13.603

> view matrix models
> #101,0.79497,0.59565,-0.11499,-70.267,-0.57272,0.7994,0.1815,68.875,0.20003,-0.078427,0.97665,-13.561

> select add #102

2574 atoms, 2564 bonds, 8 pseudobonds, 334 residues, 4 models selected  

> select subtract #102

1287 atoms, 1282 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> select subtract #101

Nothing selected  

> select add #104

1287 atoms, 1282 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> select subtract #104

Nothing selected  

> select add #103

1287 atoms, 1282 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> ui mousemode right "rotate selected models"

[Repeated 1 time(s)]

> view matrix models
> #103,0.80142,0.5867,-0.11626,-69.811,-0.56577,0.80668,0.1708,42.871,0.19399,-0.071111,0.97842,-13.55

> view matrix models
> #103,0.80485,0.58199,-0.11619,-69.422,-0.56098,0.80996,0.17107,41.111,0.19367,-0.072505,0.97838,-13.157

> select subtract #103

Nothing selected  

> select add #104

1287 atoms, 1282 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> view matrix models
> #104,0.79542,0.60048,-0.082085,-75.1,-0.58658,0.79682,0.14493,155.74,0.15244,-0.067132,0.98603,-9.473

> ui mousemode right "translate selected models"

> view matrix models
> #104,0.79542,0.60048,-0.082085,-75.392,-0.58658,0.79682,0.14493,155.75,0.15244,-0.067132,0.98603,-8.5363

> view matrix models
> #104,0.79542,0.60048,-0.082085,-75.809,-0.58658,0.79682,0.14493,153.8,0.15244,-0.067132,0.98603,-9.0262

> view matrix models
> #104,0.79542,0.60048,-0.082085,-75.842,-0.58658,0.79682,0.14493,153.72,0.15244,-0.067132,0.98603,-9.0371

> ui mousemode right "rotate selected models"

> view matrix models
> #104,0.81215,0.53815,-0.22539,-36.574,-0.56853,0.81675,-0.098491,193.48,0.13108,0.20813,0.96928,-64.964

> view matrix models
> #104,0.85378,0.47465,-0.21393,-32.469,-0.5024,0.8589,-0.099396,170.79,0.13656,0.19234,0.97178,-62.906

> view matrix models
> #104,0.86407,0.45592,-0.21334,-30.313,-0.48316,0.8701,-0.097431,163.99,0.14121,0.18727,0.97211,-62.724

> view matrix models
> #104,0.86035,0.46967,-0.19802,-35.761,-0.49448,0.86333,-0.10072,168.45,0.12365,0.18457,0.97501,-59.182

> view matrix models
> #104,0.86504,0.4957,-0.077352,-66.463,-0.50145,0.85911,-0.10236,171.13,0.015716,0.12733,0.99174,-27.805

> undo

> view matrix models
> #104,0.88191,0.46827,0.054442,-89.452,-0.46279,0.88196,-0.089236,155.59,-0.089803,0.053502,0.99452,9.6628

> undo

> view matrix models
> #104,0.8061,0.55854,-0.19552,-45.954,-0.53392,0.82894,0.16671,131.55,0.25519,-0.029987,0.96643,-34.183

> view matrix models
> #104,0.81849,0.55488,-0.14892,-56.754,-0.533,0.83014,0.16366,131.69,0.21444,-0.054575,0.97521,-22.136

> select subtract #104

Nothing selected  

> select add #103

1287 atoms, 1282 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> select subtract #103

Nothing selected  

> select add #103

1287 atoms, 1282 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> select subtract #103

Nothing selected  

> select add #102

1287 atoms, 1282 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> select subtract #102

Nothing selected  

> select add #101

1287 atoms, 1282 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Fit14-21.cxs"

> view matrix models
> #101,0.82753,0.5487,-0.11888,-65.15,-0.52246,0.83014,0.19471,49.186,0.20552,-0.099021,0.97363,-9.3102

> view matrix models
> #101,0.82892,0.51235,-0.22447,-36.248,-0.51277,0.85635,0.061053,67.538,0.22351,0.064493,0.97257,-50.384

> ui mousemode right "translate selected models"

> view matrix models
> #101,0.82892,0.51235,-0.22447,-34.741,-0.51277,0.85635,0.061053,69.194,0.22351,0.064493,0.97257,-52.202

> select add #102

2574 atoms, 2564 bonds, 8 pseudobonds, 334 residues, 4 models selected  

> select subtract #102

1287 atoms, 1282 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> select subtract #101

Nothing selected  

> select add #104

1287 atoms, 1282 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> select subtract #104

Nothing selected  

> select add #101

1287 atoms, 1282 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> select subtract #101

Nothing selected  

> select add #102

1287 atoms, 1282 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> select subtract #102

Nothing selected  

> select add #103

1287 atoms, 1282 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> select subtract #103

Nothing selected  

> select add #103

1287 atoms, 1282 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> view matrix models
> #103,0.80485,0.58199,-0.11619,-69.266,-0.56098,0.80996,0.17107,41.204,0.19367,-0.072505,0.97838,-13.061

> ui mousemode right "rotate selected models"

> view matrix models
> #103,0.79746,0.55295,-0.24146,-36.424,-0.54507,0.83183,0.10472,46.063,0.25876,0.048101,0.96474,-51.135

> view matrix models
> #103,0.77845,0.58087,-0.23792,-39.779,-0.57706,0.8114,0.092932,59.461,0.24703,0.064952,0.96683,-53.098

> view matrix models
> #103,0.77817,0.53177,-0.33418,-9.4397,-0.56103,0.82773,0.01073,68.697,0.28232,0.17914,0.94245,-81.646

> view matrix models
> #103,0.80026,0.54725,-0.24516,-34.938,-0.56483,0.82521,-0.0016921,72.482,0.20138,0.13983,0.96948,-61.805

> view matrix models
> #103,0.78771,0.56444,-0.24681,-36.082,-0.58336,0.8122,-0.0043457,79.688,0.19801,0.1474,0.96905,-62.796

> ui mousemode right "translate selected models"

> view matrix models
> #103,0.78771,0.56444,-0.24681,-35.349,-0.58336,0.8122,-0.0043457,82.149,0.19801,0.1474,0.96905,-62.705

> ui mousemode right "rotate selected models"

> view matrix models
> #103,0.75593,0.42676,-0.49642,51.886,-0.57546,0.79471,-0.1931,121.79,0.3121,0.43164,0.84633,-126.78

> ui mousemode right "translate selected models"

> view matrix models
> #103,0.75593,0.42676,-0.49642,51.325,-0.57546,0.79471,-0.1931,122.87,0.3121,0.43164,0.84633,-126.99

> ui mousemode right "rotate selected models"

> view matrix models
> #103,0.77624,0.39335,-0.49267,54.252,-0.49604,0.86339,-0.092218,71.363,0.38909,0.31597,0.86532,-119.37

> ui mousemode right "translate selected models"

> view matrix models
> #103,0.77624,0.39335,-0.49267,54.558,-0.49604,0.86339,-0.092218,71.241,0.38909,0.31597,0.86532,-120.35

> ui mousemode right "rotate selected models"

> view matrix models
> #103,0.75473,0.42642,-0.49854,52.365,-0.50483,0.86282,-0.026256,60.131,0.41895,0.27149,0.86647,-116.26

> view matrix models
> #103,0.68409,0.70255,-0.19607,-56.83,-0.70631,0.70515,0.062354,119.11,0.18207,0.095831,0.97861,-50.717

> view matrix models
> #103,0.85274,0.47253,-0.22259,-32.116,-0.44083,0.87965,0.17859,3.1698,0.28019,-0.054163,0.95841,-31.672

> view matrix models
> #103,0.83762,0.50374,-0.21128,-38.533,-0.47496,0.86267,0.17381,14.815,0.26982,-0.04524,0.96185,-32.342

> view matrix models
> #103,0.78528,0.59281,-0.17867,-55.081,-0.57203,0.80507,0.15699,50.723,0.2369,-0.021076,0.9713,-33.229

> ui mousemode right "translate selected models"

> view matrix models
> #103,0.78528,0.59281,-0.17867,-56.004,-0.57203,0.80507,0.15699,50.275,0.2369,-0.021076,0.9713,-33.629

> view matrix models
> #103,0.78528,0.59281,-0.17867,-56.029,-0.57203,0.80507,0.15699,50.305,0.2369,-0.021076,0.9713,-33.634

> view matrix models
> #103,0.78528,0.59281,-0.17867,-56.182,-0.57203,0.80507,0.15699,49.56,0.2369,-0.021076,0.9713,-33.796

> select add #102

2574 atoms, 2564 bonds, 8 pseudobonds, 334 residues, 4 models selected  

> select subtract #102

1287 atoms, 1282 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> select subtract #103

Nothing selected  

> select add #101

1287 atoms, 1282 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> view matrix models
> #101,0.82892,0.51235,-0.22447,-35.419,-0.51277,0.85635,0.061053,69.473,0.22351,0.064493,0.97257,-51.104

> undo

> ui mousemode right "rotate selected models"

> view matrix models
> #101,0.80555,0.58597,-0.08788,-73.973,-0.55741,0.79973,0.223,59.236,0.20095,-0.13065,0.97085,-2.3782

> view matrix models
> #101,0.81593,0.5756,-0.054161,-80.288,-0.55641,0.80725,0.19685,62.451,0.15703,-0.13048,0.97894,4.728

> view matrix models
> #101,0.81601,0.57363,-0.071314,-76.469,-0.55588,0.81256,0.17536,65.354,0.15854,-0.10346,0.98192,-2.3917

> ui mousemode right "translate selected models"

> view matrix models
> #101,0.81601,0.57363,-0.071314,-78.282,-0.55588,0.81256,0.17536,65.248,0.15854,-0.10346,0.98192,-2.5244

> select add #102

2574 atoms, 2564 bonds, 8 pseudobonds, 334 residues, 4 models selected  

> select subtract #102

1287 atoms, 1282 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> select subtract #101

Nothing selected  

> select add #103

1287 atoms, 1282 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> view matrix models
> #103,0.78528,0.59281,-0.17867,-58.069,-0.57203,0.80507,0.15699,50.754,0.2369,-0.021076,0.9713,-34.61

> view matrix models
> #103,0.78528,0.59281,-0.17867,-58.777,-0.57203,0.80507,0.15699,50.86,0.2369,-0.021076,0.9713,-34.839

> undo

> ui mousemode right "rotate selected models"

> view matrix models
> #103,0.8007,0.56861,-0.18855,-53.614,-0.5458,0.82218,0.16166,40.67,0.24694,-0.026532,0.96867,-34.83

> ui mousemode right "translate selected models"

> view matrix models
> #103,0.8007,0.56861,-0.18855,-53.862,-0.5458,0.82218,0.16166,39.287,0.24694,-0.026532,0.96867,-35.161

> select clear

> select add #103

1287 atoms, 1282 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> select subtract #103

Nothing selected  

> select add #104

1287 atoms, 1282 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #104,0.82649,0.55039,-0.11825,-63.351,-0.53164,0.83219,0.15756,132.15,0.18512,-0.067354,0.9804,-14.38

> ui mousemode right "translate selected models"

> view matrix models
> #104,0.82649,0.55039,-0.11825,-63.609,-0.53164,0.83219,0.15756,132.13,0.18512,-0.067354,0.9804,-13.607

> view matrix models
> #104,0.82649,0.55039,-0.11825,-70.353,-0.53164,0.83219,0.15756,133.53,0.18512,-0.067354,0.9804,-16.061

> view matrix models
> #104,0.82649,0.55039,-0.11825,-69.66,-0.53164,0.83219,0.15756,133.51,0.18512,-0.067354,0.9804,-15.803

> select add #102

2574 atoms, 2564 bonds, 8 pseudobonds, 334 residues, 4 models selected  

> select add #101

3861 atoms, 3846 bonds, 12 pseudobonds, 501 residues, 6 models selected  

> select subtract #102

2574 atoms, 2564 bonds, 8 pseudobonds, 334 residues, 4 models selected  

> select subtract #104

1287 atoms, 1282 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> view matrix models
> #101,0.81601,0.57363,-0.071314,-75.165,-0.55588,0.81256,0.17536,64.36,0.15854,-0.10346,0.98192,-1.4467

> select add #104

2574 atoms, 2564 bonds, 8 pseudobonds, 334 residues, 4 models selected  

> select subtract #104

1287 atoms, 1282 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> select subtract #101

Nothing selected  

> select add #102

1287 atoms, 1282 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> select subtract #102

Nothing selected  

> select add #103

1287 atoms, 1282 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> view matrix models
> #103,0.8007,0.56861,-0.18855,-50.005,-0.5458,0.82218,0.16166,38.358,0.24694,-0.026532,0.96867,-33.81

> select add #104

2574 atoms, 2564 bonds, 8 pseudobonds, 334 residues, 4 models selected  

> select subtract #103

1287 atoms, 1282 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> view matrix models
> #104,0.82649,0.55039,-0.11825,-67.368,-0.53164,0.83219,0.15756,131.5,0.18512,-0.067354,0.9804,-15.39

> view matrix models
> #104,0.82649,0.55039,-0.11825,-67.613,-0.53164,0.83219,0.15756,131.66,0.18512,-0.067354,0.9804,-15.438

> select add #102

2574 atoms, 2564 bonds, 8 pseudobonds, 334 residues, 4 models selected  

> select subtract #104

1287 atoms, 1282 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> view matrix models
> #102,0.77423,0.61284,-0.15811,-58.606,-0.58513,0.7883,0.19026,123.39,0.24124,-0.054788,0.96892,-26.589

> view matrix models
> #102,0.77423,0.61284,-0.15811,-62.145,-0.58513,0.7883,0.19026,123.95,0.24124,-0.054788,0.96892,-27.657

> view matrix models
> #102,0.77423,0.61284,-0.15811,-61.507,-0.58513,0.7883,0.19026,122.03,0.24124,-0.054788,0.96892,-27.564

> ui mousemode right "rotate selected models"

> view matrix models
> #102,0.77364,0.61364,-0.15786,-61.624,-0.586,0.7877,0.19011,122.37,0.24101,-0.054573,0.96899,-27.582

> select add #104

2574 atoms, 2564 bonds, 8 pseudobonds, 334 residues, 4 models selected  

> select subtract #102

1287 atoms, 1282 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> view matrix models
> #104,0.80201,0.58676,-0.11177,-72.406,-0.57023,0.80783,0.14914,146.61,0.1778,-0.055881,0.98248,-17.035

> ui mousemode right "translate selected models"

> ui mousemode right "move picked models"

> ui mousemode right "rotate selected models"

> view matrix models
> #104,0.8447,0.52077,-0.12365,-63.339,-0.50018,0.85025,0.164,119.97,0.19055,-0.076684,0.97868,-14.026

> select clear

[Repeated 1 time(s)]

> select add #102

1287 atoms, 1282 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> select subtract #102

Nothing selected  

> select add #101

1287 atoms, 1282 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> ui mousemode right "translate selected models"

> view matrix models
> #101,0.81601,0.57363,-0.071314,-76.031,-0.55588,0.81256,0.17536,63.79,0.15854,-0.10346,0.98192,-1.7113

> ui mousemode right "rotate selected models"

> view matrix models
> #101,0.81197,0.54629,-0.20559,-42.476,-0.55764,0.83007,0.0032751,93.997,0.17245,0.11199,0.97863,-53.512

> ui mousemode right "translate selected models"

> view matrix models
> #101,0.81197,0.54629,-0.20559,-41.209,-0.55764,0.83007,0.0032751,94.665,0.17245,0.11199,0.97863,-52.846

> ui mousemode right "rotate selected models"

> view matrix models
> #101,0.7973,0.56778,-0.20482,-43.397,-0.563,0.82189,0.086746,81.179,0.21759,0.046152,0.97495,-45.919

> volume #8 level 0.01539

> ui mousemode right "translate selected models"

> view matrix models
> #101,0.7973,0.56778,-0.20482,-48.697,-0.563,0.82189,0.086746,83.928,0.21759,0.046152,0.97495,-46.936

> ui mousemode right "rotate selected models"

> view matrix models
> #101,0.8349,0.53536,-0.12776,-63.881,-0.49655,0.83278,0.24477,37.07,0.23744,-0.14092,0.96113,-5.0242

> view matrix models
> #101,0.83852,0.52715,-0.13785,-60.72,-0.49607,0.84323,0.20709,41.988,0.22541,-0.10527,0.96856,-12.316

> select add #104

2574 atoms, 2564 bonds, 8 pseudobonds, 334 residues, 4 models selected  

> select subtract #104

1287 atoms, 1282 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> select subtract #101

Nothing selected  

> select add #102

1287 atoms, 1282 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> select subtract #102

Nothing selected  

> select add #103

1287 atoms, 1282 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #103,0.78762,0.58824,-0.18337,-52.949,-0.53828,0.80172,0.25979,22.252,0.29983,-0.10592,0.9481,-21.973

> ui mousemode right "translate selected models"

> view matrix models
> #103,0.78762,0.58824,-0.18337,-53.487,-0.53828,0.80172,0.25979,20.675,0.29983,-0.10592,0.9481,-22.346

> ui mousemode right "translate selected models"

> ui mousemode right "rotate selected models"

> view matrix models
> #103,0.82867,0.5357,-0.16229,-53.689,-0.48754,0.83321,0.26091,3.1004,0.27499,-0.13709,0.95162,-10.912

> select add #102

2574 atoms, 2564 bonds, 8 pseudobonds, 334 residues, 4 models selected  

> select add #101

3861 atoms, 3846 bonds, 12 pseudobonds, 501 residues, 6 models selected  

> select subtract #102

2574 atoms, 2564 bonds, 8 pseudobonds, 334 residues, 4 models selected  

> select subtract #103

1287 atoms, 1282 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> view matrix models
> #101,0.77783,0.61967,-0.10481,-76.49,-0.6006,0.78204,0.16642,84.903,0.1851,-0.066499,0.98047,-15.581

> ui mousemode right "translate selected models"

> view matrix models
> #101,0.77783,0.61967,-0.10481,-75.915,-0.6006,0.78204,0.16642,85.502,0.1851,-0.066499,0.98047,-15.325

> view matrix models
> #101,0.77783,0.61967,-0.10481,-76.724,-0.6006,0.78204,0.16642,84.754,0.1851,-0.066499,0.98047,-15.386

> view matrix models
> #101,0.77783,0.61967,-0.10481,-75.969,-0.6006,0.78204,0.16642,85.285,0.1851,-0.066499,0.98047,-15.391

> select add #103

2574 atoms, 2564 bonds, 8 pseudobonds, 334 residues, 4 models selected  

> select subtract #103

1287 atoms, 1282 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> select add #102

2574 atoms, 2564 bonds, 8 pseudobonds, 334 residues, 4 models selected  

> select subtract #101

1287 atoms, 1282 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> select add #101

2574 atoms, 2564 bonds, 8 pseudobonds, 334 residues, 4 models selected  

> select subtract #102

1287 atoms, 1282 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> select subtract #101

Nothing selected  

> select add #104

1287 atoms, 1282 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> select subtract #104

Nothing selected  

> select add #101

1287 atoms, 1282 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> select subtract #101

Nothing selected  

> select add #102

1287 atoms, 1282 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> select subtract #102

Nothing selected  

> select add #103

1287 atoms, 1282 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #103,0.83718,0.51405,-0.18678,-45.566,-0.48869,0.85641,0.1666,16.554,0.2456,-0.048197,0.96817,-28.822

> view matrix models
> #103,0.84016,0.5063,-0.19441,-42.868,-0.48845,0.86217,0.13445,21.512,0.23569,-0.017996,0.97166,-34.502

> view matrix models
> #103,0.86722,0.44855,-0.21616,-30.651,-0.42587,0.89313,0.14474,-0.10397,0.25799,-0.033461,0.96557,-34.172

> view matrix models
> #103,0.86877,0.44307,-0.22118,-28.707,-0.42585,0.8964,0.123,3.4198,0.25277,-0.012665,0.96744,-38.298

> view matrix models
> #103,0.82323,0.52778,-0.20917,-41.546,-0.50896,0.84934,0.13995,27.465,0.25152,-0.0087531,0.96781,-39.024

> view matrix models
> #103,0.81944,0.5348,-0.20619,-42.998,-0.50902,0.84437,0.16711,23.274,0.26347,-0.03198,0.96414,-35.322

> ui mousemode right "translate selected models"

> view matrix models
> #103,0.81944,0.5348,-0.20619,-43.388,-0.50902,0.84437,0.16711,23.441,0.26347,-0.03198,0.96414,-34.055

> select clear

> select add #104

1287 atoms, 1282 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> select subtract #104

Nothing selected  

> select add #103

1287 atoms, 1282 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> ui mousemode right "translate selected models"

> view matrix models
> #103,0.81944,0.5348,-0.20619,-47.481,-0.50902,0.84437,0.16711,25.285,0.26347,-0.03198,0.96414,-36.162

> ui mousemode right "rotate selected models"

> view matrix models
> #103,0.8074,0.55342,-0.20451,-49.713,-0.51479,0.83015,0.21409,20.457,0.28826,-0.067578,0.95517,-31.117

> view matrix models
> #103,0.81001,0.5482,-0.20823,-48.294,-0.51539,0.8349,0.19316,23.606,0.27974,-0.049138,0.95882,-34.394

> select clear

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> mmaker #106/9 to #101/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#101) with combination, chain 9 (#106),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> mmaker #107/9 to #102/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#102) with combination, chain 9 (#107),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> mmaker #108/9 to #103/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#103) with combination, chain 9 (#108),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> mmaker #109/9 to #104/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#104) with combination, chain 9 (#109),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> hide #!104 models

> hide #!103 models

> hide #!102 models

> hide #!101 models

> close #106-109

> show #!101 models

> show #!102 models

> show #!103 models

> show #!104 models

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Fit14-21.cxs"

> select add #102

1287 atoms, 1282 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> select subtract #102

Nothing selected  

> select add #103

1287 atoms, 1282 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> select subtract #103

Nothing selected  

> select add #101

1287 atoms, 1282 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> view matrix models
> #101,0.77992,0.58322,-0.2271,-43.894,-0.59868,0.80099,0.00099949,113.12,0.18248,0.13518,0.97387,-60.078

> ui mousemode right "translate selected models"

[Repeated 1 time(s)]

> view matrix models
> #101,0.77992,0.58322,-0.2271,-43.682,-0.59868,0.80099,0.00099949,113.25,0.18248,0.13518,0.97387,-60.527

> view matrix models
> #101,0.77992,0.58322,-0.2271,-43.489,-0.59868,0.80099,0.00099949,113.22,0.18248,0.13518,0.97387,-60.868

> view matrix models
> #101,0.77992,0.58322,-0.2271,-42.774,-0.59868,0.80099,0.00099949,113.2,0.18248,0.13518,0.97387,-60.504

> view matrix models
> #101,0.77992,0.58322,-0.2271,-44.399,-0.59868,0.80099,0.00099949,112.47,0.18248,0.13518,0.97387,-61.084

> view matrix models
> #101,0.77992,0.58322,-0.2271,-44.834,-0.59868,0.80099,0.00099949,112.47,0.18248,0.13518,0.97387,-61.233

> view matrix models
> #101,0.77992,0.58322,-0.2271,-44.42,-0.59868,0.80099,0.00099949,112.34,0.18248,0.13518,0.97387,-61.885

> view matrix models
> #101,0.77992,0.58322,-0.2271,-42.856,-0.59868,0.80099,0.00099949,113.73,0.18248,0.13518,0.97387,-61.964

> ui mousemode right "rotate selected models"

> view matrix models
> #101,0.76896,0.60685,-0.2011,-51.242,-0.57829,0.79437,0.18587,74.786,0.27254,-0.026628,0.96177,-40.185

> ui mousemode right "translate selected models"

> view matrix models
> #101,0.76896,0.60685,-0.2011,-52.054,-0.57829,0.79437,0.18587,74.635,0.27254,-0.026628,0.96177,-38.497

> view matrix models
> #101,0.76896,0.60685,-0.2011,-52.008,-0.57829,0.79437,0.18587,75.196,0.27254,-0.026628,0.96177,-38.657

> view matrix models
> #101,0.76896,0.60685,-0.2011,-52.079,-0.57829,0.79437,0.18587,74.808,0.27254,-0.026628,0.96177,-38.412

> view matrix models
> #101,0.76896,0.60685,-0.2011,-51.861,-0.57829,0.79437,0.18587,74.441,0.27254,-0.026628,0.96177,-38.605

> view matrix models
> #101,0.76896,0.60685,-0.2011,-51.589,-0.57829,0.79437,0.18587,74.228,0.27254,-0.026628,0.96177,-38.492

> view matrix models
> #101,0.76896,0.60685,-0.2011,-50.82,-0.57829,0.79437,0.18587,73.138,0.27254,-0.026628,0.96177,-38.075

> select add #102

2574 atoms, 2564 bonds, 8 pseudobonds, 334 residues, 4 models selected  

> select subtract #102

1287 atoms, 1282 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> select subtract #101

Nothing selected  

> select add #101

1287 atoms, 1282 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #101,0.78459,0.59703,-0.16722,-58.342,-0.55232,0.79557,0.24901,55.256,0.2817,-0.10301,0.95396,-20.743

> view matrix models
> #101,0.79813,0.58715,-0.13508,-65.085,-0.55179,0.80238,0.22743,57.833,0.24192,-0.10698,0.96438,-13.968

> view matrix models
> #101,0.79889,0.58571,-0.13682,-64.561,-0.55825,0.80671,0.19382,64.739,0.2239,-0.078459,0.97145,-18.352

> view matrix models
> #101,0.79781,0.58955,-0.1262,-67.326,-0.55986,0.80211,0.2078,63.367,0.22373,-0.095134,0.97,-14.187

> view matrix models
> #101,0.80108,0.58505,-0.12645,-66.888,-0.56025,0.80725,0.18565,66.622,0.21069,-0.077875,0.97445,-16.449

> select add #104

2574 atoms, 2564 bonds, 8 pseudobonds, 334 residues, 4 models selected  

> select subtract #104

1287 atoms, 1282 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> select add #103

2574 atoms, 2564 bonds, 8 pseudobonds, 334 residues, 4 models selected  

> select subtract #103

1287 atoms, 1282 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> select subtract #101

Nothing selected  

> select add #102

1287 atoms, 1282 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> view matrix models
> #102,0.77459,0.62084,-0.12067,-70.8,-0.58687,0.77668,0.22882,117.46,0.23578,-0.10643,0.96596,-13.988

> select add #101

2574 atoms, 2564 bonds, 8 pseudobonds, 334 residues, 4 models selected  

> select subtract #102

1287 atoms, 1282 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> select subtract #101

Nothing selected  

> select add #104

1287 atoms, 1282 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> view matrix models
> #104,0.80941,0.57708,-0.10881,-72.228,-0.55745,0.8133,0.16669,139.35,0.18469,-0.074262,0.97999,-13.677

> ui mousemode right "translate selected models"

> view matrix models
> #104,0.80941,0.57708,-0.10881,-66.555,-0.55745,0.8133,0.16669,140.32,0.18469,-0.074262,0.97999,-13.179

> view matrix models
> #104,0.80941,0.57708,-0.10881,-66.852,-0.55745,0.8133,0.16669,140.21,0.18469,-0.074262,0.97999,-12.368

> view matrix models
> #104,0.80941,0.57708,-0.10881,-66.898,-0.55745,0.8133,0.16669,140.81,0.18469,-0.074262,0.97999,-12.362

> view matrix models
> #104,0.80941,0.57708,-0.10881,-69.351,-0.55745,0.8133,0.16669,138.87,0.18469,-0.074262,0.97999,-13.03

> ui mousemode right "rotate selected models"

> view matrix models
> #104,0.82752,0.54892,-0.11792,-64.665,-0.5271,0.8319,0.17351,127.2,0.19334,-0.081424,0.97775,-12.659

> ui mousemode right "translate selected models"

> view matrix models
> #104,0.82752,0.54892,-0.11792,-63.542,-0.5271,0.8319,0.17351,127.84,0.19334,-0.081424,0.97775,-13.406

> view matrix models
> #104,0.82752,0.54892,-0.11792,-63.636,-0.5271,0.8319,0.17351,127.53,0.19334,-0.081424,0.97775,-13.491

> view matrix models
> #104,0.82752,0.54892,-0.11792,-64.014,-0.5271,0.8319,0.17351,127.63,0.19334,-0.081424,0.97775,-12.257

> select add #103

2574 atoms, 2564 bonds, 8 pseudobonds, 334 residues, 4 models selected  

> select subtract #103

1287 atoms, 1282 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> select add #102

2574 atoms, 2564 bonds, 8 pseudobonds, 334 residues, 4 models selected  

> select subtract #102

1287 atoms, 1282 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> select add #101

2574 atoms, 2564 bonds, 8 pseudobonds, 334 residues, 4 models selected  

> select clear

> select add #104

1287 atoms, 1282 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> select subtract #104

Nothing selected  

> select add #103

1287 atoms, 1282 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> select subtract #103

Nothing selected  

> select add #102

1287 atoms, 1282 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> select subtract #102

Nothing selected  

> select add #101

1287 atoms, 1282 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> view matrix models
> #101,0.80108,0.58505,-0.12645,-68.963,-0.56025,0.80725,0.18565,66.79,0.21069,-0.077875,0.97445,-16.693

> ui mousemode right "rotate selected models"

> view matrix models
> #101,0.79641,0.58105,-0.16767,-58.992,-0.55253,0.81182,0.18884,63.574,0.24584,-0.05775,0.96759,-26.976

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Fit14-21.cxs"

> select add #102

2574 atoms, 2564 bonds, 8 pseudobonds, 334 residues, 4 models selected  

> select subtract #102

1287 atoms, 1282 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> select subtract #101

Nothing selected  

> select add #15

105 atoms, 104 bonds, 15 residues, 1 model selected  

> select subtract #15

Nothing selected  

> select add #14

133 atoms, 132 bonds, 1 pseudobond, 17 residues, 2 models selected  

> select add #13

185 atoms, 183 bonds, 2 pseudobonds, 25 residues, 4 models selected  

> select subtract #13

133 atoms, 132 bonds, 1 pseudobond, 17 residues, 2 models selected  

> select add #16

245 atoms, 243 bonds, 1 pseudobond, 32 residues, 3 models selected  

> select subtract #16

133 atoms, 132 bonds, 1 pseudobond, 17 residues, 2 models selected  

> select add #17

260 atoms, 261 bonds, 1 pseudobond, 32 residues, 3 models selected  

> select subtract #17

133 atoms, 132 bonds, 1 pseudobond, 17 residues, 2 models selected  

> select add #57

233 atoms, 230 bonds, 2 pseudobonds, 30 residues, 4 models selected  

> view matrix models
> #14,0.79956,0.30896,0.51503,-124.43,-0.25338,0.95101,-0.17715,66.136,-0.54453,0.011146,0.83867,134.79,#57,0.93776,0.34132,0.064026,-72.158,-0.3449,0.9369,0.057137,41.174,-0.040484,-0.075664,0.99631,25.088

> show #!9 models

> hide #!9 models

> show #!9 models

> hide #!9 models

> ui mousemode right "translate selected models"

> view matrix models
> #14,0.79956,0.30896,0.51503,-124.25,-0.25338,0.95101,-0.17715,67.101,-0.54453,0.011146,0.83867,134.9,#57,0.93776,0.34132,0.064026,-71.98,-0.3449,0.9369,0.057137,42.139,-0.040484,-0.075664,0.99631,25.194

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> mmaker #106/9 to #101/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#101) with combination, chain 9 (#106),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> mmaker #107/9 to #102/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#102) with combination, chain 9 (#107),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> mmaker #108/9 to #103/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#103) with combination, chain 9 (#108),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> mmaker #109/9 to #104/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#104) with combination, chain 9 (#109),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> hide #!101 models

> hide #!102 models

> hide #!103 models

> hide #!104 models

> show #!105 models

> hide #!105 models

> select add #13

285 atoms, 281 bonds, 3 pseudobonds, 38 residues, 6 models selected  

> select subtract #14

152 atoms, 149 bonds, 2 pseudobonds, 21 residues, 4 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #13,0.84215,0.52663,-0.11598,-63.175,-0.49455,0.84001,0.22318,61.935,0.21496,-0.13059,0.96785,-3.5877,#57,0.9597,0.27324,0.065706,-60.912,-0.27798,0.95733,0.079099,19.795,-0.041289,-0.094176,0.9947,29.955

> undo

> select subtract #57

52 atoms, 51 bonds, 1 pseudobond, 8 residues, 2 models selected  

> view matrix models
> #13,0.8667,0.48347,-0.12282,-55.855,-0.44926,0.86355,0.22901,45.766,0.21678,-0.1433,0.96564,-0.31062

> ui mousemode right "translate selected models"

> view matrix models
> #13,0.8667,0.48347,-0.12282,-56.695,-0.44926,0.86355,0.22901,45.912,0.21678,-0.1433,0.96564,-0.52942

> view matrix models
> #13,0.8667,0.48347,-0.12282,-57.062,-0.44926,0.86355,0.22901,45.54,0.21678,-0.1433,0.96564,-0.58476

> select add #14

185 atoms, 183 bonds, 2 pseudobonds, 25 residues, 4 models selected  

> select subtract #13

133 atoms, 132 bonds, 1 pseudobond, 17 residues, 2 models selected  

> select add #57

233 atoms, 230 bonds, 2 pseudobonds, 30 residues, 4 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #14,0.80721,0.27703,0.52122,-120.09,-0.23052,0.96085,-0.1537,56.073,-0.54339,0.0039159,0.83947,136.07,#57,0.94873,0.30979,0.062749,-67.086,-0.31368,0.94719,0.066546,32.067,-0.038821,-0.082818,0.99581,26.505

> close #106-109

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> mmaker #106/9 to #101/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#101) with combination, chain 9 (#106),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> mmaker #107/9 to #102/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#102) with combination, chain 9 (#107),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> mmaker #108/9 to #103/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#103) with combination, chain 9 (#108),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> mmaker #109/9 to #104/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#104) with combination, chain 9 (#109),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> select add #109

1520 atoms, 1512 bonds, 6 pseudobonds, 197 residues, 6 models selected  

> ui mousemode right "translate selected models"

> view matrix models
> #14,0.80721,0.27703,0.52122,-117.88,-0.23052,0.96085,-0.1537,54.871,-0.54339,0.0039159,0.83947,136.83,#57,0.94873,0.30979,0.062749,-64.874,-0.31368,0.94719,0.066546,30.865,-0.038821,-0.082818,0.99581,27.264,#109,0.88596,0.44378,-0.13464,-46.096,-0.41694,0.88934,0.18772,87.508,0.20305,-0.11017,0.97295,-5.8636

> view matrix models
> #14,0.80721,0.27703,0.52122,-117.97,-0.23052,0.96085,-0.1537,54.686,-0.54339,0.0039159,0.83947,136.8,#57,0.94873,0.30979,0.062749,-64.966,-0.31368,0.94719,0.066546,30.68,-0.038821,-0.082818,0.99581,27.236,#109,0.88596,0.44378,-0.13464,-46.188,-0.41694,0.88934,0.18772,87.323,0.20305,-0.11017,0.97295,-5.8919

> select add #108

2807 atoms, 2794 bonds, 10 pseudobonds, 364 residues, 8 models selected  

> select subtract #108

1520 atoms, 1512 bonds, 6 pseudobonds, 197 residues, 6 models selected  

> select subtract #109

233 atoms, 230 bonds, 2 pseudobonds, 30 residues, 4 models selected  

> select add #107

1520 atoms, 1512 bonds, 6 pseudobonds, 197 residues, 6 models selected  

> view matrix models
> #14,0.80721,0.27703,0.52122,-116.3,-0.23052,0.96085,-0.1537,54.215,-0.54339,0.0039159,0.83947,137.37,#57,0.94873,0.30979,0.062749,-63.296,-0.31368,0.94719,0.066546,30.209,-0.038821,-0.082818,0.99581,27.803,#107,0.84224,0.52167,-0.13599,-56.988,-0.48183,0.84156,0.24417,77.166,0.24182,-0.14013,0.96015,-5.6765

> show #!105 models

> hide #!105 models

> undo

[Repeated 3 time(s)]

> redo

> select subtract #57

1420 atoms, 1414 bonds, 5 pseudobonds, 184 residues, 4 models selected  

> view matrix models
> #14,0.80721,0.27703,0.52122,-115.75,-0.23052,0.96085,-0.1537,53.735,-0.54339,0.0039159,0.83947,137.86,#107,0.84224,0.52167,-0.13599,-56.434,-0.48183,0.84156,0.24417,76.685,0.24182,-0.14013,0.96015,-5.1843

> undo

> select subtract #14

1287 atoms, 1282 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> view matrix models
> #107,0.84224,0.52167,-0.13599,-56.82,-0.48183,0.84156,0.24417,76.526,0.24182,-0.14013,0.96015,-5.3076

> select add #13

1339 atoms, 1333 bonds, 5 pseudobonds, 175 residues, 4 models selected  

> select subtract #13

1287 atoms, 1282 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> select add #14

1420 atoms, 1414 bonds, 5 pseudobonds, 184 residues, 4 models selected  

> select subtract #14

1287 atoms, 1282 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> select subtract #107

Nothing selected  

> select add #106

1287 atoms, 1282 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> select subtract #106

Nothing selected  

> select add #109

1287 atoms, 1282 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> select subtract #109

Nothing selected  

> select add #108

1287 atoms, 1282 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> view matrix models
> #108,0.86654,0.44574,-0.22454,-31.099,-0.40453,0.89076,0.20711,-15.072,0.29233,-0.088636,0.9522,-25.775

> view matrix models
> #108,0.86654,0.44574,-0.22454,-31.081,-0.40453,0.89076,0.20711,-14.859,0.29233,-0.088636,0.9522,-25.913

> ui mousemode right "rotate selected models"

> view matrix models
> #108,0.81688,0.54587,-0.18638,-52.082,-0.51282,0.83522,0.19858,21.591,0.26407,-0.066639,0.9622,-27.358

> ui mousemode right "translate selected models"

> view matrix models
> #108,0.81688,0.54587,-0.18638,-52.798,-0.51282,0.83522,0.19858,21.707,0.26407,-0.066639,0.9622,-27.551

> view matrix models
> #108,0.81688,0.54587,-0.18638,-53.096,-0.51282,0.83522,0.19858,21.463,0.26407,-0.066639,0.9622,-27.041

> undo

> ui mousemode right "rotate selected models"

> view matrix models
> #108,0.83075,0.52087,-0.19634,-47.764,-0.50211,0.85346,0.13959,26.895,0.24028,-0.017378,0.97055,-35.96

> view matrix models
> #108,0.83111,0.52307,-0.18884,-49.828,-0.49655,0.85089,0.17151,20.096,0.2504,-0.048776,0.96691,-29.919

> select add #107

2574 atoms, 2564 bonds, 8 pseudobonds, 334 residues, 4 models selected  

> select subtract #108

1287 atoms, 1282 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> view matrix models
> #107,0.83915,0.51056,-0.18748,-43.459,-0.47619,0.85622,0.20032,80.592,0.2628,-0.07882,0.96163,-24.18

> ui mousemode right "translate selected models"

> view matrix models
> #107,0.83915,0.51056,-0.18748,-42.361,-0.47619,0.85622,0.20032,81.311,0.2628,-0.07882,0.96163,-23.888

> view matrix models
> #107,0.83915,0.51056,-0.18748,-42.181,-0.47619,0.85622,0.20032,81.287,0.2628,-0.07882,0.96163,-24.181

> view matrix models
> #107,0.83915,0.51056,-0.18748,-42.003,-0.47619,0.85622,0.20032,81.132,0.2628,-0.07882,0.96163,-24.067

> view matrix models
> #107,0.83915,0.51056,-0.18748,-41.794,-0.47619,0.85622,0.20032,80.41,0.2628,-0.07882,0.96163,-23.95

> ui mousemode right "rotate selected models"

> view matrix models
> #107,0.84904,0.49331,-0.18917,-39.404,-0.45871,0.86593,0.19937,74.808,0.26216,-0.082498,0.96149,-22.933

> select add #106

2574 atoms, 2564 bonds, 8 pseudobonds, 334 residues, 4 models selected  

> select subtract #107

1287 atoms, 1282 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> ui mousemode right "translate selected models"

> view matrix models
> #106,0.85797,0.47978,-0.18359,-43.52,-0.44431,0.87244,0.20355,23.434,0.25783,-0.093069,0.9617,-19.928

> view matrix models
> #106,0.85797,0.47978,-0.18359,-43.756,-0.44431,0.87244,0.20355,22.893,0.25783,-0.093069,0.9617,-19.922

> select add #108

2574 atoms, 2564 bonds, 8 pseudobonds, 334 residues, 4 models selected  

> select subtract #106

1287 atoms, 1282 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> view matrix models
> #108,0.83111,0.52307,-0.18884,-47.548,-0.49655,0.85089,0.17151,20.143,0.2504,-0.048776,0.96691,-29.109

> ui mousemode right "rotate selected models"

> view matrix models
> #108,0.84903,0.49125,-0.19447,-42.585,-0.46299,0.8691,0.17408,8.6294,0.25453,-0.057757,0.96534,-27.524

> view matrix models
> #108,0.85909,0.47203,-0.19786,-39.434,-0.44273,0.87932,0.17549,1.8852,0.25682,-0.063166,0.96439,-26.53

> ui mousemode right "translate selected models"

[Repeated 1 time(s)]

> view matrix models
> #108,0.85909,0.47203,-0.19786,-39.65,-0.44273,0.87932,0.17549,1.6982,0.25682,-0.063166,0.96439,-26.584

> ui mousemode right "rotate selected models"

> view matrix models
> #108,0.86341,0.46324,-0.19983,-38.068,-0.43318,0.88375,0.17702,-1.5601,0.2586,-0.066277,0.96371,-26.079

> view matrix models
> #108,0.86593,0.46167,-0.19243,-39.664,-0.43298,0.88452,0.17366,-1.118,0.25038,-0.067062,0.96582,-24.66

> view matrix models
> #108,0.87084,0.45775,-0.17919,-42.339,-0.42133,0.88282,0.20763,-9.7492,0.25323,-0.10532,0.96165,-15.448

> select add #107

2574 atoms, 2564 bonds, 8 pseudobonds, 334 residues, 4 models selected  

> select subtract #107

1287 atoms, 1282 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> select subtract #108

Nothing selected  

> select add #106

1287 atoms, 1282 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> view matrix models
> #106,0.86292,0.47595,-0.16983,-46.562,-0.43254,0.86942,0.23877,14.302,0.2613,-0.13258,0.95611,-10.259

> select subtract #106

Nothing selected  

> select add #109

1287 atoms, 1282 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> select subtract #109

Nothing selected  

> select add #108

1287 atoms, 1282 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> select subtract #108

Nothing selected  

> select add #106

1287 atoms, 1282 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> select subtract #106

Nothing selected  

> select add #108

1287 atoms, 1282 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> select subtract #108

Nothing selected  

> select add #109

1287 atoms, 1282 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> view matrix models
> #109,0.88526,0.44041,-0.14948,-42.336,-0.41796,0.89432,0.15969,91.875,0.20402,-0.078892,0.97578,-13.975

> select add #107

2574 atoms, 2564 bonds, 8 pseudobonds, 334 residues, 4 models selected  

> select subtract #109

1287 atoms, 1282 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> view matrix models
> #107,0.84919,0.49977,-0.17063,-44.597,-0.45837,0.85799,0.23184,70.208,0.26226,-0.11866,0.95767,-13.727

> view matrix models
> #107,0.86055,0.49066,-0.13678,-51.41,-0.45796,0.86284,0.21397,72.507,0.22301,-0.1215,0.96722,-7.0555

> select subtract #107

Nothing selected  

> select add #15

105 atoms, 104 bonds, 15 residues, 1 model selected  

> select subtract #15

Nothing selected  

> select add #14

133 atoms, 132 bonds, 1 pseudobond, 17 residues, 2 models selected  

> select add #57

233 atoms, 230 bonds, 2 pseudobonds, 30 residues, 4 models selected  

> ui mousemode right "translate selected models"

> view matrix models
> #14,0.80721,0.27703,0.52122,-119.56,-0.23052,0.96085,-0.1537,55.899,-0.54339,0.0039159,0.83947,136.56,#57,0.94873,0.30979,0.062749,-66.554,-0.31368,0.94719,0.066546,31.893,-0.038821,-0.082818,0.99581,26.99

> view matrix models
> #14,0.80721,0.27703,0.52122,-119.59,-0.23052,0.96085,-0.1537,55.493,-0.54339,0.0039159,0.83947,136.55,#57,0.94873,0.30979,0.062749,-66.588,-0.31368,0.94719,0.066546,31.487,-0.038821,-0.082818,0.99581,26.982

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> mmaker #110/9 to #106/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#106) with combination, chain 9 (#110),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> mmaker #111/9 to #107/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#107) with combination, chain 9 (#111),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> mmaker #112/9 to #108/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#108) with combination, chain 9 (#112),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> mmaker #113/9 to #109/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#109) with combination, chain 9 (#113),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> hide #!106 models

> hide #!107 models

> hide #!108 models

> hide #!109 models

> select clear

> show #!108 models

> hide #!108 models

> show #!107 models

> hide #!107 models

> select add #111

1287 atoms, 1282 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> view matrix models
> #111,0.86055,0.49066,-0.13678,-52.405,-0.45796,0.86284,0.21397,73.915,0.22301,-0.1215,0.96722,-7.4318

> select subtract #111

Nothing selected  

> select add #110

1287 atoms, 1282 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> select subtract #110

Nothing selected  

> select add #113

1287 atoms, 1282 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> select subtract #113

Nothing selected  

> select add #112

1287 atoms, 1282 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #112,0.86652,0.46563,-0.17979,-43.199,-0.42128,0.87545,0.23687,-13.792,0.26769,-0.12951,0.95476,-11.329

> select subtract #112

Nothing selected  

> select add #110

1287 atoms, 1282 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> select subtract #110

Nothing selected  

> select add #112

1287 atoms, 1282 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> ui mousemode right "translate selected models"

> view matrix models
> #112,0.86652,0.46563,-0.17979,-43.088,-0.42128,0.87545,0.23687,-13.613,0.26769,-0.12951,0.95476,-12.051

> view matrix models
> #112,0.86652,0.46563,-0.17979,-43.183,-0.42128,0.87545,0.23687,-14.006,0.26769,-0.12951,0.95476,-12.018

> view matrix models
> #112,0.86652,0.46563,-0.17979,-43.566,-0.42128,0.87545,0.23687,-14.075,0.26769,-0.12951,0.95476,-12.117

> select subtract #112

Nothing selected  

> select add #111

1287 atoms, 1282 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> select subtract #111

Nothing selected  

> select add #110

1287 atoms, 1282 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> select subtract #110

Nothing selected  

> select add #113

1287 atoms, 1282 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> select add #112

2574 atoms, 2564 bonds, 8 pseudobonds, 334 residues, 4 models selected  

> select subtract #113

1287 atoms, 1282 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> view matrix models
> #112,0.86652,0.46563,-0.17979,-44.078,-0.42128,0.87545,0.23687,-13.984,0.26769,-0.12951,0.95476,-11.465

> undo

> view matrix models
> #112,0.86652,0.46563,-0.17979,-44.205,-0.42128,0.87545,0.23687,-13.991,0.26769,-0.12951,0.95476,-10.8

> ui mousemode right "rotate selected models"

> view matrix models
> #112,0.846,0.50392,-0.17419,-50.151,-0.46303,0.85636,0.22858,0.49811,0.26436,-0.11272,0.95781,-14.663

> select subtract #112

Nothing selected  

> select add #113

1287 atoms, 1282 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> select subtract #113

Nothing selected  

> select add #111

1287 atoms, 1282 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> select subtract #111

Nothing selected  

> select add #110

1287 atoms, 1282 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> view matrix models
> #110,0.82976,0.53596,-0.15571,-56.736,-0.49626,0.83616,0.23357,35.916,0.25538,-0.11653,0.95979,-13.554

> ui mousemode right "translate selected models"

> view matrix models
> #110,0.82976,0.53596,-0.15571,-55.748,-0.49626,0.83616,0.23357,36.143,0.25538,-0.11653,0.95979,-13.501

> select add #111

2574 atoms, 2564 bonds, 8 pseudobonds, 334 residues, 4 models selected  

> select subtract #111

1287 atoms, 1282 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> select subtract #110

Nothing selected  

> select add #113

1287 atoms, 1282 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #113,0.89541,0.41859,-0.15173,-38.821,-0.3942,0.90374,0.16694,83.471,0.207,-0.089664,0.97422,-11.745

> select add #112

2574 atoms, 2564 bonds, 8 pseudobonds, 334 residues, 4 models selected  

> select subtract #112

1287 atoms, 1282 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> select subtract #113

Nothing selected  

> select add #111

1287 atoms, 1282 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> select subtract #111

Nothing selected  

> select add #110

1287 atoms, 1282 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #110,0.83713,0.52182,-0.16404,-52.277,-0.49079,0.84896,0.19595,39.459,0.24151,-0.083527,0.9668,-19.825

> select clear

> select add #112

1287 atoms, 1282 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> select subtract #112

Nothing selected  

> select add #111

1287 atoms, 1282 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> select subtract #111

Nothing selected  

> select add #110

1287 atoms, 1282 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #110,0.84334,0.51056,-0.16762,-50.183,-0.47891,0.85558,0.19654,35.403,0.24376,-0.085479,0.96606,-19.674

> ui mousemode right "translate selected models"

> view matrix models
> #110,0.84334,0.51056,-0.16762,-50.432,-0.47891,0.85558,0.19654,35.796,0.24376,-0.085479,0.96606,-18.865

> view matrix models
> #110,0.84334,0.51056,-0.16762,-50.362,-0.47891,0.85558,0.19654,35.792,0.24376,-0.085479,0.96606,-19.092

> select clear

> volume #8 level 0.01003

> select add #111

1287 atoms, 1282 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> select subtract #111

Nothing selected  

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Fit14-21.cxs"

> select add #111

1287 atoms, 1282 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> select subtract #111

Nothing selected  

> select add #112

1287 atoms, 1282 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> select subtract #112

Nothing selected  

> select add #113

1287 atoms, 1282 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> select subtract #113

Nothing selected  

> select add #110

1287 atoms, 1282 bonds, 4 pseudobonds, 167 residues, 2 models selected  

> ui mousemode right zoom

> ui mousemode right "translate selected models"

> view matrix models
> #110,0.84334,0.51056,-0.16762,-48.547,-0.47891,0.85558,0.19654,34.871,0.24376,-0.085479,0.96606,-18.51

> ui mousemode right "rotate selected models"

> view matrix models
> #110,0.87331,0.455,-0.17408,-40.284,-0.42052,0.88447,0.20216,15.269,0.24595,-0.10335,0.96376,-14.312

> ui mousemode right "translate selected models"

> view matrix models
> #110,0.87331,0.455,-0.17408,-38.873,-0.42052,0.88447,0.20216,13.62,0.24595,-0.10335,0.96376,-13.766

> ui mousemode right "rotate selected models"

> ui mousemode right "translate selected models"

> view matrix models
> #110,0.87331,0.455,-0.17408,-38.593,-0.42052,0.88447,0.20216,13.07,0.24595,-0.10335,0.96376,-13.761

> ui mousemode right "rotate selected models"

> view matrix models
> #110,0.89092,0.43763,-0.12144,-48.43,-0.41835,0.89486,0.15562,19.371,0.17678,-0.087843,0.98032,-6.7596

> undo

> view matrix models
> #110,0.87782,0.45041,-0.16298,-40.61,-0.42043,0.88755,0.1884,15.043,0.22951,-0.096856,0.96847,-12.909

> undo

> view matrix models
> #110,0.88264,0.43388,-0.18082,-34.192,-0.39841,0.89468,0.20204,6.2617,0.24944,-0.10629,0.96254,-13.533

> ui mousemode right "translate selected models"

> view matrix models
> #110,0.88264,0.43388,-0.18082,-32.193,-0.39841,0.89468,0.20204,6.9244,0.24944,-0.10629,0.96254,-13.369

> view matrix models
> #110,0.88264,0.43388,-0.18082,-32.072,-0.39841,0.89468,0.20204,7.59,0.24944,-0.10629,0.96254,-13.138

> view matrix models
> #110,0.88264,0.43388,-0.18082,-32.187,-0.39841,0.89468,0.20204,6.9856,0.24944,-0.10629,0.96254,-13.349

> view matrix models
> #110,0.88264,0.43388,-0.18082,-33.11,-0.39841,0.89468,0.20204,5.9684,0.24944,-0.10629,0.96254,-13.479

> view matrix models
> #110,0.88264,0.43388,-0.18082,-33.569,-0.39841,0.89468,0.20204,5.885,0.24944,-0.10629,0.96254,-13.153

> view matrix models
> #110,0.88264,0.43388,-0.18082,-33.911,-0.39841,0.89468,0.20204,5.9067,0.24944,-0.10629,0.96254,-12.912

> view matrix models
> #110,0.88264,0.43388,-0.18082,-33.807,-0.39841,0.89468,0.20204,5.8651,0.24944,-0.10629,0.96254,-13.196

> undo

[Repeated 9 time(s)]

> select clear

> combine #13-18,57

Remapping chain ID 'o' in copy of copy of copy of pointy-1pf.pdb #14 to 'p'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID 'o' in copy of copy of copy of copy of pointy-1pf.pdb #57
to 'q'  

> hide #!1-109 target m

> select #111/p:116

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select add #114/p:116

14 atoms, 12 bonds, 2 residues, 2 models selected  

> select add #110/p:116

21 atoms, 18 bonds, 3 residues, 3 models selected  

> select add #112/p:116

28 atoms, 24 bonds, 4 residues, 4 models selected  

> select add #113/p:116

35 atoms, 30 bonds, 5 residues, 5 models selected  

> delete atoms sel

> delete bonds sel

> hide #!113 models

> show #!113 models

> show #!8 models

> hide #!8 models

> show #!8 models

> show #!9 models

> select add #9

15238 atoms, 15247 bonds, 7 pseudobonds, 978 residues, 2 models selected  

> hide #!8 models

> show #!105 models

> hide #!9 models

> hide #!108-114 target m

> select #105/a/b

Nothing selected  

> select #105/a/b/c/d/e/f/g/h/i/j/k

2144 atoms, 2153 bonds, 2 pseudobonds, 274 residues, 2 models selected  

> select clear

> combine #105/6

> hide #!105 models

> show #!105 models

> hide #!105 models

> close #115

> select #105

7579 atoms, 7588 bonds, 7 pseudobonds, 978 residues, 2 models selected  

> show #!105 models

> select subtract #105/6

6311 atoms, 6315 bonds, 6 pseudobonds, 815 residues, 2 models selected  

> delete atoms (#!105 & sel)

> delete bonds (#!105 & sel)

> combine #105

> hide #!105 models

> show #!114 models

> select add #115

1268 atoms, 1273 bonds, 1 pseudobond, 163 residues, 2 models selected  

> view matrix models
> #115,0.97661,-0.18597,-0.10797,27.642,0.18399,0.98253,-0.028113,-38.06,0.11131,0.0075906,0.99376,-33.707

Drag select of 17 residues  

> select subtract #115/6:153

122 atoms, 16 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

Drag select of 91 residues, 1 pseudobonds  

> delete atoms (#!115 & sel)

> delete bonds (#!115 & sel)

Drag select of 19 residues, 1 pseudobonds  

> delete atoms (#!115 & sel)

> delete bonds (#!115 & sel)

> select #115/6:118:1000

7 atoms, 7 bonds, 1 residue, 1 model selected  

> select #115/6:0-116

7 atoms, 6 bonds, 1 residue, 1 model selected  

> delete atoms sel

> delete bonds sel

> select add #115

282 atoms, 283 bonds, 36 residues, 1 model selected  

> view matrix models
> #115,0.97661,-0.18597,-0.10797,79.219,0.18399,0.98253,-0.028113,-79.195,0.11131,0.0075906,0.99376,-26.364

> ui mousemode right "rotate selected models"

> view matrix models
> #115,0.94197,0.32294,-0.09163,-46.591,-0.33065,0.93971,-0.087249,43.676,0.057929,0.11248,0.99196,-42.263

> ui mousemode right "translate selected models"

> view matrix models
> #115,0.94197,0.32294,-0.09163,-44.386,-0.33065,0.93971,-0.087249,35.279,0.057929,0.11248,0.99196,-42.542

> view matrix models
> #115,0.94197,0.32294,-0.09163,-45.549,-0.33065,0.93971,-0.087249,34.686,0.057929,0.11248,0.99196,-41.025

> ui mousemode right "rotate selected models"

> view matrix models
> #115,0.92743,0.37397,-0.0039783,-72.363,-0.37375,0.92717,0.025952,24.774,0.013394,-0.022582,0.99966,0.5923

> ui mousemode right "translate selected models"

> view matrix models
> #115,0.92743,0.37397,-0.0039783,-70.621,-0.37375,0.92717,0.025952,25.528,0.013394,-0.022582,0.99966,5.0242

> ui mousemode right "rotate selected models"

> view matrix models
> #115,0.93919,0.34328,-0.009152,-64.129,-0.34305,0.9391,0.019931,17.629,0.015436,-0.015579,0.99976,2.8228

> ui mousemode right "translate selected models"

> view matrix models
> #115,0.93919,0.34328,-0.009152,-65.63,-0.34305,0.9391,0.019931,17.456,0.015436,-0.015579,0.99976,3.0638

> view matrix models
> #115,0.93919,0.34328,-0.009152,-65.42,-0.34305,0.9391,0.019931,17.489,0.015436,-0.015579,0.99976,2.6834

> ui mousemode right "rotate selected models"

> view matrix models
> #115,0.93934,0.34294,-0.0055012,-66.058,-0.34295,0.93935,-0.002008,21.581,0.0044789,0.0037728,0.99998,-0.13814

> ui mousemode right "translate selected models"

> view matrix models
> #115,0.93934,0.34294,-0.0055012,-66.082,-0.34295,0.93935,-0.002008,21.53,0.0044789,0.0037728,0.99998,0.18347

> show #!8 models

> view matrix models
> #115,0.93934,0.34294,-0.0055012,-65.566,-0.34295,0.93935,-0.002008,21.372,0.0044789,0.0037728,0.99998,0.064749

> ui mousemode right "rotate selected models"

> select add #8

282 atoms, 283 bonds, 36 residues, 5 models selected  

> select subtract #8

282 atoms, 283 bonds, 36 residues, 1 model selected  

> volume #8 level 0.007112

> view matrix models
> #115,0.91944,0.27473,-0.28134,8.1648,-0.26756,0.96139,0.064378,-11.621,0.28816,0.016083,0.95745,-50.497

> view matrix models
> #115,0.90016,0.34281,-0.26868,-7.792,-0.33763,0.93891,0.066797,7.3528,0.27517,0.030588,0.96091,-52.303

> view matrix models
> #115,0.88955,0.41673,-0.1872,-40.023,-0.39509,0.90749,0.14274,12.144,0.22937,-0.05301,0.9719,-24.159

> view matrix models
> #115,0.90268,0.37921,-0.2034,-29.966,-0.36658,0.92521,0.098015,10.565,0.22535,-0.013913,0.97418,-33.756

> ui mousemode right "rotate selected models"

> ui mousemode right "translate selected models"

> view matrix models
> #115,0.90268,0.37921,-0.2034,-30.307,-0.36658,0.92521,0.098015,10.519,0.22535,-0.013913,0.97418,-33.395

> ui mousemode right "translate selected models"

> view matrix models
> #115,0.90268,0.37921,-0.2034,-30.29,-0.36658,0.92521,0.098015,10.446,0.22535,-0.013913,0.97418,-32.968

> show #!113 models

> hide #!113 models

> show #!105 models

> mmaker #105/6 to #115/6

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker copy of copy of pointy-1pf.pdb, chain 6 (#115) with copy of
pointy-1pf.pdb, chain 6 (#105), sequence alignment score = 619.1  
RMSD between 36 pruned atom pairs is 0.000 angstroms; (across all 36 pairs:
0.000)  
  

> show #!113 models

> hide #!113 models

> show #!112 models

> hide #!112 models

> show #!111 models

> hide #!111 models

> show #!109 models

> hide #!109 models

> show #!108 models

> ui mousemode right "rotate selected models"

> view matrix models
> #115,0.90312,0.42824,0.031223,-87.493,-0.42626,0.90294,-0.054836,56.874,-0.051676,0.036215,0.99801,3.9645

> view matrix models
> #115,0.90752,0.41214,0.080879,-93.705,-0.40805,0.91081,-0.062662,52.797,-0.099491,0.023865,0.99475,17.084

> view matrix models
> #115,0.93405,0.35052,0.068502,-80.863,-0.34877,0.9365,-0.036415,29.663,-0.076916,0.010122,0.99699,15.738

> mmaker #105/6 to #115/6

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker copy of copy of pointy-1pf.pdb, chain 6 (#115) with copy of
pointy-1pf.pdb, chain 6 (#105), sequence alignment score = 619.1  
RMSD between 36 pruned atom pairs is 0.000 angstroms; (across all 36 pairs:
0.000)  
  

> view matrix models
> #115,0.92179,0.37358,0.10364,-91.017,-0.37089,0.92759,-0.044837,37.862,-0.11288,0.0028914,0.9936,25.26

> view matrix models
> #115,0.943,0.31836,0.096986,-79.851,-0.31231,0.9472,-0.072582,26.686,-0.11497,0.038154,0.99264,16.881

> view matrix models
> #115,0.88998,0.39069,0.23516,-114.17,-0.37066,0.92018,-0.12601,55.146,-0.26562,0.024984,0.96375,55.212

> view matrix models
> #115,0.89213,0.37419,0.25313,-113.81,-0.36148,0.92734,-0.096843,45.98,-0.27098,-0.0051043,0.96257,64.141

> ui mousemode right "translate selected models"

> view matrix models
> #115,0.89213,0.37419,0.25313,-113.55,-0.36148,0.92734,-0.096843,45.965,-0.27098,-0.0051043,0.96257,62.919

> view matrix models
> #115,0.89213,0.37419,0.25313,-113.51,-0.36148,0.92734,-0.096843,47.055,-0.27098,-0.0051043,0.96257,62.231

> ui mousemode right "rotate selected models"

> view matrix models
> #115,0.92007,0.31804,0.22875,-100.05,-0.30712,0.94806,-0.082838,28.48,-0.24322,0.0059621,0.96995,52.577

> ui mousemode right "translate selected models"

> view matrix models
> #115,0.92007,0.31804,0.22875,-100.48,-0.30712,0.94806,-0.082838,28.367,-0.24322,0.0059621,0.96995,52.522

> mmaker #105/6 to #115/6

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker copy of copy of pointy-1pf.pdb, chain 6 (#115) with copy of
pointy-1pf.pdb, chain 6 (#105), sequence alignment score = 619.1  
RMSD between 36 pruned atom pairs is 0.000 angstroms; (across all 36 pairs:
0.000)  
  

> ui mousemode right "rotate selected models"

> view matrix models
> #115,0.92727,0.31203,0.20691,-96.208,-0.28838,0.9477,-0.13679,35.055,-0.23877,0.067168,0.96875,36.31

> ui mousemode right "translate selected models"

> view matrix models
> #115,0.92727,0.31203,0.20691,-96.309,-0.28838,0.9477,-0.13679,34.883,-0.23877,0.067168,0.96875,36.64

> mmaker #105/6 to #115/6

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker copy of copy of pointy-1pf.pdb, chain 6 (#115) with copy of
pointy-1pf.pdb, chain 6 (#105), sequence alignment score = 619.1  
RMSD between 36 pruned atom pairs is 0.000 angstroms; (across all 36 pairs:
0.000)  
  

> hide #!115 models

> show #!115 models

> hide #!105 models

> view matrix models
> #115,0.92727,0.31203,0.20691,-95.861,-0.28838,0.9477,-0.13679,34.798,-0.23877,0.067168,0.96875,36.051

> view matrix models
> #115,0.92727,0.31203,0.20691,-95.689,-0.28838,0.9477,-0.13679,34.793,-0.23877,0.067168,0.96875,36.086

> view matrix models
> #115,0.92727,0.31203,0.20691,-95.765,-0.28838,0.9477,-0.13679,34.823,-0.23877,0.067168,0.96875,36.204

> select add #13

334 atoms, 334 bonds, 1 pseudobond, 44 residues, 3 models selected  

> select subtract #13

282 atoms, 283 bonds, 36 residues, 1 model selected  

> select subtract #115

Nothing selected  

> select add #13

52 atoms, 51 bonds, 1 pseudobond, 8 residues, 2 models selected  

> select subtract #13

Nothing selected  

> select add #14

133 atoms, 132 bonds, 1 pseudobond, 17 residues, 2 models selected  

> select subtract #14

Nothing selected  

> select add #15

105 atoms, 104 bonds, 15 residues, 1 model selected  

> select subtract #15

Nothing selected  

> show #!13 models

> select add #13

52 atoms, 51 bonds, 1 pseudobond, 8 residues, 2 models selected  

> select subtract #13

Nothing selected  

> hide #!13 models

> show #!14 models

> select add #14

133 atoms, 132 bonds, 1 pseudobond, 17 residues, 2 models selected  

> select subtract #14

Nothing selected  

> hide #!14 models

> show #!57 models

> select add #57

100 atoms, 98 bonds, 1 pseudobond, 13 residues, 2 models selected  

> select subtract #57

Nothing selected  

> hide #!57 models

> combine #15-18,115

Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID '6' in copy of copy of pointy-1pf.pdb #115 to '0'  

> hide #!115 models

> hide #!114 models

> hide #!108 models

> show #!114 models

> hide #!114 models

> show #!113 models

> show #!114 models

> hide #!114 models

> show #!114 models

> hide #!114 models

> show #!112 models

> show #!111 models

> show #!110 models

> combine #15-18,115

Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID '6' in copy of copy of pointy-1pf.pdb #115 to '0'  

> mmaker #117/9 to #110/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#110) with combination, chain 9 (#117),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> combine #15-18,115

Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID '6' in copy of copy of pointy-1pf.pdb #115 to '0'  

> mmaker #118/9 to #111/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#111) with combination, chain 9 (#118),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> combine #15-18,115

Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID '6' in copy of copy of pointy-1pf.pdb #115 to '0'  

> mmaker #119/9 to #112/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#112) with combination, chain 9 (#119),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> combine #15-18,115

Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID '6' in copy of copy of pointy-1pf.pdb #115 to '0'  

> mmaker #120/9 to #113/9 pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker combination, chain 9 (#113) with combination, chain 9 (#120),
sequence alignment score = 674.3  
RMSD between 66 pruned atom pairs is 0.000 angstroms; (across all 66 pairs:
0.000)  
  

> hide #!113 models

> hide #!112 models

> hide #!110 models

> hide #!111 models

> color #116 #009051ff

> color #117 #d783ffff

> color #118 #ff85ffff

> color #118 #fffc79ff

> color #119 #ff2f92ff

> color #120 #ff7e79ff

> volume #8 level 0.01036

> select #117

1284 atoms, 1284 bonds, 1 pseudobond, 165 residues, 2 models selected  

> select subtract 1170

Expected an objects specifier or a keyword  

> select subtract #117/0

1002 atoms, 1001 bonds, 1 pseudobond, 129 residues, 2 models selected  

> combine #117

> select #117

1284 atoms, 1284 bonds, 1 pseudobond, 165 residues, 2 models selected  

> select subtract #117/0

1002 atoms, 1001 bonds, 1 pseudobond, 129 residues, 2 models selected  

> delete atoms (#!117 & sel)

> delete bonds (#!117 & sel)

> select add #121

1284 atoms, 1284 bonds, 1 pseudobond, 165 residues, 2 models selected  

> select subtract #121

Nothing selected  

> hide #!121 models

> select add #117

282 atoms, 283 bonds, 36 residues, 1 model selected  

> view matrix models
> #117,0.9047,-0.072564,-0.41983,115.59,0.069026,0.99733,-0.023637,-8.3872,0.42043,-0.0075947,0.90729,-62.78

> ui mousemode right "rotate selected models"

> view matrix models
> #117,0.91525,-0.032929,-0.40155,103.39,0.040202,0.99914,0.0096981,-9.2722,0.40089,-0.025019,0.91579,-57.583

> ui mousemode right "translate selected models"

> view matrix models
> #117,0.91525,-0.032929,-0.40155,103.29,0.040202,0.99914,0.0096981,-9.3052,0.40089,-0.025019,0.91579,-57.405

> ui mousemode right "rotate selected models"

> view matrix models
> #117,0.91818,-0.021385,-0.39558,99.643,0.032267,0.99926,0.020875,-9.8589,0.39484,-0.031931,0.9182,-55.499

> view matrix models
> #117,0.9173,-0.03494,-0.39665,102.31,0.046299,0.99875,0.019096,-12.197,0.39549,-0.035881,0.91777,-54.879

> show #!121 models

> select add #121

1566 atoms, 1567 bonds, 1 pseudobond, 201 residues, 3 models selected  

> select subtract #117

1284 atoms, 1284 bonds, 1 pseudobond, 165 residues, 2 models selected  

> select #121

1284 atoms, 1284 bonds, 1 pseudobond, 165 residues, 2 models selected  

> select #121/0

282 atoms, 283 bonds, 36 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select add #117

282 atoms, 283 bonds, 36 residues, 1 model selected  

> select subtract #117

Nothing selected  

> select add #121

1002 atoms, 1001 bonds, 1 pseudobond, 129 residues, 2 models selected  

> ui mousemode right "translate selected models"

> view matrix models
> #121,0.9047,-0.072564,-0.41983,120.63,0.069026,0.99733,-0.023637,-13.058,0.42043,-0.0075947,0.90729,-61.362

> view matrix models
> #121,0.9047,-0.072564,-0.41983,120.81,0.069026,0.99733,-0.023637,-13.106,0.42043,-0.0075947,0.90729,-61.729

> view matrix models
> #121,0.9047,-0.072564,-0.41983,122.9,0.069026,0.99733,-0.023637,-12.075,0.42043,-0.0075947,0.90729,-61.957

> view matrix models
> #121,0.9047,-0.072564,-0.41983,122.86,0.069026,0.99733,-0.023637,-11.05,0.42043,-0.0075947,0.90729,-62.093

> view matrix models
> #121,0.9047,-0.072564,-0.41983,122.95,0.069026,0.99733,-0.023637,-10.81,0.42043,-0.0075947,0.90729,-62.104

> ui mousemode right "rotate selected models"

[Repeated 1 time(s)]

> view matrix models
> #121,0.90448,-0.029235,-0.42552,115.89,0.025906,0.99957,-0.01361,-4.418,0.42574,0.0012862,0.90485,-64.39

> view matrix models
> #121,0.90474,-0.04197,-0.42389,117.93,0.038578,0.99912,-0.016583,-6.3298,0.42422,-0.0013492,0.90556,-63.721

> ui mousemode right "translate selected models"

> view matrix models
> #121,0.90474,-0.04197,-0.42389,117.47,0.038578,0.99912,-0.016583,-6.2888,0.42422,-0.0013492,0.90556,-63.824

> view matrix models
> #121,0.90474,-0.04197,-0.42389,117.29,0.038578,0.99912,-0.016583,-7.0555,0.42422,-0.0013492,0.90556,-63.574

> ui mousemode right "rotate selected models"

> view matrix models
> #121,0.90314,-0.053681,-0.42597,120.27,0.037336,0.99821,-0.046636,-0.52454,0.42772,0.026215,0.90353,-69.135

> ui mousemode right "translate selected models"

> view matrix models
> #121,0.90314,-0.053681,-0.42597,120.26,0.037336,0.99821,-0.046636,-0.5527,0.42772,0.026215,0.90353,-69.136

> view matrix models
> #121,0.90314,-0.053681,-0.42597,121.13,0.037336,0.99821,-0.046636,-0.62228,0.42772,0.026215,0.90353,-68.857

> ui mousemode right "rotate selected models"

> view matrix models
> #121,0.89072,-0.053166,-0.45143,128.75,0.040215,0.99846,-0.038244,-2.9647,0.45277,0.01591,0.89148,-69.591

> ui mousemode right "translate selected models"

> view matrix models
> #121,0.89072,-0.053166,-0.45143,126.65,0.040215,0.99846,-0.038244,-3.2338,0.45277,0.01591,0.89148,-70.259

> view matrix models
> #121,0.89072,-0.053166,-0.45143,126.55,0.040215,0.99846,-0.038244,-3.0306,0.45277,0.01591,0.89148,-70.302

> view matrix models
> #121,0.89072,-0.053166,-0.45143,126.77,0.040215,0.99846,-0.038244,-1.9358,0.45277,0.01591,0.89148,-69.985

> view matrix models
> #121,0.89072,-0.053166,-0.45143,127.68,0.040215,0.99846,-0.038244,-1.4647,0.45277,0.01591,0.89148,-69.756

> view matrix models
> #121,0.89072,-0.053166,-0.45143,126.04,0.040215,0.99846,-0.038244,-0.89468,0.45277,0.01591,0.89148,-70.342

> view matrix models
> #121,0.89072,-0.053166,-0.45143,126.17,0.040215,0.99846,-0.038244,-0.68724,0.45277,0.01591,0.89148,-70.304

> ui mousemode right "rotate selected models"

> view matrix models
> #121,0.89103,-0.024058,-0.45331,120.94,0.0096872,0.99937,-0.033998,4.5449,0.45385,0.025902,0.8907,-72.27

> view matrix models
> #121,0.88265,-0.040764,-0.46827,128.88,0.0032221,0.99673,-0.080696,15.86,0.47003,0.069718,0.8799,-81.75

> ui mousemode right "translate selected models"

> view matrix models
> #121,0.88265,-0.040764,-0.46827,129.15,0.0032221,0.99673,-0.080696,15.984,0.47003,0.069718,0.8799,-81.663

> ui mousemode right "rotate selected models"

> view matrix models
> #121,0.8834,-0.062895,-0.46438,132.42,0.024592,0.99581,-0.08809,13.273,0.46797,0.066399,0.88125,-80.883

> view matrix models
> #121,0.88155,-0.063146,-0.46785,133.55,0.058478,0.99799,-0.02451,-7.0135,0.46846,-0.0057526,0.88347,-67.681

> view matrix models
> #121,0.88172,-0.061461,-0.46774,133.17,0.056642,0.9981,-0.024376,-6.6845,0.46835,-0.0050015,0.88353,-67.815

> view matrix models
> #121,0.88196,-0.059159,-0.46759,132.66,0.054132,0.99824,-0.024192,-6.2338,0.4682,-0.0039756,0.88361,-67.997

> select subtract #121

Nothing selected  

> combine #119

> select #119/0

282 atoms, 283 bonds, 36 residues, 1 model selected  

> hide #!122 models

> show #!122 models

> delete atoms sel

> delete bonds sel

> hide #!122 models

> ui mousemode right "translate selected models"

> select add #119

1002 atoms, 1001 bonds, 1 pseudobond, 129 residues, 2 models selected  

> view matrix models
> #119,0.90206,-0.017777,-0.43125,111.03,0.027125,0.99951,0.015537,-35.264,0.43076,-0.025713,0.9021,-58.407

> view matrix models
> #119,0.90206,-0.017777,-0.43125,110.69,0.027125,0.99951,0.015537,-36.024,0.43076,-0.025713,0.9021,-58.616

> view matrix models
> #119,0.90206,-0.017777,-0.43125,112.78,0.027125,0.99951,0.015537,-36.119,0.43076,-0.025713,0.9021,-57.587

> view matrix models
> #119,0.90206,-0.017777,-0.43125,112.82,0.027125,0.99951,0.015537,-37.052,0.43076,-0.025713,0.9021,-57.569

> view matrix models
> #119,0.90206,-0.017777,-0.43125,114.33,0.027125,0.99951,0.015537,-36.778,0.43076,-0.025713,0.9021,-56.804

> view matrix models
> #119,0.90206,-0.017777,-0.43125,114.28,0.027125,0.99951,0.015537,-36.833,0.43076,-0.025713,0.9021,-56.824

> ui mousemode right "rotate selected models"

> view matrix models
> #119,0.90167,-0.032116,-0.43123,117.09,0.0261,0.99946,-0.019864,-29.423,0.43163,0.0066559,0.90203,-63.158

> ui mousemode right "translate selected models"

> view matrix models
> #119,0.90167,-0.032116,-0.43123,116.53,0.0261,0.99946,-0.019864,-29.33,0.43163,0.0066559,0.90203,-63.349

> show #!122 models

> hide #!116 models

> select #122

1284 atoms, 1284 bonds, 1 pseudobond, 165 residues, 2 models selected  

> select subtract #122/0

1002 atoms, 1001 bonds, 1 pseudobond, 129 residues, 2 models selected  

> delete atoms (#!122 & sel)

> delete bonds (#!122 & sel)

> select add #122

282 atoms, 283 bonds, 36 residues, 1 model selected  

> ui mousemode right "translate selected models"

> view matrix models
> #122,0.90206,-0.017777,-0.43125,106.75,0.027125,0.99951,0.015537,-32.572,0.43076,-0.025713,0.9021,-59.859

> show #!116 models

> ui mousemode right "rotate selected models"

> view matrix models
> #122,0.90223,-0.024717,-0.43054,107.76,0.034642,0.99928,0.015228,-33.953,0.42986,-0.028654,0.90244,-59.248

> view matrix models
> #122,0.9043,-0.019749,-0.42643,105.74,0.03258,0.99921,0.022815,-34.956,0.42564,-0.034524,0.90423,-57.763

> select clear

[Repeated 1 time(s)]

> hide #!120 models

> show #!120 models

> combine #120

> select #120/0

282 atoms, 283 bonds, 36 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select #123

1284 atoms, 1284 bonds, 1 pseudobond, 165 residues, 2 models selected  

> select subtract #123/0

1002 atoms, 1001 bonds, 1 pseudobond, 129 residues, 2 models selected  

> delete atoms (#!123 & sel)

> delete bonds (#!123 & sel)

> select add #123

282 atoms, 283 bonds, 36 residues, 1 model selected  

> ui mousemode right "translate selected models"

> view matrix models
> #123,0.91402,-0.10959,-0.39059,121.34,0.090831,0.99366,-0.066248,69.445,0.39537,0.025074,0.91818,-63.777

> view matrix models
> #123,0.91402,-0.10959,-0.39059,121.12,0.090831,0.99366,-0.066248,69.852,0.39537,0.025074,0.91818,-63.789

> view matrix models
> #123,0.91402,-0.10959,-0.39059,121.06,0.090831,0.99366,-0.066248,69.853,0.39537,0.025074,0.91818,-63.805

> ui mousemode right "rotate selected models"

> view matrix models
> #123,0.92417,-0.052791,-0.37831,107.16,0.053136,0.99854,-0.0095338,65.813,0.37826,-0.011291,0.92563,-55.689

> view matrix models
> #123,0.92469,-0.048413,-0.37762,106.19,0.051513,0.99867,-0.0018945,64.679,0.37721,-0.0177,0.92596,-54.46

> ui mousemode right "translate selected models"

> view matrix models
> #123,0.92469,-0.048413,-0.37762,106.98,0.051513,0.99867,-0.0018945,65.071,0.37721,-0.0177,0.92596,-55.547

> view matrix models
> #123,0.92469,-0.048413,-0.37762,106.82,0.051513,0.99867,-0.0018945,64.704,0.37721,-0.0177,0.92596,-55.548

> select add #121

1284 atoms, 1284 bonds, 1 pseudobond, 165 residues, 3 models selected  

> select subtract #123

1002 atoms, 1001 bonds, 1 pseudobond, 129 residues, 2 models selected  

> view matrix models
> #121,0.88196,-0.059159,-0.46759,133.8,0.054132,0.99824,-0.024192,-7.8202,0.4682,-0.0039756,0.88361,-67.864

> view matrix models
> #121,0.88196,-0.059159,-0.46759,133.4,0.054132,0.99824,-0.024192,-8.182,0.4682,-0.0039756,0.88361,-67.951

> select subtract #121

Nothing selected  

> select add #122

282 atoms, 283 bonds, 36 residues, 1 model selected  

> select subtract #122

Nothing selected  

> select add #119

1002 atoms, 1001 bonds, 1 pseudobond, 129 residues, 2 models selected  

> view matrix models
> #119,0.90167,-0.032116,-0.43123,116.48,0.0261,0.99946,-0.019864,-30.084,0.43163,0.0066559,0.90203,-63.277

> view matrix models
> #119,0.90167,-0.032116,-0.43123,117.23,0.0261,0.99946,-0.019864,-30.38,0.43163,0.0066559,0.90203,-62.998

> select clear

> select add #118

1284 atoms, 1284 bonds, 1 pseudobond, 165 residues, 2 models selected  

> combine #118

> select #118/0

282 atoms, 283 bonds, 36 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select #118/0

Nothing selected  

> select #124

1284 atoms, 1284 bonds, 1 pseudobond, 165 residues, 2 models selected  

> select subtract #124/0

1002 atoms, 1001 bonds, 1 pseudobond, 129 residues, 2 models selected  

> delete atoms (#!124 & sel)

> delete bonds (#!124 & sel)

> hide #!124 models

> show #!124 models

Drag select of 8 postprocess_masked330_onepf.mrc , 42 residues  

> select clear

[Repeated 1 time(s)]

> select add #116

1284 atoms, 1284 bonds, 1 pseudobond, 165 residues, 2 models selected  

> ui mousemode right "translate selected models"

> view matrix models
> #116,0.92461,-0.034563,-0.37933,99.365,0.042229,0.99904,0.011903,14.271,0.37856,-0.027025,0.92518,-54.438

> select add #121

2286 atoms, 2285 bonds, 2 pseudobonds, 294 residues, 4 models selected  

> ui mousemode right "translate selected models"

> view matrix models
> #116,0.92461,-0.034563,-0.37933,100.04,0.042229,0.99904,0.011903,13.411,0.37856,-0.027025,0.92518,-54.188,#121,0.88196,-0.059159,-0.46759,134.08,0.054132,0.99824,-0.024192,-9.0412,0.4682,-0.0039756,0.88361,-67.701

> undo

> select subtract #116

1002 atoms, 1001 bonds, 1 pseudobond, 129 residues, 2 models selected  

> view matrix models
> #121,0.88196,-0.059159,-0.46759,135,0.054132,0.99824,-0.024192,-9.5991,0.4682,-0.0039756,0.88361,-67.372

> view matrix models
> #121,0.88196,-0.059159,-0.46759,136.19,0.054132,0.99824,-0.024192,-9.4144,0.4682,-0.0039756,0.88361,-66.863

> ui mousemode right "rotate selected models"

> view matrix models
> #121,0.88213,-0.053304,-0.46797,135.12,0.04776,0.99858,-0.023712,-8.2674,0.46857,-0.0014331,0.88342,-67.385

> ui mousemode right "rotate selected models"

> view matrix models
> #121,0.87915,-0.07731,-0.47023,140.76,0.03842,0.99504,-0.091762,8.1454,0.47499,0.062606,0.87776,-79.76

> view matrix models
> #121,0.87241,-0.075627,-0.48289,144.4,0.037871,0.99545,-0.087481,7.3114,0.48731,0.058032,0.8713,-80.105

> ui mousemode right "translate selected models"

> view matrix models
> #121,0.87241,-0.075627,-0.48289,143.95,0.037871,0.99545,-0.087481,7.3836,0.48731,0.058032,0.8713,-79.408

> select add #124

1284 atoms, 1284 bonds, 1 pseudobond, 165 residues, 3 models selected  

> select subtract #121

282 atoms, 283 bonds, 36 residues, 1 model selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #124,0.91939,-0.0091586,-0.39325,101.04,0.029906,0.99846,0.046665,34.003,0.39221,-0.054663,0.91825,-51.194

> ui mousemode right "translate selected models"

> view matrix models
> #124,0.91939,-0.0091586,-0.39325,101.86,0.029906,0.99846,0.046665,34.582,0.39221,-0.054663,0.91825,-50.886

> select add #122

564 atoms, 566 bonds, 72 residues, 2 models selected  

> select subtract #122

282 atoms, 283 bonds, 36 residues, 1 model selected  

> select subtract #124

Nothing selected  

> select add #119

1002 atoms, 1001 bonds, 1 pseudobond, 129 residues, 2 models selected  

> ui mousemode right "rotate selected models"

> ui mousemode right "translate selected models"

> view matrix models
> #119,0.90167,-0.032116,-0.43123,118.27,0.0261,0.99946,-0.019864,-31.964,0.43163,0.0066559,0.90203,-62.734

> ui mousemode right "rotate selected models"

> view matrix models
> #119,0.89821,-0.087235,-0.43082,129.4,0.082583,0.99615,-0.02953,-40.967,0.43173,-0.0090533,0.90196,-59.747

Drag select of 8 postprocess_masked330_onepf.mrc , 218 residues, 3 pseudobonds  
Drag select of 8 postprocess_masked330_onepf.mrc , 261 residues, 2 pseudobonds  
Drag select of 8 postprocess_masked330_onepf.mrc , 113 residues, 1 pseudobonds  

> select clear

> select add #120

1002 atoms, 1001 bonds, 1 pseudobond, 129 residues, 2 models selected  

> select subtract #120

Nothing selected  

> select add #123

282 atoms, 283 bonds, 36 residues, 1 model selected  

> view matrix models
> #123,0.92836,0.00011939,-0.37168,96.776,0.0036233,0.99995,0.0093714,71.791,0.37166,-0.010047,0.92832,-56.192

> undo

> ui mousemode right "translate selected models"

> view matrix models
> #123,0.92469,-0.048413,-0.37762,107.91,0.051513,0.99867,-0.0018945,66.239,0.37721,-0.0177,0.92596,-55.183

> view matrix models
> #123,0.92469,-0.048413,-0.37762,108.07,0.051513,0.99867,-0.0018945,66.764,0.37721,-0.0177,0.92596,-55.366

> ui mousemode right "rotate selected models"

> view matrix models
> #123,0.92957,-0.044719,-0.36591,104.29,0.051134,0.99866,0.007855,65.013,0.36507,-0.026013,0.93062,-52.447

> select add #124

564 atoms, 566 bonds, 72 residues, 2 models selected  

> select subtract #123

282 atoms, 283 bonds, 36 residues, 1 model selected  
Drag select of 8 postprocess_masked330_onepf.mrc  

> select add #124

282 atoms, 283 bonds, 36 residues, 3 models selected  

> select clear

> select add #124

282 atoms, 283 bonds, 36 residues, 1 model selected  

> view matrix models
> #124,0.91548,-0.020115,-0.40185,106.09,0.023953,0.9997,0.0045302,43.437,0.40164,-0.013773,0.91569,-59.173

> undo

> ui mousemode right "translate selected models"

> view matrix models
> #124,0.91939,-0.0091586,-0.39325,101.75,0.029906,0.99846,0.046665,35.292,0.39221,-0.054663,0.91825,-50.855

> ui mousemode right "rotate selected models"

> view matrix models
> #124,0.91665,-0.0066601,-0.39963,103.06,0.011752,0.99988,0.010292,45.436,0.39951,-0.014131,0.91662,-58.837

> view matrix models
> #124,0.91969,0.002297,-0.39264,99.644,0.0081759,0.99965,0.024999,43.422,0.39256,-0.026201,0.91935,-55.942

> view matrix models
> #124,0.91916,-0.02019,-0.39336,103.68,0.03212,0.9992,0.023769,39.022,0.39256,-0.034482,0.91908,-54.491

> view matrix models
> #124,0.91666,-0.023597,-0.39896,105.8,0.034339,0.99921,0.019798,39.327,0.39818,-0.031849,0.91675,-55.605

> select clear

> select add #124

282 atoms, 283 bonds, 36 residues, 1 model selected  

> view matrix models
> #124,0.9157,-0.038788,-0.39998,108.75,0.049541,0.99863,0.016576,37.04,0.39879,-0.034994,0.91637,-55.122

> ui mousemode right "translate selected models"

> view matrix models
> #124,0.9157,-0.038788,-0.39998,108.45,0.049541,0.99863,0.016576,36.045,0.39879,-0.034994,0.91637,-55.162

> view matrix models
> #124,0.9157,-0.038788,-0.39998,108.6,0.049541,0.99863,0.016576,36.058,0.39879,-0.034994,0.91637,-55.041

> view matrix models
> #124,0.9157,-0.038788,-0.39998,108.55,0.049541,0.99863,0.016576,35.878,0.39879,-0.034994,0.91637,-55.039

> view matrix models
> #124,0.9157,-0.038788,-0.39998,108.87,0.049541,0.99863,0.016576,35.836,0.39879,-0.034994,0.91637,-54.912

> select clear

Drag select of 8 postprocess_masked330_onepf.mrc  

> select clear

> select add #116

1284 atoms, 1284 bonds, 1 pseudobond, 165 residues, 2 models selected  

> ui mousemode right "translate selected models"

> view matrix models
> #116,0.92461,-0.034563,-0.37933,99.954,0.042229,0.99904,0.011903,14.079,0.37856,-0.027025,0.92518,-54.444

> undo

> select clear

> select add #121

1002 atoms, 1001 bonds, 1 pseudobond, 129 residues, 2 models selected  

> view matrix models
> #121,0.87241,-0.075627,-0.48289,142.17,0.037871,0.99545,-0.087481,8.3856,0.48731,0.058032,0.8713,-79.861

> select subtract #121

Nothing selected  

> select add #122

282 atoms, 283 bonds, 36 residues, 1 model selected  

> select subtract #122

Nothing selected  

> select add #119

1002 atoms, 1001 bonds, 1 pseudobond, 129 residues, 2 models selected  

> view matrix models
> #119,0.89821,-0.087235,-0.43082,127.96,0.082583,0.99615,-0.02953,-39.586,0.43173,-0.0090533,0.90196,-60.122

> ui mousemode right "rotate selected models"

> view matrix models
> #119,0.89858,-0.066033,-0.43381,124.45,0.062225,0.9978,-0.022989,-37.049,0.43437,-0.0063365,0.90071,-60.929

> select add #118

2004 atoms, 2002 bonds, 2 pseudobonds, 258 residues, 4 models selected  

> select subtract #119

1002 atoms, 1001 bonds, 1 pseudobond, 129 residues, 2 models selected  

> select subtract #118

Nothing selected  

> select add #124

282 atoms, 283 bonds, 36 residues, 1 model selected  

> view matrix models
> #124,0.91665,-0.034923,-0.39816,107.69,0.049372,0.99844,0.026091,34.12,0.39663,-0.043574,0.91695,-53.143

> select subtract #124

Nothing selected  

> select add #121

1002 atoms, 1001 bonds, 1 pseudobond, 129 residues, 2 models selected  

> select subtract #121

Nothing selected  

> select add #117

282 atoms, 283 bonds, 36 residues, 1 model selected  

> view matrix models
> #117,0.91988,-0.024219,-0.39145,99.015,0.045676,0.99792,0.045596,-16.899,0.38953,-0.059822,0.91907,-49.903

> view matrix models
> #117,0.91603,-0.02896,-0.40006,102.19,0.036059,0.9993,0.010226,-8.6155,0.39948,-0.023793,0.91643,-57.457

> select add #123

564 atoms, 566 bonds, 72 residues, 2 models selected  

> select subtract #117

282 atoms, 283 bonds, 36 residues, 1 model selected  

> view matrix models
> #123,0.9285,-0.026146,-0.37042,102.21,0.047608,0.99767,0.048916,58.181,0.36828,-0.063053,0.92758,-46.245

> view matrix models
> #123,0.9281,0.00020957,-0.37233,98.188,0.015993,0.99905,0.040427,65.752,0.37198,-0.043475,0.92722,-50.218

> select clear

[Repeated 1 time(s)]

> select add #123

282 atoms, 283 bonds, 36 residues, 1 model selected  

> select subtract #123

Nothing selected  

> select add #120

1002 atoms, 1001 bonds, 1 pseudobond, 129 residues, 2 models selected  

> view matrix models
> #120,0.92841,-0.11312,-0.35392,110.3,0.090699,0.99271,-0.079353,69.809,0.36032,0.041571,0.9319,-63.019

> undo

> ui mousemode right "translate selected models"

> view matrix models
> #120,0.91402,-0.10959,-0.39059,116.52,0.090831,0.99366,-0.066248,67.833,0.39537,0.025074,0.91818,-64.754

> view matrix models
> #120,0.91402,-0.10959,-0.39059,116.38,0.090831,0.99366,-0.066248,67.839,0.39537,0.025074,0.91818,-64.465

> ui mousemode right "rotate selected models"

> view matrix models
> #120,0.92635,-0.10878,-0.36061,107.6,0.090384,0.99361,-0.067546,68.203,0.36565,0.029978,0.93027,-61.752

> select add #121

2004 atoms, 2002 bonds, 2 pseudobonds, 258 residues, 4 models selected  

> select subtract #120

1002 atoms, 1001 bonds, 1 pseudobond, 129 residues, 2 models selected  

> view matrix models
> #121,0.87287,-0.10668,-0.47615,146.63,0.079919,0.99389,-0.076168,-2.2496,0.48137,0.028431,0.87606,-73.965

> select add #123

1284 atoms, 1284 bonds, 1 pseudobond, 165 residues, 3 models selected  

> select subtract #123

1002 atoms, 1001 bonds, 1 pseudobond, 129 residues, 2 models selected  

> select subtract #121

Nothing selected  

> select add #120

1002 atoms, 1001 bonds, 1 pseudobond, 129 residues, 2 models selected  

> select subtract #120

Nothing selected  

> select add #120

1002 atoms, 1001 bonds, 1 pseudobond, 129 residues, 2 models selected  

> view matrix models
> #120,0.92387,-0.081627,-0.37391,105.64,0.084114,0.99641,-0.0096927,57.208,0.37336,-0.022496,0.92742,-52.752

> ui mousemode right "translate selected models"

> view matrix models
> #120,0.92387,-0.081627,-0.37391,105.59,0.084114,0.99641,-0.0096927,56.783,0.37336,-0.022496,0.92742,-54.21

> select add #124

1284 atoms, 1284 bonds, 1 pseudobond, 165 residues, 3 models selected  

> select subtract #124

1002 atoms, 1001 bonds, 1 pseudobond, 129 residues, 2 models selected  

> select add #118

2004 atoms, 2002 bonds, 2 pseudobonds, 258 residues, 4 models selected  

> select subtract #120

1002 atoms, 1001 bonds, 1 pseudobond, 129 residues, 2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #118,0.92351,-0.1047,-0.369,113.05,0.10165,0.99443,-0.027747,34.431,0.36985,-0.011884,0.92902,-55.978

> view matrix models
> #118,0.92103,-0.10521,-0.37502,114.88,0.10468,0.99427,-0.021841,32.641,0.37516,-0.019141,0.92676,-55.228

> select add #124

1284 atoms, 1284 bonds, 1 pseudobond, 165 residues, 3 models selected  

> select subtract #124

1002 atoms, 1001 bonds, 1 pseudobond, 129 residues, 2 models selected  

> select add #119

2004 atoms, 2002 bonds, 2 pseudobonds, 258 residues, 4 models selected  

> select subtract #119

1002 atoms, 1001 bonds, 1 pseudobond, 129 residues, 2 models selected  

> view matrix models
> #118,0.92032,-0.11143,-0.37495,116.2,0.11102,0.99356,-0.022759,31.66,0.37507,-0.020683,0.92676,-54.916

> undo

> ui mousemode right "translate selected models"

> view matrix models
> #118,0.92103,-0.10521,-0.37502,113.12,0.10468,0.99427,-0.021841,32.74,0.37516,-0.019141,0.92676,-55.659

> select add #121

2004 atoms, 2002 bonds, 2 pseudobonds, 258 residues, 4 models selected  

> select subtract #118

1002 atoms, 1001 bonds, 1 pseudobond, 129 residues, 2 models selected  

> view matrix models
> #121,0.87287,-0.10668,-0.47615,145.76,0.079919,0.99389,-0.076168,-1.8199,0.48137,0.028431,0.87606,-74.151

> select subtract #121

Nothing selected  

> select add #119

1002 atoms, 1001 bonds, 1 pseudobond, 129 residues, 2 models selected  

> view matrix models
> #119,0.89858,-0.066033,-0.43381,123.76,0.062225,0.9978,-0.022989,-36.999,0.43437,-0.0063365,0.90071,-61.107

> view matrix models
> #119,0.89858,-0.066033,-0.43381,123.83,0.062225,0.9978,-0.022989,-36.378,0.43437,-0.0063365,0.90071,-61.021

> view matrix models
> #119,0.89858,-0.066033,-0.43381,123.81,0.062225,0.9978,-0.022989,-36.606,0.43437,-0.0063365,0.90071,-60.97

> select clear

> select add #122

282 atoms, 283 bonds, 36 residues, 1 model selected  

> view matrix models
> #122,0.9043,-0.019749,-0.42643,107.34,0.03258,0.99921,0.022815,-33.206,0.42564,-0.034524,0.90423,-57.227

> select add #121

1284 atoms, 1284 bonds, 1 pseudobond, 165 residues, 3 models selected  

> select subtract #121

282 atoms, 283 bonds, 36 residues, 1 model selected  

> select subtract #122

Nothing selected  

> select add #117

282 atoms, 283 bonds, 36 residues, 1 model selected  

> view matrix models
> #117,0.91603,-0.02896,-0.40006,101.6,0.036059,0.9993,0.010226,-8.4664,0.39948,-0.023793,0.91643,-57.632

> view matrix models
> #117,0.91603,-0.02896,-0.40006,102.11,0.036059,0.9993,0.010226,-8.4766,0.39948,-0.023793,0.91643,-57.476

> view matrix models
> #117,0.91603,-0.02896,-0.40006,102.04,0.036059,0.9993,0.010226,-7.6711,0.39948,-0.023793,0.91643,-57.475

> view matrix models
> #117,0.91603,-0.02896,-0.40006,102.06,0.036059,0.9993,0.010226,-7.6802,0.39948,-0.023793,0.91643,-57.56

> ui mousemode right "rotate selected models"

> view matrix models
> #117,0.91624,-0.02555,-0.39983,101.4,0.035644,0.99921,0.017831,-9.0077,0.39905,-0.030588,0.91642,-56.324

> select clear

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Fit14-22.cxs"

> select add #121

1002 atoms, 1001 bonds, 1 pseudobond, 129 residues, 2 models selected  

> view matrix models
> #121,0.87136,-0.11557,-0.47683,147.9,0.080636,0.99238,-0.093172,1.7738,0.48396,0.042737,0.87404,-77.002

> select add #123

1284 atoms, 1284 bonds, 1 pseudobond, 165 residues, 3 models selected  

> select subtract #121

282 atoms, 283 bonds, 36 residues, 1 model selected  

> ui mousemode right "translate selected models"

> view matrix models
> #123,0.9281,0.00020957,-0.37233,98.137,0.015993,0.99905,0.040427,65.021,0.37198,-0.043475,0.92722,-49.922

> view matrix models
> #123,0.9281,0.00020957,-0.37233,97.795,0.015993,0.99905,0.040427,64.654,0.37198,-0.043475,0.92722,-50.013

> view matrix models
> #123,0.9281,0.00020957,-0.37233,97.612,0.015993,0.99905,0.040427,64.482,0.37198,-0.043475,0.92722,-50.06

> view matrix models
> #123,0.9281,0.00020957,-0.37233,97.556,0.015993,0.99905,0.040427,64.352,0.37198,-0.043475,0.92722,-49.913

> select clear

> select add #123

282 atoms, 283 bonds, 36 residues, 1 model selected  

> view matrix models
> #123,0.9281,0.00020957,-0.37233,97.356,0.015993,0.99905,0.040427,62.486,0.37198,-0.043475,0.92722,-49.919

> view matrix models
> #123,0.9281,0.00020957,-0.37233,97.044,0.015993,0.99905,0.040427,62.524,0.37198,-0.043475,0.92722,-49.641

> select add #121

1284 atoms, 1284 bonds, 1 pseudobond, 165 residues, 3 models selected  

> select subtract #121

282 atoms, 283 bonds, 36 residues, 1 model selected  

> select subtract #123

Nothing selected  

> select add #117

282 atoms, 283 bonds, 36 residues, 1 model selected  

> view matrix models
> #117,0.91624,-0.02555,-0.39983,101.02,0.035644,0.99921,0.017831,-10.63,0.39905,-0.030588,0.91642,-56.316

> view matrix models
> #117,0.91624,-0.02555,-0.39983,101.04,0.035644,0.99921,0.017831,-10.668,0.39905,-0.030588,0.91642,-56.384

> view matrix models
> #117,0.91624,-0.02555,-0.39983,101.3,0.035644,0.99921,0.017831,-10.686,0.39905,-0.030588,0.91642,-56.33

> view matrix models
> #117,0.91624,-0.02555,-0.39983,101.36,0.035644,0.99921,0.017831,-10.353,0.39905,-0.030588,0.91642,-56.315

> select add #123

564 atoms, 566 bonds, 72 residues, 2 models selected  

> select subtract #117

282 atoms, 283 bonds, 36 residues, 1 model selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #123,0.92215,-0.0042673,-0.38682,101.69,0.017046,0.99942,0.02961,64.282,0.38646,-0.033899,0.92168,-53.069

> select subtract #123

Nothing selected  

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Fit14-22.cxs"

> select add #123

282 atoms, 283 bonds, 36 residues, 1 model selected  

> ui mousemode right "translate selected models"

> view matrix models
> #123,0.92215,-0.0042673,-0.38682,101.39,0.017046,0.99942,0.02961,65.539,0.38646,-0.033899,0.92168,-53.098

> ui mousemode right "rotate selected models"

> view matrix models
> #123,0.91969,-0.050565,-0.38938,110.18,0.064011,0.99771,0.021627,58.089,0.38739,-0.044815,0.92082,-51.275

> view matrix models
> #123,0.92398,-0.037161,-0.38064,105.43,0.061329,0.99679,0.051556,53.166,0.3775,-0.070981,0.92328,-45.368

> select add #124

564 atoms, 566 bonds, 72 residues, 2 models selected  

> select subtract #123

282 atoms, 283 bonds, 36 residues, 1 model selected  

> view matrix models
> #124,0.91616,-0.03992,-0.39883,108.75,0.054203,0.99823,0.024593,33.487,0.39714,-0.044149,0.9167,-53.1

> view matrix models
> #124,0.92234,-0.031977,-0.38506,103.62,0.044769,0.9987,0.024298,35.316,0.38378,-0.03965,0.92257,-52.336

> view matrix models
> #124,0.92928,-0.018194,-0.36892,96.898,0.029584,0.99924,0.02524,38.033,0.36818,-0.034369,0.92912,-51.389

> select clear

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Fit14-22.cxs"

> select add #122

282 atoms, 283 bonds, 36 residues, 1 model selected  

> select subtract #122

Nothing selected  

> select add #119

1002 atoms, 1001 bonds, 1 pseudobond, 129 residues, 2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #119,0.89867,-0.021061,-0.43811,116.1,0.0135,0.9997,-0.020366,-27.496,0.43841,0.012388,0.89869,-64.958

> select add #124

1284 atoms, 1284 bonds, 1 pseudobond, 165 residues, 3 models selected  

> select subtract #119

282 atoms, 283 bonds, 36 residues, 1 model selected  

> view matrix models
> #124,0.92546,-0.080234,-0.37025,108.39,0.09408,0.99537,0.019459,27.092,0.36698,-0.052841,0.92873,-47.955

> select add #116

1566 atoms, 1567 bonds, 1 pseudobond, 201 residues, 3 models selected  

> select subtract #116

282 atoms, 283 bonds, 36 residues, 1 model selected  

> select subtract #124

Nothing selected  

> select add #123

282 atoms, 283 bonds, 36 residues, 1 model selected  

> view matrix models
> #123,0.92216,-0.061529,-0.38188,110.14,0.087812,0.99479,0.051767,48.258,0.3767,-0.08127,0.92276,-43.373

> select add #121

1284 atoms, 1284 bonds, 1 pseudobond, 165 residues, 3 models selected  

> select subtract #123

1002 atoms, 1001 bonds, 1 pseudobond, 129 residues, 2 models selected  

> view matrix models
> #121,0.87298,-0.078357,-0.48143,141.41,0.040581,0.99526,-0.088401,8.4814,0.48607,0.057635,0.87202,-79.863

> view matrix models
> #121,0.87271,-0.087712,-0.48029,143.02,0.050651,0.99469,-0.089619,6.7697,0.4856,0.053884,0.87252,-79.153

> ui mousemode right "translate selected models"

> view matrix models
> #121,0.87271,-0.087712,-0.48029,143.68,0.050651,0.99469,-0.089619,6.8585,0.4856,0.053884,0.87252,-78.888

> ui mousemode right "rotate selected models"

> view matrix models
> #121,0.87369,-0.081045,-0.47969,142.09,0.055882,0.99622,-0.066535,0.80429,0.48326,0.031325,0.87491,-74.595

> select add #123

1284 atoms, 1284 bonds, 1 pseudobond, 165 residues, 3 models selected  

> select subtract #121

282 atoms, 283 bonds, 36 residues, 1 model selected  

> ui mousemode right "translate selected models"

> view matrix models
> #123,0.92216,-0.061529,-0.38188,110.46,0.087812,0.99479,0.051767,48.637,0.3767,-0.08127,0.92276,-44.16

> view matrix models
> #123,0.92216,-0.061529,-0.38188,110.45,0.087812,0.99479,0.051767,48.841,0.3767,-0.08127,0.92276,-44.175

> select add #122

564 atoms, 566 bonds, 72 residues, 2 models selected  

> select subtract #123

282 atoms, 283 bonds, 36 residues, 1 model selected  

> select subtract #122

Nothing selected  

> select add #119

1002 atoms, 1001 bonds, 1 pseudobond, 129 residues, 2 models selected  

> ui mousemode right "rotate selected models"

> ui mousemode right "translate selected models"

> view matrix models
> #119,0.89867,-0.021061,-0.43811,117.04,0.0135,0.9997,-0.020366,-27.942,0.43841,0.012388,0.89869,-64.365

> select add #122

1284 atoms, 1284 bonds, 1 pseudobond, 165 residues, 3 models selected  

> select subtract #119

282 atoms, 283 bonds, 36 residues, 1 model selected  

> select add #124

564 atoms, 566 bonds, 72 residues, 2 models selected  

> select subtract #122

282 atoms, 283 bonds, 36 residues, 1 model selected  

> view matrix models
> #124,0.92546,-0.080234,-0.37025,107.03,0.09408,0.99537,0.019459,26.987,0.36698,-0.052841,0.92873,-48.381

> view matrix models
> #124,0.92546,-0.080234,-0.37025,107.39,0.09408,0.99537,0.019459,27.064,0.36698,-0.052841,0.92873,-48.269

> show #!115 models

> hide #!115 models

> select add #116

1566 atoms, 1567 bonds, 1 pseudobond, 201 residues, 3 models selected  

> select subtract #116

282 atoms, 283 bonds, 36 residues, 1 model selected  

> select add #115

564 atoms, 566 bonds, 72 residues, 2 models selected  

> show #!115 models

> select subtract #124

282 atoms, 283 bonds, 36 residues, 1 model selected  

> view matrix models
> #115,0.92727,0.31203,0.20691,-95.353,-0.28838,0.9477,-0.13679,33.838,-0.23877,0.067168,0.96875,36.2

> view matrix models
> #115,0.92727,0.31203,0.20691,-95.535,-0.28838,0.9477,-0.13679,33.067,-0.23877,0.067168,0.96875,36.01

> view matrix models
> #115,0.92727,0.31203,0.20691,-95.507,-0.28838,0.9477,-0.13679,33.439,-0.23877,0.067168,0.96875,36.055

> combine #15-18,115

Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID '6' in copy of copy of pointy-1pf.pdb #115 to '0'  

> select subtract #115

Nothing selected  

> hide #!115 models

> hide #!116 models

> color #125 #0096ffff

> select add #122

282 atoms, 283 bonds, 36 residues, 1 model selected  

> select add #119

1284 atoms, 1284 bonds, 1 pseudobond, 165 residues, 3 models selected  

> select subtract #122

1002 atoms, 1001 bonds, 1 pseudobond, 129 residues, 2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #119,0.8901,-0.10474,-0.44357,135.86,0.09777,0.99446,-0.038631,-40.538,0.44515,-0.0089816,0.89541,-61.01

> view matrix models
> #119,0.89191,-0.08955,-0.44326,132.53,0.080737,0.99598,-0.038758,-37.305,0.44495,-0.001219,0.89556,-62.478

> select add #123

1284 atoms, 1284 bonds, 1 pseudobond, 165 residues, 3 models selected  

> select subtract #119

282 atoms, 283 bonds, 36 residues, 1 model selected  

> view matrix models
> #123,0.92549,-0.012914,-0.37856,100.96,0.038441,0.99746,0.059952,56.562,0.37682,-0.070037,0.92363,-46.261

> select clear

> select add #124

282 atoms, 283 bonds, 36 residues, 1 model selected  

> view matrix models
> #124,0.92777,-0.058108,-0.36859,102.88,0.071217,0.99722,0.022047,30.762,0.36629,-0.046705,0.92933,-49.284

> select add #122

564 atoms, 566 bonds, 72 residues, 2 models selected  

> select subtract #124

282 atoms, 283 bonds, 36 residues, 1 model selected  

> select subtract #122

Nothing selected  

> select add #119

1002 atoms, 1001 bonds, 1 pseudobond, 129 residues, 2 models selected  

> view matrix models
> #119,0.88903,-0.11848,-0.44225,138.43,0.11014,0.99292,-0.044584,-41.575,0.4444,-0.0090734,0.89578,-60.914

> ui mousemode right "translate selected models"

> view matrix models
> #119,0.88903,-0.11848,-0.44225,138.96,0.11014,0.99292,-0.044584,-43.532,0.4444,-0.0090734,0.89578,-60.784

> view matrix models
> #119,0.88903,-0.11848,-0.44225,137.68,0.11014,0.99292,-0.044584,-41.245,0.4444,-0.0090734,0.89578,-61.113

> ui mousemode right "rotate selected models"

> view matrix models
> #119,0.89196,-0.08897,-0.44328,131.67,0.080148,0.99603,-0.038641,-36.887,0.44496,-0.0010616,0.89555,-62.708

> view matrix models
> #119,0.89181,-0.090451,-0.44327,131.98,0.081974,0.9959,-0.038294,-37.307,0.44492,-0.0021859,0.89557,-62.489

> select add #124

1284 atoms, 1284 bonds, 1 pseudobond, 165 residues, 3 models selected  

> select subtract #119

282 atoms, 283 bonds, 36 residues, 1 model selected  

> view matrix models
> #124,0.92782,-0.051919,-0.36941,101.98,0.071293,0.99669,0.038979,27.663,0.36616,-0.062501,0.92845,-46.424

> select subtract #124

Nothing selected  

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Fit14-22.cxs"

Drag select of 8 postprocess_masked330_onepf.mrc , 414 residues, 4 pseudobonds  
Drag select of 8 postprocess_masked330_onepf.mrc , 214 residues  
Drag select of 8 postprocess_masked330_onepf.mrc , 337 residues, 2 pseudobonds  
Drag select of 8 postprocess_masked330_onepf.mrc , 359 residues, 4 pseudobonds  
Drag select of 8 postprocess_masked330_onepf.mrc , 376 residues, 4 pseudobonds  

> select clear

> select add #123

282 atoms, 283 bonds, 36 residues, 1 model selected  

> ui mousemode right "translate selected models"

> view matrix models
> #123,0.92549,-0.012914,-0.37856,99.838,0.038441,0.99746,0.059952,55.462,0.37682,-0.070037,0.92363,-46.487

> view matrix models
> #123,0.92549,-0.012914,-0.37856,99.476,0.038441,0.99746,0.059952,55.326,0.37682,-0.070037,0.92363,-47.44

> select add #121

1284 atoms, 1284 bonds, 1 pseudobond, 165 residues, 3 models selected  

> select subtract #123

1002 atoms, 1001 bonds, 1 pseudobond, 129 residues, 2 models selected  

> view matrix models
> #121,0.87369,-0.081045,-0.47969,142.58,0.055882,0.99622,-0.066535,0.25016,0.48326,0.031325,0.87491,-74.476

> select clear

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Fit14-22.cxs"

> select clear

> select add #124

282 atoms, 283 bonds, 36 residues, 1 model selected  

> view matrix models
> #124,0.92782,-0.051919,-0.36941,102.21,0.071293,0.99669,0.038979,27.588,0.36616,-0.062501,0.92845,-46.929

> select clear

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Fit14-22.cxs"

> hide #!8 models

Drag select of 825 residues, 5 pseudobonds  

> ui tool show "Color Zone"

> show #!8 models

> color zone #8 near sel distance 9.04

> select clear

> select #8

2 models selected  

> color #8.1 dark gray

> transparency #8.1 50

> select clear

> select add #123

282 atoms, 283 bonds, 36 residues, 1 model selected  

> select subtract #123

Nothing selected  

> select add #120

1002 atoms, 1001 bonds, 1 pseudobond, 129 residues, 2 models selected  

> view matrix models
> #120,0.92387,-0.081627,-0.37391,105.8,0.084114,0.99641,-0.0096927,56.633,0.37336,-0.022496,0.92742,-55.111

> select clear

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Fit14-22.cxs"

> select add #121

1002 atoms, 1001 bonds, 1 pseudobond, 129 residues, 2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #121,0.87299,-0.10805,-0.47561,147.04,0.083504,0.99387,-0.072516,-3.759,0.48053,0.02359,0.87666,-72.795

> ui mousemode right "translate selected models"

> view matrix models
> #121,0.87299,-0.10805,-0.47561,147.6,0.083504,0.99387,-0.072516,-4.1159,0.48053,0.02359,0.87666,-72.597

> view matrix models
> #121,0.87299,-0.10805,-0.47561,146.54,0.083504,0.99387,-0.072516,-4.2049,0.48053,0.02359,0.87666,-72.807

> view matrix models
> #121,0.87299,-0.10805,-0.47561,146.46,0.083504,0.99387,-0.072516,-4.5364,0.48053,0.02359,0.87666,-72.839

> view matrix models
> #121,0.87299,-0.10805,-0.47561,146.51,0.083504,0.99387,-0.072516,-4.8739,0.48053,0.02359,0.87666,-72.815

> view matrix models
> #121,0.87299,-0.10805,-0.47561,146.64,0.083504,0.99387,-0.072516,-4.9295,0.48053,0.02359,0.87666,-72.784

> select clear

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Fit14-22.cxs"

> select add #125

1284 atoms, 1284 bonds, 1 pseudobond, 165 residues, 2 models selected  

> select subtract #125

Nothing selected  

> select add #125

1284 atoms, 1284 bonds, 1 pseudobond, 165 residues, 2 models selected  

> select subtract #125

Nothing selected  

> show #!116 models

> hide #!116 models

> show #!115 models

> select add #115

282 atoms, 283 bonds, 36 residues, 1 model selected  

> view matrix models
> #115,0.92727,0.31203,0.20691,-95.167,-0.28838,0.9477,-0.13679,34.62,-0.23877,0.067168,0.96875,36.188

> select subtract #115

Nothing selected  

> show #!116 models

> combine #15-18,115

Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID '6' in copy of copy of pointy-1pf.pdb #115 to '0'  

> hide #!115 models

> hide #!116 models

> show #!116 models

> hide #!125 models

> show #!125 models

> hide #!116 models

> show #!116 models

> hide #!116 models

> show #!116 models

> hide #!116 models

> hide #!126 models

> show #!126 models

> hide #!125 models

> color #126 #0433ffff

> color #126 #73fdffff

> select add #121

1002 atoms, 1001 bonds, 1 pseudobond, 129 residues, 2 models selected  

> select add #120

2004 atoms, 2002 bonds, 2 pseudobonds, 258 residues, 4 models selected  

> select subtract #120

1002 atoms, 1001 bonds, 1 pseudobond, 129 residues, 2 models selected  

> select add #119

2004 atoms, 2002 bonds, 2 pseudobonds, 258 residues, 4 models selected  

> view matrix models
> #119,0.89181,-0.090451,-0.44327,129.1,0.081974,0.9959,-0.038294,-36.844,0.44492,-0.0021859,0.89557,-63.207,#121,0.87299,-0.10805,-0.47561,143.77,0.083504,0.99387,-0.072516,-4.4672,0.48053,0.02359,0.87666,-73.501

> ui mousemode right "rotate selected models"

> view matrix models
> #119,0.8949,-0.044758,-0.44401,119.32,0.035898,0.99895,-0.028347,-29.958,0.44482,0.0094288,0.89557,-65.55,#121,0.8762,-0.062417,-0.4779,135.44,0.037875,0.99743,-0.060831,1.8313,0.48047,0.0352,0.87631,-75.486

> ui mousemode right "translate selected models"

> view matrix models
> #119,0.8949,-0.044758,-0.44401,119.68,0.035898,0.99895,-0.028347,-29.609,0.44482,0.0094288,0.89557,-65.453,#121,0.8762,-0.062417,-0.4779,135.8,0.037875,0.99743,-0.060831,2.1796,0.48047,0.0352,0.87631,-75.389

> select subtract #119

1002 atoms, 1001 bonds, 1 pseudobond, 129 residues, 2 models selected  

> view matrix models
> #121,0.8762,-0.062417,-0.4779,135.6,0.037875,0.99743,-0.060831,2.2551,0.48047,0.0352,0.87631,-74.477

> view matrix models
> #121,0.8762,-0.062417,-0.4779,135.73,0.037875,0.99743,-0.060831,2.2735,0.48047,0.0352,0.87631,-74.788

> select add #122

1284 atoms, 1284 bonds, 1 pseudobond, 165 residues, 3 models selected  

> select subtract #121

282 atoms, 283 bonds, 36 residues, 1 model selected  

> select add #119

1284 atoms, 1284 bonds, 1 pseudobond, 165 residues, 3 models selected  

> select subtract #122

1002 atoms, 1001 bonds, 1 pseudobond, 129 residues, 2 models selected  

> view matrix models
> #119,0.8949,-0.044758,-0.44401,119.71,0.035898,0.99895,-0.028347,-29.488,0.44482,0.0094288,0.89557,-66.481

> volume #8 level 0.007923

> select add #120

2004 atoms, 2002 bonds, 2 pseudobonds, 258 residues, 4 models selected  

> select subtract #119

1002 atoms, 1001 bonds, 1 pseudobond, 129 residues, 2 models selected  

> select subtract #120

Nothing selected  

> select add #123

282 atoms, 283 bonds, 36 residues, 1 model selected  

> view matrix models
> #123,0.92549,-0.012914,-0.37856,100.69,0.038441,0.99746,0.059952,55.009,0.37682,-0.070037,0.92363,-47.169

> show #!115 models

> hide #!115 models

> show #!105 models

> hide #!105 models

> select add #119

1284 atoms, 1284 bonds, 1 pseudobond, 165 residues, 3 models selected  

> select subtract #123

1002 atoms, 1001 bonds, 1 pseudobond, 129 residues, 2 models selected  

> select add #121

2004 atoms, 2002 bonds, 2 pseudobonds, 258 residues, 4 models selected  

> view matrix models
> #119,0.8949,-0.044758,-0.44401,120.86,0.035898,0.99895,-0.028347,-30.58,0.44482,0.0094288,0.89557,-66.263,#121,0.8762,-0.062417,-0.4779,136.87,0.037875,0.99743,-0.060831,1.1815,0.48047,0.0352,0.87631,-74.57

> view matrix models
> #119,0.8949,-0.044758,-0.44401,121.36,0.035898,0.99895,-0.028347,-30.596,0.44482,0.0094288,0.89557,-66.061,#121,0.8762,-0.062417,-0.4779,137.38,0.037875,0.99743,-0.060831,1.1648,0.48047,0.0352,0.87631,-74.368

> select add #123

2286 atoms, 2285 bonds, 2 pseudobonds, 294 residues, 5 models selected  

> select subtract #121

1284 atoms, 1284 bonds, 1 pseudobond, 165 residues, 3 models selected  

> select subtract #119

282 atoms, 283 bonds, 36 residues, 1 model selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #123,0.92104,-0.059003,-0.38496,110.55,0.084613,0.99516,0.049915,48.201,0.38015,-0.078546,0.92158,-46

> view matrix models
> #123,0.91194,-0.068577,-0.40455,117.63,0.12514,0.98545,0.11503,29.677,0.39078,-0.15553,0.90725,-32.389

> select add #124

564 atoms, 566 bonds, 72 residues, 2 models selected  

> select subtract #123

282 atoms, 283 bonds, 36 residues, 1 model selected  

> view matrix models
> #124,0.94022,-0.046567,-0.33738,92.864,0.069863,0.99591,0.057236,24.581,0.33333,-0.077385,0.93963,-40.053

> view matrix models
> #124,0.87002,-0.039375,-0.49145,134.31,0.099563,0.9903,0.096914,12.257,0.48287,-0.13325,0.8655,-46.116

> view matrix models
> #124,0.91711,-0.033902,-0.39719,106.47,0.046804,0.99864,0.022833,35.098,0.39587,-0.03953,0.91745,-54.593

> undo

[Repeated 1 time(s)]

> select add #126

1566 atoms, 1567 bonds, 1 pseudobond, 201 residues, 3 models selected  

> select subtract #124

1284 atoms, 1284 bonds, 1 pseudobond, 165 residues, 2 models selected  

> view matrix models
> #126,0.93098,-0.0098259,-0.36495,90.44,0.031282,0.99811,0.052926,8.5109,0.36374,-0.060689,0.92952,-45.694

> undo

> select subtract #126

Nothing selected  

> show #!116 models

> hide #!116 models

> show #!115 models

> select add #115

282 atoms, 283 bonds, 36 residues, 1 model selected  

> view matrix models
> #115,0.92218,0.33214,0.19815,-97.622,-0.3168,0.94259,-0.10562,35.55,-0.22186,0.034621,0.97446,40.071

> view matrix models
> #115,0.91431,0.35997,0.18562,-100.78,-0.35204,0.93296,-0.075181,39.108,-0.20024,0.0033923,0.97974,42.781

> view matrix models
> #115,0.91434,0.35986,0.18572,-100.77,-0.35685,0.93279,-0.050579,35.411,-0.19144,-0.020027,0.9813,46.721

> ui mousemode right "translate selected models"

> view matrix models
> #115,0.91434,0.35986,0.18572,-100.57,-0.35685,0.93279,-0.050579,35.554,-0.19144,-0.020027,0.9813,46.195

> select add #124

564 atoms, 566 bonds, 72 residues, 2 models selected  

> select subtract #115

282 atoms, 283 bonds, 36 residues, 1 model selected  

> view matrix models
> #124,0.94022,-0.046567,-0.33738,92.97,0.069863,0.99591,0.057236,25.003,0.33333,-0.077385,0.93963,-40.463

> view matrix models
> #124,0.94022,-0.046567,-0.33738,92.903,0.069863,0.99591,0.057236,24.874,0.33333,-0.077385,0.93963,-40.235

> ui mousemode right "rotate selected models"

> view matrix models
> #124,0.94213,-0.041922,-0.33263,90.854,0.070585,0.99472,0.074555,21.69,0.32775,-0.093719,0.94011,-36.464

> view matrix models
> #124,0.91777,-0.017004,-0.39674,103.44,0.038185,0.99823,0.045549,32.899,0.39527,-0.056953,0.9168,-51.587

> ui mousemode right "translate selected models"

> view matrix models
> #124,0.91777,-0.017004,-0.39674,102.99,0.038185,0.99823,0.045549,31.723,0.39527,-0.056953,0.9168,-50.83

> view matrix models
> #124,0.91777,-0.017004,-0.39674,103.51,0.038185,0.99823,0.045549,32.046,0.39527,-0.056953,0.9168,-50.866

> select add #123

564 atoms, 566 bonds, 72 residues, 2 models selected  

> select subtract #124

282 atoms, 283 bonds, 36 residues, 1 model selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #123,0.91066,-0.075486,-0.4062,119.36,0.12474,0.98752,0.096146,32.943,0.39388,-0.13823,0.90871,-36.197

> combine #15-18,115

Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID '6' in copy of copy of pointy-1pf.pdb #115 to '0'  

> hide #!115 models

> hide #!126 models

> close #125-126

> color #127 #00fa92ff

> select add #121

1284 atoms, 1284 bonds, 1 pseudobond, 165 residues, 3 models selected  

> select subtract #121

282 atoms, 283 bonds, 36 residues, 1 model selected  

> select add #117

564 atoms, 566 bonds, 72 residues, 2 models selected  

> select subtract #123

282 atoms, 283 bonds, 36 residues, 1 model selected  

> view matrix models
> #117,0.91729,-0.00669,-0.39815,97.653,0.033935,0.99753,0.061422,-17.902,0.39676,-0.069853,0.91526,-49.01

> ui mousemode right "translate selected models"

> view matrix models
> #117,0.91729,-0.00669,-0.39815,97.472,0.033935,0.99753,0.061422,-18.153,0.39676,-0.069853,0.91526,-48.362

> select subtract #117

Nothing selected  

> select add #122

282 atoms, 283 bonds, 36 residues, 1 model selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #122,0.90875,0.00045019,-0.41735,101.35,0.032501,0.99689,0.071844,-41.984,0.41608,-0.078853,0.9059,-48.166

> select subtract #122

Nothing selected  

> show #!115 models

> hide #!115 models

> show #!105 models

> hide #!105 models

> select add #121

1002 atoms, 1001 bonds, 1 pseudobond, 129 residues, 2 models selected  

> view matrix models
> #121,0.89889,0.012427,-0.438,110.35,0.043345,0.99217,0.11711,-35.095,0.43603,-0.12425,0.89131,-37.897

> view matrix models
> #121,0.89767,-0.023967,-0.44002,117.95,0.063498,0.99513,0.075335,-31.314,0.43608,-0.095566,0.89482,-44.086

> ui mousemode right "translate selected models"

> view matrix models
> #121,0.89767,-0.023967,-0.44002,118.67,0.063498,0.99513,0.075335,-30.069,0.43608,-0.095566,0.89482,-46.27

> view matrix models
> #121,0.89767,-0.023967,-0.44002,119.6,0.063498,0.99513,0.075335,-29.951,0.43608,-0.095566,0.89482,-45.795

> ui mousemode right "rotate selected models"

> view matrix models
> #121,0.89445,-0.062965,-0.4427,128.24,0.096433,0.9939,0.053474,-32.039,0.43664,-0.090522,0.89507,-46.922

> ui mousemode right "translate selected models"

> view matrix models
> #121,0.89445,-0.062965,-0.4427,126.63,0.096433,0.9939,0.053474,-32.049,0.43664,-0.090522,0.89507,-47.285

> ui mousemode right "rotate selected models"

> view matrix models
> #121,0.89614,-0.058446,-0.43991,124.86,0.077744,0.99664,0.02596,-23.144,0.43691,-0.057464,0.89767,-54.17

> view matrix models
> #121,0.92861,-0.057477,-0.36659,103.11,0.052178,0.99834,-0.024357,-7.9996,0.36738,0.0034897,0.93006,-58.089

> view matrix models
> #121,0.91814,-0.082705,-0.38752,114.32,-0.01244,0.97148,-0.23681,53.538,0.39605,0.22224,0.89093,-97.726

> view matrix models
> #121,0.87635,-0.13011,-0.46378,147.43,0.034912,0.97745,-0.20825,36.875,0.48041,0.16631,0.86113,-98.336

> view matrix models
> #121,0.88329,-0.11319,-0.45495,140.98,0.047816,0.98711,-0.15276,21.116,0.46638,0.11318,0.87732,-88.614

> ui mousemode right "translate selected models"

> view matrix models
> #121,0.88329,-0.11319,-0.45495,139.97,0.047816,0.98711,-0.15276,20.11,0.46638,0.11318,0.87732,-85.783

> view matrix models
> #121,0.88329,-0.11319,-0.45495,141.39,0.047816,0.98711,-0.15276,20.917,0.46638,0.11318,0.87732,-86.485

> view matrix models
> #121,0.88329,-0.11319,-0.45495,140.66,0.047816,0.98711,-0.15276,22.078,0.46638,0.11318,0.87732,-86.54

> ui mousemode right "rotate selected models"

> view matrix models
> #121,0.88408,-0.089957,-0.45859,136.81,0.027969,0.98972,-0.14022,23.109,0.46649,0.11114,0.87751,-86.216

> ui mousemode right "translate selected models"

> view matrix models
> #121,0.88408,-0.089957,-0.45859,138.31,0.027969,0.98972,-0.14022,21.715,0.46649,0.11114,0.87751,-86.196

> view matrix models
> #121,0.88408,-0.089957,-0.45859,138.26,0.027969,0.98972,-0.14022,21.65,0.46649,0.11114,0.87751,-86.141

> ui mousemode right "rotate selected models"

> view matrix models
> #121,0.88802,-0.048413,-0.45725,129.26,0.021548,0.99773,-0.06379,5.9197,0.4593,0.046794,0.88705,-74.334

> ui mousemode right "translate selected models"

> view matrix models
> #121,0.88802,-0.048413,-0.45725,128.77,0.021548,0.99773,-0.06379,7.0849,0.4593,0.046794,0.88705,-73.919

> ui mousemode right "rotate selected models"

> view matrix models
> #121,0.88646,-0.035583,-0.46144,127.5,-0.046374,0.98519,-0.16506,43.99,0.46048,0.16772,0.87168,-94.091

> view matrix models
> #121,0.86295,-0.056907,-0.50207,144.64,0.029489,0.99762,-0.062389,5.1914,0.50442,0.039033,0.86257,-76.736

> view matrix models
> #121,0.88854,-0.04248,-0.45683,127.45,-0.012706,0.99304,-0.11706,25.83,0.45862,0.10981,0.88182,-84.731

> view matrix models
> #121,0.88978,-0.10071,-0.44515,135.92,0.037356,0.98815,-0.1489,22.951,0.45487,0.11586,0.88299,-85.35

> view matrix models
> #121,0.86878,-0.10464,-0.48401,148.87,0.031943,0.98723,-0.1561,25.699,0.49416,0.12015,0.86103,-89.777

> ui mousemode right "translate selected models"

> view matrix models
> #121,0.86878,-0.10464,-0.48401,147.98,0.031943,0.98723,-0.1561,25.404,0.49416,0.12015,0.86103,-89.668

> ui mousemode right "rotate selected models"

> view matrix models
> #121,0.86331,-0.11097,-0.49232,152,0.069643,0.99239,-0.10156,5.6019,0.49984,0.053389,0.86447,-78.808

> view matrix models
> #121,0.8853,-0.087163,-0.45678,135.73,0.042486,0.99333,-0.1072,12.146,0.46307,0.075502,0.8831,-79.256

> view matrix models
> #121,0.8833,-0.11119,-0.45543,140.45,0.080096,0.99298,-0.087079,0.4029,0.46192,0.040438,0.886,-72.924

> ui mousemode right "translate selected models"

> view matrix models
> #121,0.8833,-0.11119,-0.45543,139.69,0.080096,0.99298,-0.087079,-1.3014,0.46192,0.040438,0.886,-74.029

> view matrix models
> #121,0.8833,-0.11119,-0.45543,139.77,0.080096,0.99298,-0.087079,-1.1626,0.46192,0.040438,0.886,-74.039

> ui mousemode right "move picked models"

> ui mousemode right "rotate selected models"

> view matrix models
> #121,0.88544,-0.084378,-0.45702,134.54,0.055692,0.99556,-0.075906,1.0876,0.4614,0.041758,0.88621,-74.227

> select add #123

1284 atoms, 1284 bonds, 1 pseudobond, 165 residues, 3 models selected  

> select subtract #121

282 atoms, 283 bonds, 36 residues, 1 model selected  

> view matrix models
> #123,0.91361,-0.05461,-0.4029,114.63,0.10421,0.98929,0.10222,35.541,0.393,-0.13538,0.90952,-36.658

> ui mousemode right "translate selected models"

> view matrix models
> #123,0.91361,-0.05461,-0.4029,114.92,0.10421,0.98929,0.10222,36.709,0.393,-0.13538,0.90952,-36.547

> select add #122

564 atoms, 566 bonds, 72 residues, 2 models selected  

> select subtract #122

282 atoms, 283 bonds, 36 residues, 1 model selected  

> select add #119

1284 atoms, 1284 bonds, 1 pseudobond, 165 residues, 3 models selected  

> select subtract #123

1002 atoms, 1001 bonds, 1 pseudobond, 129 residues, 2 models selected  

> view matrix models
> #119,0.8949,-0.044758,-0.44401,122.94,0.035898,0.99895,-0.028347,-30.555,0.44482,0.0094288,0.89557,-66.044

> ui mousemode right "rotate selected models"

> view matrix models
> #119,0.839,-0.049578,-0.54187,155.21,0.065711,0.99778,0.01045,-44.334,0.54015,-0.044374,0.8404,-64.16

> view matrix models
> #119,0.83899,-0.11583,-0.53168,165.77,0.071402,0.99207,-0.10345,-21.279,0.53945,0.048834,0.8406,-81.824

> ui mousemode right zoom

> ui mousemode right "translate selected models"

> view matrix models
> #119,0.83899,-0.11583,-0.53168,166.27,0.071402,0.99207,-0.10345,-20.559,0.53945,0.048834,0.8406,-81.628

> ui mousemode right "rotate selected models"

> view matrix models
> #119,0.83985,-0.07496,-0.53761,159.51,0.026332,0.99488,-0.09758,-13.033,0.54218,0.067796,0.83753,-85.179

> view matrix models
> #119,0.83348,-0.127,-0.53775,170.76,0.080703,0.99077,-0.10891,-21.115,0.54662,0.047373,0.83604,-81.896

> ui mousemode right "translate selected models"

> view matrix models
> #119,0.83348,-0.127,-0.53775,170.4,0.080703,0.99077,-0.10891,-21.351,0.54662,0.047373,0.83604,-82.065

> ui mousemode right "rotate selected models"

> view matrix models
> #119,0.72918,-0.13718,-0.67043,220.7,0.038124,0.98632,-0.16035,-1.3123,0.68326,0.091361,0.72444,-95.844

> view matrix models
> #119,0.81287,-0.12714,-0.5684,180.88,0.048912,0.98734,-0.1509,-5.6383,0.58039,0.094864,0.80879,-92.519

> view matrix models
> #119,0.81375,-0.13377,-0.56562,181.4,0.061593,0.98752,-0.14494,-9.4879,0.57795,0.083109,0.81183,-90.394

> select add #123

1284 atoms, 1284 bonds, 1 pseudobond, 165 residues, 3 models selected  

> select subtract #123

1002 atoms, 1001 bonds, 1 pseudobond, 129 residues, 2 models selected  

> select add #120

2004 atoms, 2002 bonds, 2 pseudobonds, 258 residues, 4 models selected  

> select subtract #119

1002 atoms, 1001 bonds, 1 pseudobond, 129 residues, 2 models selected  

> view matrix models
> #120,0.9231,-0.086863,-0.37462,107.1,0.089332,0.99594,-0.010807,55.876,0.37404,-0.02349,0.92711,-55.001

> ui mousemode right "rotate selected models"

> ui mousemode right "translate selected models"

> view matrix models
> #120,0.9231,-0.086863,-0.37462,108.8,0.089332,0.99594,-0.010807,57.179,0.37404,-0.02349,0.92711,-54.497

> view matrix models
> #120,0.9231,-0.086863,-0.37462,110.1,0.089332,0.99594,-0.010807,58,0.37404,-0.02349,0.92711,-54.051

> view matrix models
> #120,0.9231,-0.086863,-0.37462,110.67,0.089332,0.99594,-0.010807,55.951,0.37404,-0.02349,0.92711,-53.945

> select add #121

2004 atoms, 2002 bonds, 2 pseudobonds, 258 residues, 4 models selected  

> select subtract #120

1002 atoms, 1001 bonds, 1 pseudobond, 129 residues, 2 models selected  

> view matrix models
> #121,0.88544,-0.084378,-0.45702,134.87,0.055692,0.99556,-0.075906,2.0157,0.4614,0.041758,0.88621,-74

> select add #122

1284 atoms, 1284 bonds, 1 pseudobond, 165 residues, 3 models selected  

> select subtract #121

282 atoms, 283 bonds, 36 residues, 1 model selected  

> select subtract #122

Nothing selected  

> select add #119

1002 atoms, 1001 bonds, 1 pseudobond, 129 residues, 2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #119,0.81422,-0.14339,-0.56258,182.52,0.06003,0.98462,-0.16407,-4.7294,0.57745,0.099818,0.8103,-93.166

> ui mousemode right "translate selected models"

> view matrix models
> #119,0.81422,-0.14339,-0.56258,182.4,0.06003,0.98462,-0.16407,-4.7258,0.57745,0.099818,0.8103,-92.79

> select add #118

2004 atoms, 2002 bonds, 2 pseudobonds, 258 residues, 4 models selected  

> select subtract #118

1002 atoms, 1001 bonds, 1 pseudobond, 129 residues, 2 models selected  

> select subtract #119

Nothing selected  

> select add #124

282 atoms, 283 bonds, 36 residues, 1 model selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #124,0.91794,-0.0081059,-0.39665,101.95,0.038646,0.99686,0.069064,27.781,0.39484,-0.078725,0.91537,-46.834

> select add #120

1284 atoms, 1284 bonds, 1 pseudobond, 165 residues, 3 models selected  

> select add #119

2286 atoms, 2285 bonds, 2 pseudobonds, 294 residues, 5 models selected  

> select subtract #119

1284 atoms, 1284 bonds, 1 pseudobond, 165 residues, 3 models selected  

> select subtract #120

282 atoms, 283 bonds, 36 residues, 1 model selected  

> select subtract #124

Nothing selected  

> select add #120

1002 atoms, 1001 bonds, 1 pseudobond, 129 residues, 2 models selected  

> view matrix models
> #120,0.95689,-0.10419,-0.27113,86.014,0.09717,0.99449,-0.039222,60.389,0.27372,0.011186,0.96174,-46.986

> view matrix models
> #120,0.94496,-0.079262,-0.31743,93.114,0.073446,0.99684,-0.030267,62.995,0.31882,0.0052875,0.9478,-52.292

> undo

> view matrix models
> #120,0.92633,-0.065721,-0.37094,105.23,0.061648,0.99784,-0.02284,63.719,0.37164,-0.0017109,0.92838,-57.859

> ui mousemode right "translate selected models"

> view matrix models
> #120,0.92633,-0.065721,-0.37094,105.62,0.061648,0.99784,-0.02284,64.88,0.37164,-0.0017109,0.92838,-57.769

> view matrix models
> #120,0.92633,-0.065721,-0.37094,104.55,0.061648,0.99784,-0.02284,63.832,0.37164,-0.0017109,0.92838,-55.601

> volume #8 level 0.01214

> ui mousemode right "rotate selected models"

> view matrix models
> #120,0.91258,-0.070384,-0.4028,114.73,0.068723,0.99746,-0.018595,61.588,0.40308,-0.010712,0.9151,-57.646

> select add #122

1284 atoms, 1284 bonds, 1 pseudobond, 165 residues, 3 models selected  

> select subtract #122

1002 atoms, 1001 bonds, 1 pseudobond, 129 residues, 2 models selected  

> select subtract #120

Nothing selected  

> select add #119

1002 atoms, 1001 bonds, 1 pseudobond, 129 residues, 2 models selected  

> view matrix models
> #119,0.81339,-0.13712,-0.56533,181.93,0.053278,0.9853,-0.16232,-3.8245,0.57927,0.10191,0.80874,-93.246

> undo

> ui mousemode right "translate selected models"

> view matrix models
> #119,0.81422,-0.14339,-0.56258,181.58,0.06003,0.98462,-0.16407,-4.2519,0.57745,0.099818,0.8103,-90.599

> ui mousemode right "rotate selected models"

> view matrix models
> #119,0.81811,-0.12992,-0.5602,177.74,0.067954,0.98916,-0.13016,-13.632,0.57104,0.068415,0.81807,-84.874

> ui mousemode right "translate selected models"

> view matrix models
> #119,0.81811,-0.12992,-0.5602,178.05,0.067954,0.98916,-0.13016,-13.354,0.57104,0.068415,0.81807,-85.534

> select add #123

1284 atoms, 1284 bonds, 1 pseudobond, 165 residues, 3 models selected  

> select add #121

2286 atoms, 2285 bonds, 2 pseudobonds, 294 residues, 5 models selected  

> select subtract #119

1284 atoms, 1284 bonds, 1 pseudobond, 165 residues, 3 models selected  

> view matrix models
> #121,0.88544,-0.084378,-0.45702,134.78,0.055692,0.99556,-0.075906,3.6556,0.4614,0.041758,0.88621,-73.791,#123,0.91361,-0.05461,-0.4029,114.83,0.10421,0.98929,0.10222,38.349,0.393,-0.13538,0.90952,-36.338

> ui mousemode right "rotate selected models"

> view matrix models
> #121,0.88894,-0.049699,-0.45531,126.38,0.023099,0.9977,-0.063803,7.4999,0.45743,0.0462,0.88804,-74.28,#123,0.91846,-0.020977,-0.39496,107.81,0.070906,0.99115,0.11225,42.703,0.3891,-0.1311,0.91182,-36.593

> ui mousemode right "translate selected models"

> view matrix models
> #121,0.88894,-0.049699,-0.45531,127.25,0.023099,0.9977,-0.063803,7.8354,0.45743,0.0462,0.88804,-74.13,#123,0.91846,-0.020977,-0.39496,108.69,0.070906,0.99115,0.11225,43.039,0.3891,-0.1311,0.91182,-36.443

> view matrix models
> #121,0.88894,-0.049699,-0.45531,127.87,0.023099,0.9977,-0.063803,8.2995,0.45743,0.0462,0.88804,-74.686,#123,0.91846,-0.020977,-0.39496,109.31,0.070906,0.99115,0.11225,43.503,0.3891,-0.1311,0.91182,-36.999

> select add #120

2286 atoms, 2285 bonds, 2 pseudobonds, 294 residues, 5 models selected  

> select subtract #120

1284 atoms, 1284 bonds, 1 pseudobond, 165 residues, 3 models selected  

> select subtract #121

282 atoms, 283 bonds, 36 residues, 1 model selected  

> view matrix models
> #123,0.91846,-0.020977,-0.39496,109.03,0.070906,0.99115,0.11225,42.402,0.3891,-0.1311,0.91182,-37.165

> ui mousemode right "rotate selected models"

> view matrix models
> #123,0.90591,-0.049207,-0.42061,121.08,0.077971,0.99563,0.051456,51.645,0.41624,-0.079409,0.90578,-50.107

> ui mousemode right "translate selected models"

> view matrix models
> #123,0.90591,-0.049207,-0.42061,120.65,0.077971,0.99563,0.051456,51.711,0.41624,-0.079409,0.90578,-49.372

> view matrix models
> #123,0.90591,-0.049207,-0.42061,119.08,0.077971,0.99563,0.051456,52.641,0.41624,-0.079409,0.90578,-49.305

> view matrix models
> #123,0.90591,-0.049207,-0.42061,119.4,0.077971,0.99563,0.051456,52.368,0.41624,-0.079409,0.90578,-48.565

> ui mousemode right "rotate selected models"

> view matrix models
> #123,0.90506,-0.05049,-0.42228,120.1,0.065139,0.99767,0.020323,60.378,0.42027,-0.045901,0.90624,-55.108

> select add #121

1284 atoms, 1284 bonds, 1 pseudobond, 165 residues, 3 models selected  

> select subtract #123

1002 atoms, 1001 bonds, 1 pseudobond, 129 residues, 2 models selected  

> view matrix models
> #121,0.88724,-0.045824,-0.45903,128.24,0.03359,0.99883,-0.034786,0.035567,0.46009,0.015444,0.88774,-69.307

> view matrix models
> #121,0.88716,-0.050461,-0.45869,129.07,0.045602,0.99872,-0.02167,-5.0748,0.4592,-0.001693,0.88833,-65.979

> select add #122

1284 atoms, 1284 bonds, 1 pseudobond, 165 residues, 3 models selected  

> select subtract #122

1002 atoms, 1001 bonds, 1 pseudobond, 129 residues, 2 models selected  

> select subtract #121

Nothing selected  

> select add #119

1002 atoms, 1001 bonds, 1 pseudobond, 129 residues, 2 models selected  

> view matrix models
> #119,0.86608,-0.1254,-0.48392,151.84,0.070863,0.98905,-0.12947,-14.07,0.49485,0.077839,0.86548,-81.316

> view matrix models
> #119,0.86723,-0.11817,-0.48369,150.18,0.075002,0.99135,-0.10771,-19.777,0.49223,0.057133,0.86859,-77.461

> ui mousemode right "translate selected models"

> view matrix models
> #119,0.86723,-0.11817,-0.48369,149.13,0.075002,0.99135,-0.10771,-19.922,0.49223,0.057133,0.86859,-77.878

> ui mousemode right "rotate selected models"

> view matrix models
> #119,0.86854,-0.094755,-0.48647,144.96,0.079982,0.99549,-0.051102,-33.23,0.48912,0.0054759,0.8722,-68.126

> view matrix models
> #119,0.87323,-0.095361,-0.47789,142.37,0.079504,0.99541,-0.053355,-32.659,0.48078,0.008597,0.8768,-67.943

> ui mousemode right "translate selected models"

> view matrix models
> #119,0.87323,-0.095361,-0.47789,142.5,0.079504,0.99541,-0.053355,-32.539,0.48078,0.008597,0.8768,-68.567

> view matrix models
> #119,0.87323,-0.095361,-0.47789,143.67,0.079504,0.99541,-0.053355,-32.52,0.48078,0.008597,0.8768,-68.117

> select add #124

1284 atoms, 1284 bonds, 1 pseudobond, 165 residues, 3 models selected  

> select subtract #119

282 atoms, 283 bonds, 36 residues, 1 model selected  

> view matrix models
> #124,0.91794,-0.0081059,-0.39665,102.07,0.038646,0.99686,0.069064,28.808,0.39484,-0.078725,0.91537,-46.941

> view matrix models
> #124,0.91794,-0.0081059,-0.39665,102,0.038646,0.99686,0.069064,28.784,0.39484,-0.078725,0.91537,-46.569

> select clear

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Fit14-23.cxs"

> select add #122

282 atoms, 283 bonds, 36 residues, 1 model selected  

> select add #119

1284 atoms, 1284 bonds, 1 pseudobond, 165 residues, 3 models selected  

> select subtract #122

1002 atoms, 1001 bonds, 1 pseudobond, 129 residues, 2 models selected  

> view matrix models
> #119,0.87323,-0.095361,-0.47789,143.88,0.079504,0.99541,-0.053355,-34.936,0.48078,0.008597,0.8768,-68.11

> view matrix models
> #119,0.87323,-0.095361,-0.47789,144.85,0.079504,0.99541,-0.053355,-34.987,0.48078,0.008597,0.8768,-67.669

> ui mousemode right "rotate selected models"

> view matrix models
> #119,0.87223,-0.064318,-0.48484,140.55,0.045551,0.99769,-0.050404,-29.049,0.48697,0.021879,0.87315,-70.729

> select add #118

2004 atoms, 2002 bonds, 2 pseudobonds, 258 residues, 4 models selected  

> select subtract #119

1002 atoms, 1001 bonds, 1 pseudobond, 129 residues, 2 models selected  

> select add #124

1284 atoms, 1284 bonds, 1 pseudobond, 165 residues, 3 models selected  

> select subtract #118

282 atoms, 283 bonds, 36 residues, 1 model selected  

> ui mousemode right "translate selected models"

> view matrix models
> #124,0.91794,-0.0081059,-0.39665,102.19,0.038646,0.99686,0.069064,27.9,0.39484,-0.078725,0.91537,-46.52

> select add #122

564 atoms, 566 bonds, 72 residues, 2 models selected  

> select add #123

846 atoms, 849 bonds, 108 residues, 3 models selected  

> select subtract #122

564 atoms, 566 bonds, 72 residues, 2 models selected  

> select subtract #123

282 atoms, 283 bonds, 36 residues, 1 model selected  

> select subtract #124

Nothing selected  

> select add #119

1002 atoms, 1001 bonds, 1 pseudobond, 129 residues, 2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #119,0.86832,-0.11278,-0.48302,150.22,0.089611,0.99345,-0.070861,-33.134,0.48785,0.018246,0.87274,-70.135

> ui mousemode right "translate selected models"

> view matrix models
> #119,0.86832,-0.11278,-0.48302,150.55,0.089611,0.99345,-0.070861,-31.671,0.48785,0.018246,0.87274,-69.991

> ui mousemode right "rotate selected models"

> view matrix models
> #119,0.87151,-0.069317,-0.48545,142.1,0.043422,0.99698,-0.064404,-24.169,0.48845,0.03505,0.87189,-73.145

> ui mousemode right "translate selected models"

> view matrix models
> #119,0.87151,-0.069317,-0.48545,141.82,0.043422,0.99698,-0.064404,-23.927,0.48845,0.03505,0.87189,-73.248

> ui mousemode right "rotate selected models"

> view matrix models
> #119,0.8695,-0.10739,-0.48212,148.82,0.087776,0.99414,-0.063135,-32.751,0.48607,0.012577,0.87383,-68.87

> ui mousemode right "translate selected models"

[Repeated 1 time(s)]

> view matrix models
> #119,0.8695,-0.10739,-0.48212,147.46,0.087776,0.99414,-0.063135,-34.321,0.48607,0.012577,0.87383,-69.632

> select clear

> select add #120

1002 atoms, 1001 bonds, 1 pseudobond, 129 residues, 2 models selected  

> ui mousemode right "translate selected models"

> view matrix models
> #120,0.91258,-0.070384,-0.4028,114.1,0.068723,0.99746,-0.018595,61.64,0.40308,-0.010712,0.9151,-58.767

> view matrix models
> #120,0.91258,-0.070384,-0.4028,114.76,0.068723,0.99746,-0.018595,62.129,0.40308,-0.010712,0.9151,-58.577

> select clear

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Fit14-24.cxs"

> ui windowfill toggle

[Repeated 1 time(s)]

> select add #123

282 atoms, 283 bonds, 36 residues, 1 model selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #123,0.90704,-0.024556,-0.42033,114.96,0.063743,0.9948,0.079436,50.063,0.4162,-0.098845,0.90389,-44.915

> ui windowfill toggle

> view matrix models
> #123,0.90272,-0.020471,-0.42975,116.88,0.063028,0.99438,0.085027,49.226,0.42559,-0.10384,0.89894,-44.991

> ui mousemode right zoom

> ui windowfill toggle

> select add #122

564 atoms, 566 bonds, 72 residues, 2 models selected  

> select subtract #122

282 atoms, 283 bonds, 36 residues, 1 model selected  

> select subtract #123

Nothing selected  

> select add #119

1002 atoms, 1001 bonds, 1 pseudobond, 129 residues, 2 models selected  

> ui mousemode right "translate selected models"

> view matrix models
> #119,0.8695,-0.10739,-0.48212,148.78,0.087776,0.99414,-0.063135,-35.809,0.48607,0.012577,0.87383,-68.79

> ui mousemode right "rotate selected models"

> view matrix models
> #119,0.86998,-0.07559,-0.48727,143.66,0.051918,0.99673,-0.061928,-29.185,0.49035,0.028578,0.87105,-72.156

> ui mousemode right "translate selected models"

> view matrix models
> #119,0.86998,-0.07559,-0.48727,143.01,0.051918,0.99673,-0.061928,-28.473,0.49035,0.028578,0.87105,-72.57

> ui mousemode right "rotate selected models"

> view matrix models
> #119,0.86857,-0.028892,-0.49473,135.91,-0.00084377,0.99821,-0.059776,-18.358,0.49557,0.052337,0.86699,-77.344

> ui mousemode right "translate selected models"

> view matrix models
> #119,0.86857,-0.028892,-0.49473,136.31,-0.00084377,0.99821,-0.059776,-17.501,0.49557,0.052337,0.86699,-77.241

> select add #121

2004 atoms, 2002 bonds, 2 pseudobonds, 258 residues, 4 models selected  

> select subtract #119

1002 atoms, 1001 bonds, 1 pseudobond, 129 residues, 2 models selected  

> view matrix models
> #121,0.88716,-0.050461,-0.45869,130.45,0.045602,0.99872,-0.02167,-8.2246,0.4592,-0.001693,0.88833,-65.591

> view matrix models
> #121,0.88716,-0.050461,-0.45869,131.66,0.045602,0.99872,-0.02167,-8.194,0.4592,-0.001693,0.88833,-65.078

> select add #124

1284 atoms, 1284 bonds, 1 pseudobond, 165 residues, 3 models selected  

> select subtract #121

282 atoms, 283 bonds, 36 residues, 1 model selected  

> view matrix models
> #124,0.91794,-0.0081059,-0.39665,103.02,0.038646,0.99686,0.069064,30.586,0.39484,-0.078725,0.91537,-46.181

> view matrix models
> #124,0.91794,-0.0081059,-0.39665,102.88,0.038646,0.99686,0.069064,30.209,0.39484,-0.078725,0.91537,-46.187

> ui mousemode right "rotate selected models"

> view matrix models
> #124,0.91337,-0.063878,-0.40209,114.22,0.098036,0.99306,0.06493,19.951,0.39515,-0.098725,0.91329,-42.478

> select add #123

564 atoms, 566 bonds, 72 residues, 2 models selected  

> select subtract #124

282 atoms, 283 bonds, 36 residues, 1 model selected  

> view matrix models
> #123,0.89919,-0.081655,-0.42988,127.94,0.12442,0.98959,0.072282,40.355,0.4195,-0.11848,0.89999,-41.516

> select add #122

564 atoms, 566 bonds, 72 residues, 2 models selected  

> select subtract #122

282 atoms, 283 bonds, 36 residues, 1 model selected  

> select subtract #123

Nothing selected  

> select add #119

1002 atoms, 1001 bonds, 1 pseudobond, 129 residues, 2 models selected  

> ui mousemode right "translate selected models"

> view matrix models
> #119,0.86857,-0.028892,-0.49473,137.03,-0.00084377,0.99821,-0.059776,-16.436,0.49557,0.052337,0.86699,-77.068

> ui mousemode right "rotate selected models"

> view matrix models
> #119,0.87368,-0.029223,-0.48563,134.2,-0.0093225,0.99701,-0.076767,-11.014,0.48642,0.071596,0.87079,-79.632

> ui mousemode right "translate selected models"

> view matrix models
> #119,0.87368,-0.029223,-0.48563,134.17,-0.0093225,0.99701,-0.076767,-10.925,0.48642,0.071596,0.87079,-80.089

> select add #121

2004 atoms, 2002 bonds, 2 pseudobonds, 258 residues, 4 models selected  

> select subtract #119

1002 atoms, 1001 bonds, 1 pseudobond, 129 residues, 2 models selected  

> view matrix models
> #121,0.88716,-0.050461,-0.45869,131.86,0.045602,0.99872,-0.02167,-8.4136,0.4592,-0.001693,0.88833,-65.797

> select add #118

2004 atoms, 2002 bonds, 2 pseudobonds, 258 residues, 4 models selected  

> select add #124

2286 atoms, 2285 bonds, 2 pseudobonds, 294 residues, 5 models selected  

> select subtract #121

1284 atoms, 1284 bonds, 1 pseudobond, 165 residues, 3 models selected  

> select subtract #118

282 atoms, 283 bonds, 36 residues, 1 model selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #124,0.91456,-0.055919,-0.40056,112.36,0.1003,0.99082,0.090688,15.06,0.39181,-0.12312,0.91177,-37.412

> ui mousemode right "translate selected models"

[Repeated 1 time(s)]

> view matrix models
> #124,0.91456,-0.055919,-0.40056,112.44,0.1003,0.99082,0.090688,15.05,0.39181,-0.12312,0.91177,-37.662

> select add #121

1284 atoms, 1284 bonds, 1 pseudobond, 165 residues, 3 models selected  

> select subtract #124

1002 atoms, 1001 bonds, 1 pseudobond, 129 residues, 2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #121,0.88557,-0.063237,-0.46018,134.93,0.043485,0.99763,-0.053408,-1.3233,0.46247,0.027286,0.88622,-71.562

> select add #119

2004 atoms, 2002 bonds, 2 pseudobonds, 258 residues, 4 models selected  

> select subtract #121

1002 atoms, 1001 bonds, 1 pseudobond, 129 residues, 2 models selected  

> select subtract #119

Nothing selected  

> select add #124

282 atoms, 283 bonds, 36 residues, 1 model selected  

> ui mousemode right "translate selected models"

> view matrix models
> #124,0.91456,-0.055919,-0.40056,112.69,0.1003,0.99082,0.090688,14.925,0.39181,-0.12312,0.91177,-37.649

> select add #123

564 atoms, 566 bonds, 72 residues, 2 models selected  

> hide #!127 models

> show #!127 models

> hide #!127 models

> show #!116 models

> hide #!116 models

> show #!115 models

> view matrix models
> #123,0.89919,-0.081655,-0.42988,127.53,0.12442,0.98959,0.072282,39.773,0.4195,-0.11848,0.89999,-40.411,#124,0.91456,-0.055919,-0.40056,112.28,0.1003,0.99082,0.090688,14.344,0.39181,-0.12312,0.91177,-36.544

> undo

> select add #115

846 atoms, 849 bonds, 108 residues, 3 models selected  

> view matrix models
> #115,0.91434,0.35986,0.18572,-100.94,-0.35685,0.93279,-0.050579,35.266,-0.19144,-0.020027,0.9813,47.453,#123,0.89919,-0.081655,-0.42988,127.58,0.12442,0.98959,0.072282,40.067,0.4195,-0.11848,0.89999,-40.258,#124,0.91456,-0.055919,-0.40056,112.33,0.1003,0.99082,0.090688,14.637,0.39181,-0.12312,0.91177,-36.391

> ui mousemode right "rotate selected models"

> view matrix models
> #115,0.92,0.34657,0.18301,-97.808,-0.3391,0.93801,-0.071712,34.437,-0.19652,0.0039179,0.98049,41.917,#123,0.89585,-0.095361,-0.43399,130.92,0.12696,0.99092,0.044338,44.604,0.42582,-0.09482,0.89982,-44.777,#124,0.91167,-0.069629,-0.40498,116.02,0.10374,0.99262,0.062867,18.875,0.39761,-0.099326,0.91216,-41.585

> ui mousemode right "translate selected models"

> view matrix models
> #115,0.92,0.34657,0.18301,-97.698,-0.3391,0.93801,-0.071712,34.423,-0.19652,0.0039179,0.98049,41.727,#123,0.89585,-0.095361,-0.43399,131.03,0.12696,0.99092,0.044338,44.59,0.42582,-0.09482,0.89982,-44.967,#124,0.91167,-0.069629,-0.40498,116.13,0.10374,0.99262,0.062867,18.861,0.39761,-0.099326,0.91216,-41.775

> view matrix models
> #115,0.92,0.34657,0.18301,-97.7,-0.3391,0.93801,-0.071712,34.42,-0.19652,0.0039179,0.98049,41.771,#123,0.89585,-0.095361,-0.43399,131.03,0.12696,0.99092,0.044338,44.587,0.42582,-0.09482,0.89982,-44.923,#124,0.91167,-0.069629,-0.40498,116.13,0.10374,0.99262,0.062867,18.857,0.39761,-0.099326,0.91216,-41.731

> select subtract #123

564 atoms, 566 bonds, 72 residues, 2 models selected  

> select subtract #124

282 atoms, 283 bonds, 36 residues, 1 model selected  

> select subtract #115

Nothing selected  

> show #!127 models

> close #127

> combine #15-18,115

Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #16 to '7'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #17 to '8'  
Remapping chain ID '6' in copy of copy of copy of pointy-1pf.pdb #18 to '9'  
Remapping chain ID '6' in copy of copy of pointy-1pf.pdb #115 to '0'  

> color #125 #73fa79ff

> hide #!115 models

> select add #119

1002 atoms, 1001 bonds, 1 pseudobond, 129 residues, 2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #119,0.87394,-0.082442,-0.47899,142.92,0.04481,0.99498,-0.089494,-19.07,0.48396,0.056749,0.87325,-77.254

> ui mousemode right "translate selected models"

> view matrix models
> #119,0.87394,-0.082442,-0.47899,140.98,0.04481,0.99498,-0.089494,-19.676,0.48396,0.056749,0.87325,-77.769

> view matrix models
> #119,0.87394,-0.082442,-0.47899,141.28,0.04481,0.99498,-0.089494,-19.414,0.48396,0.056749,0.87325,-77.682

> ui mousemode right "rotate selected models"

> view matrix models
> #119,0.87353,-0.076161,-0.48077,140.53,0.037723,0.99531,-0.08913,-18.095,0.48531,0.059721,0.8723,-78.333

> select add #121

2004 atoms, 2002 bonds, 2 pseudobonds, 258 residues, 4 models selected  

> select subtract #119

1002 atoms, 1001 bonds, 1 pseudobond, 129 residues, 2 models selected  

> view matrix models
> #121,0.88486,-0.069724,-0.4606,136.39,0.043371,0.99677,-0.067567,1.7385,0.46383,0.039811,0.88503,-73.988

> view matrix models
> #121,0.89439,-0.073387,-0.44122,131.2,0.047746,0.99648,-0.068955,1.1781,0.44473,0.040606,0.89474,-72.191

> view matrix models
> #121,0.89436,-0.081313,-0.43989,132.45,0.048548,0.99518,-0.085251,4.571,0.4447,0.054889,0.894,-74.756

> select add #124

1284 atoms, 1284 bonds, 1 pseudobond, 165 residues, 3 models selected  

> select subtract #121

282 atoms, 283 bonds, 36 residues, 1 model selected  

> ui mousemode right "translate selected models"

> view matrix models
> #124,0.91167,-0.069629,-0.40498,116.4,0.10374,0.99262,0.062867,18.95,0.39761,-0.099326,0.91216,-42.243

> view matrix models
> #124,0.91167,-0.069629,-0.40498,116.55,0.10374,0.99262,0.062867,18.493,0.39761,-0.099326,0.91216,-42.477

> select add #123

564 atoms, 566 bonds, 72 residues, 2 models selected  

> select subtract #124

282 atoms, 283 bonds, 36 residues, 1 model selected  

> view matrix models
> #123,0.89585,-0.095361,-0.43399,131.29,0.12696,0.99092,0.044338,44.47,0.42582,-0.09482,0.89982,-45.523

> ui mousemode right zoom

> select clear

> select add #121

1002 atoms, 1001 bonds, 1 pseudobond, 129 residues, 2 models selected  

> select add #119

2004 atoms, 2002 bonds, 2 pseudobonds, 258 residues, 4 models selected  

> select add #124

2286 atoms, 2285 bonds, 2 pseudobonds, 294 residues, 5 models selected  

> select add #123

2568 atoms, 2568 bonds, 2 pseudobonds, 330 residues, 6 models selected  

> ui mousemode right "translate selected models"

> view matrix models
> #119,0.87353,-0.076161,-0.48077,140.56,0.037723,0.99531,-0.08913,-17.065,0.48531,0.059721,0.8723,-78.282,#121,0.89436,-0.081313,-0.43989,132.48,0.048548,0.99518,-0.085251,5.6013,0.4447,0.054889,0.894,-74.705,#123,0.89585,-0.095361,-0.43399,131.32,0.12696,0.99092,0.044338,45.5,0.42582,-0.09482,0.89982,-45.473,#124,0.91167,-0.069629,-0.40498,116.59,0.10374,0.99262,0.062867,19.523,0.39761,-0.099326,0.91216,-42.426

> select subtract #123

2286 atoms, 2285 bonds, 2 pseudobonds, 294 residues, 5 models selected  

> select subtract #121

1284 atoms, 1284 bonds, 1 pseudobond, 165 residues, 3 models selected  

> select subtract #119

282 atoms, 283 bonds, 36 residues, 1 model selected  

> ui mousemode right zoom

> ui windowfill toggle

[Repeated 1 time(s)]

> select add #118

1284 atoms, 1284 bonds, 1 pseudobond, 165 residues, 3 models selected  

> select subtract #118

282 atoms, 283 bonds, 36 residues, 1 model selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #124,0.91679,-0.047597,-0.39653,110.27,0.096487,0.98986,0.10426,13.659,0.38755,-0.13385,0.91208,-34.596

> view matrix models
> #124,0.91555,-0.050721,-0.39899,111.5,0.098372,0.99013,0.099864,14.068,0.38998,-0.13068,0.9115,-35.502

> view matrix models
> #124,0.91599,-0.049101,-0.39818,110.99,0.09877,0.98953,0.10519,13.091,0.38885,-0.13568,0.91125,-34.387

> view matrix models
> #124,0.91719,-0.040329,-0.39641,108.94,0.090661,0.98989,0.10906,13.9,0.38801,-0.13597,0.91157,-34.233

> view matrix models
> #124,0.91625,-0.047214,-0.39781,110.55,0.097027,0.98962,0.10603,13.263,0.38867,-0.13574,0.91132,-34.354

> ui mousemode right zoom

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Fit14-25.cxs"

[Repeated 1 time(s)]

> select subtract #124

Nothing selected  

> select add #122

282 atoms, 283 bonds, 36 residues, 1 model selected  

> select subtract #122

Nothing selected  

> select add #119

1002 atoms, 1001 bonds, 1 pseudobond, 129 residues, 2 models selected  

> ui mousemode right "translate selected models"

> view matrix models
> #119,0.87353,-0.076161,-0.48077,140.63,0.037723,0.99531,-0.08913,-18.977,0.48531,0.059721,0.8723,-77.971

> view matrix models
> #119,0.87353,-0.076161,-0.48077,141.07,0.037723,0.99531,-0.08913,-18.529,0.48531,0.059721,0.8723,-77.814

> ui mousemode right zoom

> select add #118

2004 atoms, 2002 bonds, 2 pseudobonds, 258 residues, 4 models selected  

> select subtract #119

1002 atoms, 1001 bonds, 1 pseudobond, 129 residues, 2 models selected  

> select subtract #118

Nothing selected  

> select add #124

282 atoms, 283 bonds, 36 residues, 1 model selected  

> ui mousemode right "translate selected models"

> view matrix models
> #124,0.91625,-0.047214,-0.39781,110.67,0.097027,0.98962,0.10603,13.25,0.38867,-0.13574,0.91132,-34.679

> ui mousemode right "rotate selected models"

> view matrix models
> #124,0.9194,-0.037918,-0.3915,107.3,0.097742,0.98615,0.13403,8.4502,0.38099,-0.16149,0.91037,-28.638

> ui mousemode right zoom

> select subtract #124

Nothing selected  

> select add #118

1002 atoms, 1001 bonds, 1 pseudobond, 129 residues, 2 models selected  

> ui mousemode right "translate selected models"

> view matrix models
> #118,0.92103,-0.10521,-0.37502,111.48,0.10468,0.99427,-0.021841,32.821,0.37516,-0.019141,0.92676,-55.871

> view matrix models
> #118,0.92103,-0.10521,-0.37502,111.18,0.10468,0.99427,-0.021841,32.858,0.37516,-0.019141,0.92676,-56.015

> view matrix models
> #118,0.92103,-0.10521,-0.37502,110.7,0.10468,0.99427,-0.021841,32.877,0.37516,-0.019141,0.92676,-56.412

> select subtract #118

Nothing selected  

> select add #123

282 atoms, 283 bonds, 36 residues, 1 model selected  

> select subtract #123

Nothing selected  

> select add #123

282 atoms, 283 bonds, 36 residues, 1 model selected  

> select subtract #123

Nothing selected  

> select add #120

1002 atoms, 1001 bonds, 1 pseudobond, 129 residues, 2 models selected  

> view matrix models
> #120,0.91258,-0.070384,-0.4028,112.91,0.068723,0.99746,-0.018595,62.294,0.40308,-0.010712,0.9151,-59.243

> view matrix models
> #120,0.91258,-0.070384,-0.4028,112.9,0.068723,0.99746,-0.018595,62.263,0.40308,-0.010712,0.9151,-59.247

> view matrix models
> #120,0.91258,-0.070384,-0.4028,112.9,0.068723,0.99746,-0.018595,62.138,0.40308,-0.010712,0.9151,-59.259

> view matrix models
> #120,0.91258,-0.070384,-0.4028,112.91,0.068723,0.99746,-0.018595,62.353,0.40308,-0.010712,0.9151,-59.238

> ui mousemode right "rotate selected models"

> view matrix models
> #120,0.90062,-0.14785,-0.40869,131.32,0.14354,0.98878,-0.041387,53.273,0.41022,-0.02139,0.91173,-57.985

> ui mousemode right "translate selected models"

> view matrix models
> #120,0.90062,-0.14785,-0.40869,129.53,0.14354,0.98878,-0.041387,53.563,0.41022,-0.02139,0.91173,-58.175

> view matrix models
> #120,0.90062,-0.14785,-0.40869,129,0.14354,0.98878,-0.041387,53.36,0.41022,-0.02139,0.91173,-58.324

> select add #122

1284 atoms, 1284 bonds, 1 pseudobond, 165 residues, 3 models selected  

> select subtract #122

1002 atoms, 1001 bonds, 1 pseudobond, 129 residues, 2 models selected  

> select subtract #120

Nothing selected  

> select add #119

1002 atoms, 1001 bonds, 1 pseudobond, 129 residues, 2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #119,0.87499,-0.043646,-0.48217,134.86,0.002118,0.99626,-0.086338,-11.967,0.48414,0.074523,0.87181,-80.296

> ui mousemode right "translate selected models"

> view matrix models
> #119,0.87499,-0.043646,-0.48217,135.01,0.002118,0.99626,-0.086338,-11.92,0.48414,0.074523,0.87181,-80.226

> select subtract #119

Nothing selected  

> select add #121

1002 atoms, 1001 bonds, 1 pseudobond, 129 residues, 2 models selected  

> ui mousemode right zoom

> select subtract #121

Nothing selected  

> select add #119

1002 atoms, 1001 bonds, 1 pseudobond, 129 residues, 2 models selected  

> select subtract #119

Nothing selected  

> select add #122

282 atoms, 283 bonds, 36 residues, 1 model selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #122,0.91015,0.045559,-0.41176,92.406,-0.013327,0.99664,0.080813,-34.613,0.41406,-0.068065,0.9077,-49.929

> ui mousemode right "translate selected models"

> view matrix models
> #122,0.91015,0.045559,-0.41176,90.92,-0.013327,0.99664,0.080813,-35.101,0.41406,-0.068065,0.9077,-50.31

> select add #121

1284 atoms, 1284 bonds, 1 pseudobond, 165 residues, 3 models selected  

> select subtract #122

1002 atoms, 1001 bonds, 1 pseudobond, 129 residues, 2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #121,0.89332,-0.10288,-0.43749,136.32,0.07393,0.99382,-0.082748,0.1382,0.4433,0.041577,0.89541,-72.167

> select add #118

2004 atoms, 2002 bonds, 2 pseudobonds, 258 residues, 4 models selected  

> select subtract #118

1002 atoms, 1001 bonds, 1 pseudobond, 129 residues, 2 models selected  

> select subtract #121

Nothing selected  

> select add #124

282 atoms, 283 bonds, 36 residues, 1 model selected  

> select add #122

564 atoms, 566 bonds, 72 residues, 2 models selected  

> select subtract #122

282 atoms, 283 bonds, 36 residues, 1 model selected  

> select add #120

1284 atoms, 1284 bonds, 1 pseudobond, 165 residues, 3 models selected  

> select subtract #120

282 atoms, 283 bonds, 36 residues, 1 model selected  

> select add #119

1284 atoms, 1284 bonds, 1 pseudobond, 165 residues, 3 models selected  

> ui mousemode right "translate selected models"

> view matrix models
> #119,0.87499,-0.043646,-0.48217,136.25,0.002118,0.99626,-0.086338,-12.511,0.48414,0.074523,0.87181,-79.281,#124,0.9194,-0.037918,-0.3915,108.54,0.097742,0.98615,0.13403,7.8594,0.38099,-0.16149,0.91037,-27.693

> view matrix models
> #119,0.87499,-0.043646,-0.48217,135.94,0.002118,0.99626,-0.086338,-12.082,0.48414,0.074523,0.87181,-79.265,#124,0.9194,-0.037918,-0.3915,108.23,0.097742,0.98615,0.13403,8.2882,0.38099,-0.16149,0.91037,-27.678

> select subtract #119

282 atoms, 283 bonds, 36 residues, 1 model selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #124,0.92694,0.025484,-0.37435,92.817,0.034002,0.98788,0.15144,17.263,0.37368,-0.15311,0.91484,-28.494

> ui windowfill toggle

[Repeated 1 time(s)]

> select add #119

1284 atoms, 1284 bonds, 1 pseudobond, 165 residues, 3 models selected  

> select subtract #124

1002 atoms, 1001 bonds, 1 pseudobond, 129 residues, 2 models selected  

> ui mousemode right "translate selected models"

> view matrix models
> #119,0.87499,-0.043646,-0.48217,133.74,0.002118,0.99626,-0.086338,-12.07,0.48414,0.074523,0.87181,-79.521

> view matrix models
> #119,0.87499,-0.043646,-0.48217,134.08,0.002118,0.99626,-0.086338,-11.169,0.48414,0.074523,0.87181,-79.556

> view matrix models
> #119,0.87499,-0.043646,-0.48217,134.14,0.002118,0.99626,-0.086338,-11.173,0.48414,0.074523,0.87181,-80.021

> view matrix models
> #119,0.87499,-0.043646,-0.48217,133.89,0.002118,0.99626,-0.086338,-11.169,0.48414,0.074523,0.87181,-80.105

> select add #123

1284 atoms, 1284 bonds, 1 pseudobond, 165 residues, 3 models selected  

> select subtract #119

282 atoms, 283 bonds, 36 residues, 1 model selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #123,0.9054,-0.069638,-0.41882,122.26,0.12209,0.9875,0.099735,36.658,0.40663,-0.14143,0.90258,-34.336

> ui mousemode right "translate selected models"

> view matrix models
> #123,0.9054,-0.069638,-0.41882,122.68,0.12209,0.9875,0.099735,36.735,0.40663,-0.14143,0.90258,-35.036

> view matrix models
> #123,0.9054,-0.069638,-0.41882,122.48,0.12209,0.9875,0.099735,36.516,0.40663,-0.14143,0.90258,-34.718

> ui mousemode right "rotate selected models"

> view matrix models
> #123,0.90895,-0.059133,-0.41269,118.86,0.12346,0.98367,0.13098,31.038,0.39821,-0.17001,0.9014,-28.011

> ui mousemode right "translate selected models"

> view matrix models
> #123,0.90895,-0.059133,-0.41269,118.98,0.12346,0.98367,0.13098,31.138,0.39821,-0.17001,0.9014,-28.26

> view matrix models
> #123,0.90895,-0.059133,-0.41269,119.02,0.12346,0.98367,0.13098,31.246,0.39821,-0.17001,0.9014,-28.33

> select add #122

564 atoms, 566 bonds, 72 residues, 2 models selected  

> select subtract #123

282 atoms, 283 bonds, 36 residues, 1 model selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #122,0.90882,0.0046606,-0.41717,99.109,0.026487,0.99728,0.068845,-40.793,0.41635,-0.073617,0.90622,-49.544

> ui mousemode right "translate selected models"

> view matrix models
> #122,0.90882,0.0046606,-0.41717,99.408,0.026487,0.99728,0.068845,-43.208,0.41635,-0.073617,0.90622,-49.653

> ui mousemode right "rotate selected models"

> view matrix models
> #122,0.90916,0.0084511,-0.41636,98.55,0.026905,0.99651,0.078976,-45.059,0.41558,-0.083004,0.90576,-47.828

> select subtract #122

Nothing selected  

> select add #123

282 atoms, 283 bonds, 36 residues, 1 model selected  

> select add #121

1284 atoms, 1284 bonds, 1 pseudobond, 165 residues, 3 models selected  

> ui mousemode right "translate selected models"

> view matrix models
> #121,0.89332,-0.10288,-0.43749,135.19,0.07393,0.99382,-0.082748,-0.0097375,0.4433,0.041577,0.89541,-72.144,#123,0.90895,-0.059133,-0.41269,117.89,0.12346,0.98367,0.13098,31.098,0.39821,-0.17001,0.9014,-28.307

> view matrix models
> #121,0.89332,-0.10288,-0.43749,134.68,0.07393,0.99382,-0.082748,0.52871,0.4433,0.041577,0.89541,-72.326,#123,0.90895,-0.059133,-0.41269,117.39,0.12346,0.98367,0.13098,31.637,0.39821,-0.17001,0.9014,-28.49

> select subtract #121

282 atoms, 283 bonds, 36 residues, 1 model selected  

> select add #118

1284 atoms, 1284 bonds, 1 pseudobond, 165 residues, 3 models selected  

> select subtract #118

282 atoms, 283 bonds, 36 residues, 1 model selected  

> select add #124

564 atoms, 566 bonds, 72 residues, 2 models selected  

> view matrix models
> #123,0.90895,-0.059133,-0.41269,117.4,0.12346,0.98367,0.13098,31.662,0.39821,-0.17001,0.9014,-29.07,#124,0.92694,0.025484,-0.37435,92.828,0.034002,0.98788,0.15144,17.288,0.37368,-0.15311,0.91484,-29.075

> view matrix models
> #123,0.90895,-0.059133,-0.41269,117.47,0.12346,0.98367,0.13098,31.484,0.39821,-0.17001,0.9014,-29.042,#124,0.92694,0.025484,-0.37435,92.895,0.034002,0.98788,0.15144,17.11,0.37368,-0.15311,0.91484,-29.047

> view matrix models
> #123,0.90895,-0.059133,-0.41269,117.85,0.12346,0.98367,0.13098,31.693,0.39821,-0.17001,0.9014,-28.7,#124,0.92694,0.025484,-0.37435,93.274,0.034002,0.98788,0.15144,17.318,0.37368,-0.15311,0.91484,-28.705

> view matrix models
> #123,0.90895,-0.059133,-0.41269,117.95,0.12346,0.98367,0.13098,31.566,0.39821,-0.17001,0.9014,-29.05,#124,0.92694,0.025484,-0.37435,93.375,0.034002,0.98788,0.15144,17.192,0.37368,-0.15311,0.91484,-29.054

> select subtract #124

282 atoms, 283 bonds, 36 residues, 1 model selected  

> view matrix models
> #123,0.90895,-0.059133,-0.41269,118.26,0.12346,0.98367,0.13098,31.48,0.39821,-0.17001,0.9014,-29.625

> select add #121

1284 atoms, 1284 bonds, 1 pseudobond, 165 residues, 3 models selected  

> select subtract #121

282 atoms, 283 bonds, 36 residues, 1 model selected  

> select add #117

564 atoms, 566 bonds, 72 residues, 2 models selected  

> select subtract #123

282 atoms, 283 bonds, 36 residues, 1 model selected  

> view matrix models
> #117,0.91729,-0.00669,-0.39815,97.549,0.033935,0.99753,0.061422,-18.17,0.39676,-0.069853,0.91526,-48.808

> ui mousemode right "rotate selected models"

> view matrix models
> #117,0.92027,0.0054453,-0.39124,93.617,0.032927,0.99528,0.091303,-23.189,0.38989,-0.096906,0.91575,-42.975

> ui mousemode right "translate selected models"

> select subtract #117

Nothing selected  

> select add #120

1002 atoms, 1001 bonds, 1 pseudobond, 129 residues, 2 models selected  

> select subtract #120

Nothing selected  

> select add #123

282 atoms, 283 bonds, 36 residues, 1 model selected  

> view matrix models
> #123,0.90895,-0.059133,-0.41269,117.87,0.12346,0.98367,0.13098,30.755,0.39821,-0.17001,0.9014,-29.591

> view matrix models
> #123,0.90895,-0.059133,-0.41269,118.33,0.12346,0.98367,0.13098,30.447,0.39821,-0.17001,0.9014,-29.52

> ui mousemode right "rotate selected models"

> view matrix models
> #123,0.91126,-0.026043,-0.411,111.96,0.092167,0.98558,0.1419,34.231,0.40138,-0.16719,0.90052,-30.456

> ui mousemode right "translate selected models"

> view matrix models
> #123,0.91126,-0.026043,-0.411,111.96,0.092167,0.98558,0.1419,33.962,0.40138,-0.16719,0.90052,-30.431

> show #!105 models

> hide #!105 models

> show #!9 models

> hide #!9 models

> ui mousemode right "rotate selected models"

> view matrix models
> #123,0.90813,-0.041458,-0.41663,116.24,0.091779,0.9906,0.10148,40.764,0.40851,-0.13039,0.90339,-38.59

> ui mousemode right "translate selected models"

> view matrix models
> #123,0.90813,-0.041458,-0.41663,116.5,0.091779,0.9906,0.10148,41.565,0.40851,-0.13039,0.90339,-38.508

> select add #118

1284 atoms, 1284 bonds, 1 pseudobond, 165 residues, 3 models selected  

> select subtract #118

282 atoms, 283 bonds, 36 residues, 1 model selected  

> select subtract #123

Nothing selected  

> select add #124

282 atoms, 283 bonds, 36 residues, 1 model selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #124,0.92266,0.013109,-0.38539,98.375,0.033998,0.99276,0.11516,23.164,0.38411,-0.11936,0.91554,-36.943

> ui mousemode right "translate selected models"

> view matrix models
> #124,0.92266,0.013109,-0.38539,98.543,0.033998,0.99276,0.11516,23.783,0.38411,-0.11936,0.91554,-36.905

> view matrix models
> #124,0.92266,0.013109,-0.38539,98.363,0.033998,0.99276,0.11516,23.47,0.38411,-0.11936,0.91554,-36.845

> select subtract #124

Nothing selected  

> select add #122

282 atoms, 283 bonds, 36 residues, 1 model selected  

> select subtract #122

Nothing selected  

> select add #119

1002 atoms, 1001 bonds, 1 pseudobond, 129 residues, 2 models selected  

> view matrix models
> #119,0.87499,-0.043646,-0.48217,133.24,0.002118,0.99626,-0.086338,-10.889,0.48414,0.074523,0.87181,-80.333

> view matrix models
> #119,0.87499,-0.043646,-0.48217,133.14,0.002118,0.99626,-0.086338,-10.342,0.48414,0.074523,0.87181,-80.421

> select add #121

2004 atoms, 2002 bonds, 2 pseudobonds, 258 residues, 4 models selected  

> select subtract #119

1002 atoms, 1001 bonds, 1 pseudobond, 129 residues, 2 models selected  

> view matrix models
> #121,0.89332,-0.10288,-0.43749,133.84,0.07393,0.99382,-0.082748,0.666,0.4433,0.041577,0.89541,-72.534

> view matrix models
> #121,0.89332,-0.10288,-0.43749,133.81,0.07393,0.99382,-0.082748,0.87303,0.4433,0.041577,0.89541,-72.439

> view matrix models
> #121,0.89332,-0.10288,-0.43749,133.62,0.07393,0.99382,-0.082748,0.88251,0.4433,0.041577,0.89541,-72.484

> view matrix models
> #121,0.89332,-0.10288,-0.43749,133.34,0.07393,0.99382,-0.082748,0.95939,0.4433,0.041577,0.89541,-72.673

> view matrix models
> #121,0.89332,-0.10288,-0.43749,133.15,0.07393,0.99382,-0.082748,0.9177,0.4433,0.041577,0.89541,-72.095

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Fit14-26.cxs"

> select subtract #121

Nothing selected  

> select clear

> select add #121

1002 atoms, 1001 bonds, 1 pseudobond, 129 residues, 2 models selected  

> select add #122

1284 atoms, 1284 bonds, 1 pseudobond, 165 residues, 3 models selected  

> select subtract #122

1002 atoms, 1001 bonds, 1 pseudobond, 129 residues, 2 models selected  

> select subtract #121

Nothing selected  

> select add #119

1002 atoms, 1001 bonds, 1 pseudobond, 129 residues, 2 models selected  

> view matrix models
> #119,0.87499,-0.043646,-0.48217,134.13,0.002118,0.99626,-0.086338,-9.943,0.48414,0.074523,0.87181,-79.933

> view matrix models
> #119,0.87499,-0.043646,-0.48217,134.24,0.002118,0.99626,-0.086338,-9.9587,0.48414,0.074523,0.87181,-79.9

> ui mousemode right "rotate selected models"

> view matrix models
> #119,0.87406,-0.045335,-0.4837,135.07,0.0058225,0.99654,-0.082881,-11.475,0.48579,0.069626,0.8713,-79.201

> select subtract #119

Nothing selected  

> select add #121

1002 atoms, 1001 bonds, 1 pseudobond, 129 residues, 2 models selected  

> select subtract #121

Nothing selected  

> select add #117

282 atoms, 283 bonds, 36 residues, 1 model selected  

> select subtract #117

Nothing selected  

> select add #121

1002 atoms, 1001 bonds, 1 pseudobond, 129 residues, 2 models selected  

> ui mousemode right "translate selected models"

> view matrix models
> #121,0.89332,-0.10288,-0.43749,132.87,0.07393,0.99382,-0.082748,0.94643,0.4433,0.041577,0.89541,-71.794

> view matrix models
> #121,0.89332,-0.10288,-0.43749,132.81,0.07393,0.99382,-0.082748,0.72133,0.4433,0.041577,0.89541,-71.721

> view matrix models
> #121,0.89332,-0.10288,-0.43749,132.84,0.07393,0.99382,-0.082748,0.9532,0.4433,0.041577,0.89541,-71.701

> view matrix models
> #121,0.89332,-0.10288,-0.43749,132.86,0.07393,0.99382,-0.082748,0.91412,0.4433,0.041577,0.89541,-71.733

> ui mousemode right "rotate selected models"

> view matrix models
> #121,0.89493,-0.089023,-0.43724,129.84,0.067776,0.99565,-0.063993,-1.9784,0.44104,0.027634,0.89706,-68.947

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Fit14-26.cxs"

Window position QRect(-565,671 321x152) outside any known screen, using
primary screen  

> view matrix models
> #121,0.76265,-0.51489,-0.39149,228.89,0.48516,0.85565,-0.18024,-37.395,0.42778,-0.052474,0.90236,-52.029

> undo

Drag select of 825 residues, 5 pseudobonds  

> color zone #8 near sel distance 9.04

> select clear

> select add #123

282 atoms, 283 bonds, 36 residues, 1 model selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #123,0.90821,-0.047929,-0.41576,117.41,0.083457,0.99421,0.067694,48.92,0.41011,-0.096179,0.90695,-45.273

> view matrix models
> #123,0.91066,-0.035014,-0.41167,113.98,0.079071,0.99275,0.090477,45.759,0.40552,-0.11495,0.90683,-41.176

> view matrix models
> #123,0.90881,-0.041283,-0.41516,116.06,0.072623,0.99555,0.059979,52.268,0.41084,-0.08466,0.90777,-47.517

> ui mousemode right "rotate selected models"

> ui mousemode right "translate selected models"

> view matrix models
> #123,0.90881,-0.041283,-0.41516,115.84,0.072623,0.99555,0.059979,52.244,0.41084,-0.08466,0.90777,-46.516

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Fit14-26.cxs"

> select #8

2 models selected  

> transparency #8.1 50

> select #8

2 models selected  

> select clear

> select add #122

282 atoms, 283 bonds, 36 residues, 1 model selected  

> select subtract #122

Nothing selected  

> select add #119

1002 atoms, 1001 bonds, 1 pseudobond, 129 residues, 2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #119,0.8742,-0.043893,-0.48358,134.74,0.011478,0.9975,-0.069789,-15.477,0.48543,0.055459,0.87251,-76.674

> view matrix models
> #119,0.87615,-0.048359,-0.47961,134.38,0.022612,0.99798,-0.05932,-19.982,0.48151,0.041128,0.87547,-73.739

> view matrix models
> #119,0.87607,-0.017987,-0.48185,129.06,-0.0084903,0.99857,-0.052711,-15.05,0.48211,0.05027,0.87467,-75.44

> ui mousemode right "translate selected models"

> view matrix models
> #119,0.87607,-0.017987,-0.48185,128.39,-0.0084903,0.99857,-0.052711,-15.517,0.48211,0.05027,0.87467,-75.634

> select clear

> select add #121

1002 atoms, 1001 bonds, 1 pseudobond, 129 residues, 2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #121,0.89788,-0.063422,-0.43564,124.03,0.041764,0.99738,-0.059121,2.044,0.43825,0.03489,0.89818,-69.983

> undo

> select clear

> undo

> redo

Drag select of 8 postprocess_masked330_onepf.mrc , 4 residues  
Drag select of 8 postprocess_masked330_onepf.mrc , 5 residues  

> select clear

> select add #121

1002 atoms, 1001 bonds, 1 pseudobond, 129 residues, 2 models selected  

> view matrix models
> #121,0.91926,-0.083226,-0.38476,113.08,0.066245,0.99616,-0.057206,-3.1407,0.38804,0.027099,0.92124,-62.873

> view matrix models
> #121,0.90389,-0.09145,-0.41787,124.53,0.072858,0.99552,-0.06027,-3.754,0.42151,0.024032,0.9065,-66.168

> view matrix models
> #121,0.90641,-0.048122,-0.41964,116.11,0.028264,0.99817,-0.053416,3.506,0.42145,0.036556,0.90612,-68.463

> view matrix models
> #121,0.87156,-0.071379,-0.48506,140.99,0.014552,0.99268,-0.11993,20.878,0.49007,0.097467,0.86622,-86.062

> view matrix models
> #121,0.86303,-0.0598,-0.5016,143.89,0.010981,0.99495,-0.099722,17.073,0.50504,0.080555,0.85933,-84.513

> view matrix models
> #121,0.84038,0.083471,-0.53554,128.12,-0.18893,0.97121,-0.1451,71.866,0.50801,0.22311,0.83195,-106.74

> undo

> view matrix models
> #121,0.80379,-0.14193,-0.57774,187.17,0.042172,0.98228,-0.18263,29.924,0.59342,0.12244,0.79553,-97.688

> view matrix models
> #121,0.80264,-0.11919,-0.58443,184.43,0.009606,0.98229,-0.18713,37.523,0.59639,0.14459,0.78957,-101.31

> ui mousemode right "translate selected models"

> view matrix models
> #121,0.80264,-0.11919,-0.58443,185.32,0.009606,0.98229,-0.18713,38.525,0.59639,0.14459,0.78957,-100.58

> view matrix models
> #121,0.80264,-0.11919,-0.58443,184.88,0.009606,0.98229,-0.18713,37.882,0.59639,0.14459,0.78957,-101.14

> view matrix models
> #121,0.80264,-0.11919,-0.58443,185.07,0.009606,0.98229,-0.18713,37.806,0.59639,0.14459,0.78957,-101.63

> undo

> ui mousemode right "rotate selected models"

> view matrix models
> #121,0.80496,-0.10683,-0.58363,181.88,0.016702,0.98735,-0.15769,29.48,0.59309,0.11719,0.79656,-96.664

> view matrix models
> #121,0.80633,-0.098094,-0.58327,179.86,0.033826,0.99218,-0.1201,17.408,0.59049,0.077114,0.80335,-89.871

> view matrix models
> #121,0.82782,-0.11825,-0.54839,172.21,-0.012346,0.97345,-0.22855,52.484,0.56086,0.19597,0.80438,-106.65

> view matrix models
> #121,0.86289,-0.10086,-0.49523,150.89,-0.0022311,0.97912,-0.20329,44.198,0.50539,0.17652,0.84464,-99.73

> view matrix models
> #121,0.94355,-0.037637,-0.3291,88.538,0.034872,0.99929,-0.014302,-5.6488,0.3294,0.002018,0.94419,-50.544

> view matrix models
> #121,0.92847,-0.043142,-0.36889,100.76,0.031387,0.99879,-0.03781,-0.063818,0.37008,0.023527,0.9287,-59.852

> view matrix models
> #121,0.94351,-0.052865,-0.3271,91.042,0.028385,0.99646,-0.07917,9.3978,0.33012,0.065413,0.94167,-62.265

> view matrix models
> #121,0.92861,-0.055897,-0.36682,102.75,0.026476,0.99605,-0.084757,11.002,0.37011,0.068995,0.92642,-68.062

> view matrix models
> #121,0.92649,-0.050866,-0.37288,103.45,0.027777,0.99736,-0.067039,6.8859,0.3753,0.051753,0.92546,-65.646

> view matrix models
> #121,0.92378,-0.049584,-0.37969,105.15,0.034592,0.99833,-0.046211,1.0718,0.38135,0.029555,0.92396,-62.352

> view matrix models
> #121,0.92354,-0.054778,-0.37958,106.17,0.039817,0.99809,-0.047161,0.23736,0.38144,0.028441,0.92396,-62.158

> undo

> ui mousemode right "translate selected models"

> view matrix models
> #121,0.92378,-0.049584,-0.37969,105.65,0.034592,0.99833,-0.046211,0.91774,0.38135,0.029555,0.92396,-62.249

> view matrix models
> #121,0.92378,-0.049584,-0.37969,105.3,0.034592,0.99833,-0.046211,0.32237,0.38135,0.029555,0.92396,-62.342

> select clear

> select add #119

1002 atoms, 1001 bonds, 1 pseudobond, 129 residues, 2 models selected  

> view matrix models
> #119,0.87607,-0.017987,-0.48185,129.04,-0.0084903,0.99857,-0.052711,-16.243,0.48211,0.05027,0.87467,-75.532

> ui mousemode right "rotate selected models"

> view matrix models
> #119,0.87549,-0.029908,-0.4823,131.52,-0.0085159,0.99697,-0.077282,-10.943,0.48315,0.071767,0.87259,-79.422

> ui mousemode right "translate selected models"

> view matrix models
> #119,0.87549,-0.029908,-0.4823,131.64,-0.0085159,0.99697,-0.077282,-10.624,0.48315,0.071767,0.87259,-79.376

> select add #125

2286 atoms, 2285 bonds, 2 pseudobonds, 294 residues, 4 models selected  

> view matrix models
> #119,0.87549,-0.029908,-0.4823,131.95,-0.0085159,0.99697,-0.077282,-10.372,0.48315,0.071767,0.87259,-79.306,#125,0.92461,-0.034563,-0.37933,99.539,0.042229,0.99904,0.011903,14.564,0.37856,-0.027025,0.92518,-54.057

> ui mousemode right "rotate selected models"

> view matrix models
> #119,0.8743,-0.020796,-0.48494,130.73,-0.009271,0.99818,-0.059521,-14.003,0.48529,0.056535,0.87252,-76.416,#125,0.92412,-0.025212,-0.38126,98.499,0.039418,0.99879,0.029496,11.614,0.38005,-0.042287,0.924,-51.625

> undo

[Repeated 2 time(s)]

> redo

> select subtract #119

1284 atoms, 1284 bonds, 1 pseudobond, 165 residues, 2 models selected  

> view matrix models
> #125,0.92427,-0.027984,-0.38071,98.348,0.040247,0.99889,0.024288,12.275,0.3796,-0.037772,0.92438,-52.18

> ui mousemode right "translate selected models"

> view matrix models
> #125,0.92427,-0.027984,-0.38071,98.656,0.040247,0.99889,0.024288,12.099,0.3796,-0.037772,0.92438,-51.984

> select add #121

2286 atoms, 2285 bonds, 2 pseudobonds, 294 residues, 4 models selected  

> select subtract #125

1002 atoms, 1001 bonds, 1 pseudobond, 129 residues, 2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #121,0.92324,-0.050219,-0.38092,105.78,0.044038,0.99872,-0.024931,-6.0128,0.38169,0.0062428,0.92427,-58.031

> select clear

> select down

Nothing selected  

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Fit14-27.cxs"

> select add #124

282 atoms, 283 bonds, 36 residues, 1 model selected  

> select subtract #124

Nothing selected  

> select add #118

1002 atoms, 1001 bonds, 1 pseudobond, 129 residues, 2 models selected  

> view matrix models
> #118,0.92302,-0.085924,-0.37504,106.62,0.09897,0.99497,0.015624,26.307,0.37181,-0.051538,0.92688,-49.571

> select clear

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Fit14-27.cxs"

——— End of log from Fri Jan 12 07:27:46 2024 ———

opened ChimeraX session  

> show #!1 models

> hide #!1 models

> show #!4 models

> ui tool show "Color Zone"

> hide #!4 models

> hide #!8 models

> select clear

Drag select of 825 residues, 5 pseudobonds  

> show #!7 models

> hide #!7 models

> show #!4 models

> color zone #4 near sel distance 9.04

> volume splitbyzone #4

Opened post266flipy.mrc 0 as #126.1, grid size 274,274,274, pixel 1.51, shown
at level 0.0209, step 1, values float32  
Opened post266flipy.mrc 1 as #126.2, grid size 274,274,274, pixel 1.51, shown
at level 0.0209, step 1, values float32  
Opened post266flipy.mrc 2 as #126.3, grid size 274,274,274, pixel 1.51, shown
at level 0.0209, step 1, values float32  
Opened post266flipy.mrc 3 as #126.4, grid size 274,274,274, pixel 1.51, shown
at level 0.0209, step 1, values float32  
Opened post266flipy.mrc 4 as #126.5, grid size 274,274,274, pixel 1.51, shown
at level 0.0209, step 1, values float32  
Opened post266flipy.mrc 5 as #126.6, grid size 274,274,274, pixel 1.51, shown
at level 0.0209, step 1, values float32  

> hide #!126 models

> hide #!126.1 models

> volume #126.6 level 0.01818

> show #!126 models

> close #126

> color (#!117-125 & sel) orange red

> show #!4 models

> color zone #4 near sel distance 9.04

> color zone #4 near sel distance 8.96

> color zone #4 near sel distance 4.06

> volume splitbyzone #4

Opened post266flipy.mrc 0 as #126.1, grid size 274,274,274, pixel 1.51, shown
at level 0.0209, step 1, values float32  
Opened post266flipy.mrc 1 as #126.2, grid size 274,274,274, pixel 1.51, shown
at level 0.0209, step 1, values float32  

> hide #!126.1 models

> color sel bychain

> hide #!126 models

> show #!9 models

> hide #!9 models

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Fit14-27-1.pdb" #117 fromat pdb

Expected a keyword  

> select ~sel & ##selected

Nothing selected  

> select ~sel & ##selected

Nothing selected  

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Fit14-27-1.pdb" #117 format pdb

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Fit14-27-2.pdb" #118 format pdb

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Fit14-27-3.pdb" #119 format pdb

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Fit14-27-4.pdb" #120 format pdb

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Fit14-27-6.pdb" #121 format pdb

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Fit14-27-5.pdb" #121 format pdb

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Fit14-27-5.pdb" #122 format pdb

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Fit14-27-5.pdb" #121 format pdb

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Fit14-27-6.pdb" #122 format pdb

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Fit14-27-7.pdb" #123 format pdb

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Fit14-27-8.pdb" #124 format pdb

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Fit14-27-8.pdb" #125 format pdb

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Fit14-27-8.pdb" #124 format pdb

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Fit14-27-9.pdb" #125 format pdb

> show #!8 models

> select add #8

2 models selected  

> color #8.1 light gray

> transparency #8.1 50

> select clear

> select add #8

2 models selected  

> select subtract #8

Nothing selected  

> hide #!8 models

Drag select of 825 residues, 5 pseudobonds  

> show #!8 models

> color zone #8 near sel distance 9.04

> select #8

2 models selected  

> transparency #8.1 50

> select clear

> ui windowfill toggle

> open "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Fit14-27-1-stitchedtemp3-lightrefine2.pdb"

Summary of feedback from opening /Users/chaaban/Library/CloudStorage/OneDrive-
MRCLaboratoryofMolecularBiology/Documents/Carter
Lab/Diorge/Membranes/Fit14-27-1-stitchedtemp3-lightrefine2.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 PRO 0 118
LEU 0 142 1 25  
Start residue of secondary structure not found: HELIX 2 2 PRO 0 145 GLU 0 149
1 5  
PDB SEQRES record for chain D is incomplete. Ignoring input sequence records
as basis for sequence.  
  
Chain information for Fit14-27-1-stitchedtemp3-lightrefine2.pdb #127  
---  
Chain | Description  
9 E M | No description available  
D | No description available  
I | No description available  
N O T | No description available  
U | No description available  
  

> hide #!117-125,127 atoms

> show #!117-125,127 cartoons

> ui windowfill toggle

> close #127

> open "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Fit14-27-1-stitchedtemp3-lightrefine2.pdb"

Summary of feedback from opening /Users/chaaban/Library/CloudStorage/OneDrive-
MRCLaboratoryofMolecularBiology/Documents/Carter
Lab/Diorge/Membranes/Fit14-27-1-stitchedtemp3-lightrefine2.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 PRO 0 118
LEU 0 142 1 25  
Start residue of secondary structure not found: HELIX 2 2 PRO 0 145 GLU 0 149
1 5  
PDB SEQRES record for chain D is incomplete. Ignoring input sequence records
as basis for sequence.  
  
Chain information for Fit14-27-1-stitchedtemp3-lightrefine2.pdb #127  
---  
Chain | Description  
9 E M | No description available  
D | No description available  
I | No description available  
N O T | No description available  
U | No description available  
  

> hide #!117-125,127 atoms

> show #!117-125,127 cartoons

> hide #!109-125 target m

Drag select of 4 residues  

> delete atoms sel

> delete bonds sel

> kdssp

Unknown command: kdssp  

> ksdssp #127

Unknown command: ksdssp #127  

> color #!127 bychain

[Repeated 2 time(s)]Drag select of 820 residues  

> color zone #8 near sel distance 9.04

> select #8

2 models selected  

> transparency #8.1 50

> select clear

> open "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Fit14-27-1-stitchedtemp3-lightrefine3.pdb"

Summary of feedback from opening /Users/chaaban/Library/CloudStorage/OneDrive-
MRCLaboratoryofMolecularBiology/Documents/Carter
Lab/Diorge/Membranes/Fit14-27-1-stitchedtemp3-lightrefine3.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 PRO 0 118
LEU 0 142 1 25  
Start residue of secondary structure not found: HELIX 2 2 PRO 0 145 GLU 0 149
1 5  
PDB SEQRES record for chain D is incomplete. Ignoring input sequence records
as basis for sequence.  
  
Chain information for Fit14-27-1-stitchedtemp3-lightrefine3.pdb #128  
---  
Chain | Description  
9 E M | No description available  
D | No description available  
I | No description available  
N O T | No description available  
U | No description available  
  

> hide #!127 models

> hide #!128 atoms

> show #!128 cartoons

> color #!128 bychain

> close #127-128

> open "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Fit14-27-1-stitchedtemp3-lightrefine4.pdb"

Summary of feedback from opening /Users/chaaban/Library/CloudStorage/OneDrive-
MRCLaboratoryofMolecularBiology/Documents/Carter
Lab/Diorge/Membranes/Fit14-27-1-stitchedtemp3-lightrefine4.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 PRO 0 118
LEU 0 142 1 25  
Start residue of secondary structure not found: HELIX 2 2 PRO 0 145 GLU 0 149
1 5  
PDB SEQRES record for chain D is incomplete. Ignoring input sequence records
as basis for sequence.  
  
Chain information for Fit14-27-1-stitchedtemp3-lightrefine4.pdb #127  
---  
Chain | Description  
9 E M | No description available  
D | No description available  
I | No description available  
N O T | No description available  
U | No description available  
  

> hide #!127 atoms

> show #!127 cartoons

> color #!127 bychain

[Repeated 1 time(s)]

> color zone #8 near #127 distance 9.04

> volume splitbyzone #8

Opened postprocess_masked330_onepf.mrc 0 as #128.1, grid size 274,274,274,
pixel 1.51, shown at level 0.0121, step 1, values float32  
Opened postprocess_masked330_onepf.mrc 1 as #128.2, grid size 274,274,274,
pixel 1.51, shown at level 0.0121, step 1, values float32  
Opened postprocess_masked330_onepf.mrc 2 as #128.3, grid size 274,274,274,
pixel 1.51, shown at level 0.0121, step 1, values float32  
Opened postprocess_masked330_onepf.mrc 3 as #128.4, grid size 274,274,274,
pixel 1.51, shown at level 0.0121, step 1, values float32  
Opened postprocess_masked330_onepf.mrc 4 as #128.5, grid size 274,274,274,
pixel 1.51, shown at level 0.0121, step 1, values float32  
Opened postprocess_masked330_onepf.mrc 5 as #128.6, grid size 274,274,274,
pixel 1.51, shown at level 0.0121, step 1, values float32  
Opened postprocess_masked330_onepf.mrc 6 as #128.7, grid size 274,274,274,
pixel 1.51, shown at level 0.0121, step 1, values float32  
Opened postprocess_masked330_onepf.mrc 7 as #128.8, grid size 274,274,274,
pixel 1.51, shown at level 0.0121, step 1, values float32  
Opened postprocess_masked330_onepf.mrc 8 as #128.9, grid size 274,274,274,
pixel 1.51, shown at level 0.0121, step 1, values float32  
Opened postprocess_masked330_onepf.mrc 9 as #128.10, grid size 274,274,274,
pixel 1.51, shown at level 0.0121, step 1, values float32  

> hide #!128.9 models

> hide #!128.8 models

> hide #!128.7 models

> hide #!128.6 models

> hide #!128.5 models

> hide #!128.4 models

> hide #!128.3 models

> hide #!128 models

> show #!128 models

> hide #!128.1 models

> hide #!128.2 models

> show #!115 models

> hide #!115 models

> show #!105 models

> matchmaker \105/6 to \127/U

Missing or invalid "matchAtoms" argument: invalid atoms specifier  

> matchmaker #105/6 to #127/U

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker Fit14-27-1-stitchedtemp3-lightrefine4.pdb, chain U (#127) with copy
of pointy-1pf.pdb, chain 6 (#105), sequence alignment score = 707.1  
RMSD between 73 pruned atom pairs is 0.586 angstroms; (across all 139 pairs:
8.194)  
  

> select #128.10

2 models selected  

> transparency #128.10.1 50

> select clear

Drag select of 128.10 postprocess_masked330_onepf.mrc 9 , 14 residues  

> select #128.10

2 models selected  

> select clear

> select ~sel & ##selected

Nothing selected  

> select ~sel & ##selected

Nothing selected  

> matchmaker #105/6:104-140 to #127/U:104-140

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker Fit14-27-1-stitchedtemp3-lightrefine4.pdb, chain U (#127) with copy
of pointy-1pf.pdb, chain 6 (#105), sequence alignment score = 177.7  
RMSD between 25 pruned atom pairs is 0.722 angstroms; (across all 37 pairs:
3.228)  
  

> matchmaker #105/6:90-140 to #127/U:90-140

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker Fit14-27-1-stitchedtemp3-lightrefine4.pdb, chain U (#127) with copy
of pointy-1pf.pdb, chain 6 (#105), sequence alignment score = 248.4  
RMSD between 24 pruned atom pairs is 0.635 angstroms; (across all 51 pairs:
5.850)  
  

> matchmaker #105/6:90-120 to #127/U:90-120

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker Fit14-27-1-stitchedtemp3-lightrefine4.pdb, chain U (#127) with copy
of pointy-1pf.pdb, chain 6 (#105), sequence alignment score = 143.8  
RMSD between 23 pruned atom pairs is 0.781 angstroms; (across all 31 pairs:
2.936)  
  

> matchmaker #105/6:90-130 to #127/U:90-130

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker Fit14-27-1-stitchedtemp3-lightrefine4.pdb, chain U (#127) with copy
of pointy-1pf.pdb, chain 6 (#105), sequence alignment score = 195.4  
RMSD between 22 pruned atom pairs is 0.704 angstroms; (across all 41 pairs:
5.102)  
  

> matchmaker #105/6:94-130 to #127/U:94-130

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker Fit14-27-1-stitchedtemp3-lightrefine4.pdb, chain U (#127) with copy
of pointy-1pf.pdb, chain 6 (#105), sequence alignment score = 174.9  
RMSD between 18 pruned atom pairs is 0.729 angstroms; (across all 37 pairs:
5.288)  
  

> matchmaker #105/6:100-130 to #127/U:100-130

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker Fit14-27-1-stitchedtemp3-lightrefine4.pdb, chain U (#127) with copy
of pointy-1pf.pdb, chain 6 (#105), sequence alignment score = 145.2  
RMSD between 13 pruned atom pairs is 0.964 angstroms; (across all 31 pairs:
3.840)  
  

> matchmaker #105/6:100-140 to #127/U:100-140

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker Fit14-27-1-stitchedtemp3-lightrefine4.pdb, chain U (#127) with copy
of pointy-1pf.pdb, chain 6 (#105), sequence alignment score = 198.2  
RMSD between 24 pruned atom pairs is 0.635 angstroms; (across all 41 pairs:
3.786)  
  

> matchmaker #105/6:100-135 to #127/U:100-135

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker Fit14-27-1-stitchedtemp3-lightrefine4.pdb, chain U (#127) with copy
of pointy-1pf.pdb, chain 6 (#105), sequence alignment score = 171.7  
RMSD between 19 pruned atom pairs is 0.497 angstroms; (across all 36 pairs:
4.239)  
  

> matchmaker #105/6:96-135 to #127/U:96-135

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker Fit14-27-1-stitchedtemp3-lightrefine4.pdb, chain U (#127) with copy
of pointy-1pf.pdb, chain 6 (#105), sequence alignment score = 191.5  
RMSD between 18 pruned atom pairs is 0.484 angstroms; (across all 40 pairs:
5.045)  
  

> matchmaker #105/6:96-132 to #127/U:96-132

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker Fit14-27-1-stitchedtemp3-lightrefine4.pdb, chain U (#127) with copy
of pointy-1pf.pdb, chain 6 (#105), sequence alignment score = 175.6  
RMSD between 13 pruned atom pairs is 0.964 angstroms; (across all 37 pairs:
4.157)  
  

> matchmaker #105/6:96-133 to #127/U:96-133

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker Fit14-27-1-stitchedtemp3-lightrefine4.pdb, chain U (#127) with copy
of pointy-1pf.pdb, chain 6 (#105), sequence alignment score = 181.6  
RMSD between 15 pruned atom pairs is 0.488 angstroms; (across all 38 pairs:
5.005)  
  

> matchmaker #104/6:96-133 to #104/U:96-133

No 'to' model specified  

> matchmaker #105/6:94-133 to #127/U:94-133

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker Fit14-27-1-stitchedtemp3-lightrefine4.pdb, chain U (#127) with copy
of pointy-1pf.pdb, chain 6 (#105), sequence alignment score = 191.5  
RMSD between 16 pruned atom pairs is 1.015 angstroms; (across all 40 pairs:
4.428)  
  

> matchmaker #105/6:95-133 to #127/U:95-133

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker Fit14-27-1-stitchedtemp3-lightrefine4.pdb, chain U (#127) with copy
of pointy-1pf.pdb, chain 6 (#105), sequence alignment score = 186.9  
RMSD between 14 pruned atom pairs is 0.493 angstroms; (across all 39 pairs:
5.248)  
  

> select ~sel & ##selected

Nothing selected  

> select ~sel & ##selected

Nothing selected  

> matchmaker #105/6:94-133 to #127/U:94-133

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker Fit14-27-1-stitchedtemp3-lightrefine4.pdb, chain U (#127) with copy
of pointy-1pf.pdb, chain 6 (#105), sequence alignment score = 191.5  
RMSD between 16 pruned atom pairs is 1.015 angstroms; (across all 40 pairs:
4.428)  
  

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/temppf.pdb" relModel #8 format pdb

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/tempvol.mrc" relModel #8 format mrc

Expected a models specifier or a keyword  

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/temppf.pdb" #105 relModel #8 format pdb

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/temppf.pdb" #128.10 relModel #8 format mrc

Expected a keyword  

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/temppf.mrc" #128.10 relModel #8 format mrc

Expected a keyword  

> close #128.1-9

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/temppf.mrc" #128 relModel #8 format mrc

Expected a keyword  

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/temppf.mrc" #128 format mrc

> volume splitbyzone #8

Opened postprocess_masked330_onepf.mrc 0 as #129.1, grid size 274,274,274,
pixel 1.51, shown at level 0.0121, step 1, values float32  
Opened postprocess_masked330_onepf.mrc 1 as #129.2, grid size 274,274,274,
pixel 1.51, shown at level 0.0121, step 1, values float32  
Opened postprocess_masked330_onepf.mrc 2 as #129.3, grid size 274,274,274,
pixel 1.51, shown at level 0.0121, step 1, values float32  
Opened postprocess_masked330_onepf.mrc 3 as #129.4, grid size 274,274,274,
pixel 1.51, shown at level 0.0121, step 1, values float32  
Opened postprocess_masked330_onepf.mrc 4 as #129.5, grid size 274,274,274,
pixel 1.51, shown at level 0.0121, step 1, values float32  
Opened postprocess_masked330_onepf.mrc 5 as #129.6, grid size 274,274,274,
pixel 1.51, shown at level 0.0121, step 1, values float32  
Opened postprocess_masked330_onepf.mrc 6 as #129.7, grid size 274,274,274,
pixel 1.51, shown at level 0.0121, step 1, values float32  
Opened postprocess_masked330_onepf.mrc 7 as #129.8, grid size 274,274,274,
pixel 1.51, shown at level 0.0121, step 1, values float32  
Opened postprocess_masked330_onepf.mrc 8 as #129.9, grid size 274,274,274,
pixel 1.51, shown at level 0.0121, step 1, values float32  
Opened postprocess_masked330_onepf.mrc 9 as #129.10, grid size 274,274,274,
pixel 1.51, shown at level 0.0121, step 1, values float32  

> hide #!128.10 models

> hide #!129.2 models

> show #!129.2 models

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/temppfnext.mrc" #129.2 format mrc

> open "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Fit14-27-1-stitchedtemp3-lightrefine4-newrefinedpf-
> alsoneighbour-2.pdb"

Summary of feedback from opening /Users/chaaban/Library/CloudStorage/OneDrive-
MRCLaboratoryofMolecularBiology/Documents/Carter
Lab/Diorge/Membranes/Fit14-27-1-stitchedtemp3-lightrefine4-newrefinedpf-
alsoneighbour-2.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 PRO 0 118
LEU 0 142 1 25  
Start residue of secondary structure not found: HELIX 2 2 PRO 0 145 GLU 0 149
1 5  
PDB SEQRES record for chain D is incomplete. Ignoring input sequence records
as basis for sequence.  
  
Chain information for Fit14-27-1-stitchedtemp3-lightrefine4-newrefinedpf-
alsoneighbour-2.pdb #130  
---  
Chain | Description  
6 | No description available  
9 E M | No description available  
D | No description available  
I | No description available  
N O T | No description available  
  

> hide #!105,127,130 atoms

> show #!105,127,130 cartoons

> hide #!129 models

> hide #!128 models

> hide #!127 models

> hide #!105 models

> show #!9 models

> hide #!9 models

> show #!8 models

> color zone #8 near #130 distance 9.04

> color #!130 bychain

> color zone #8 near #130 distance 9.04

> select #8

2 models selected  

> transparency #8.1 50

> ui windowfill toggle

> select clear

> ui windowfill toggle

[Repeated 1 time(s)]

> ksdssp #130

Unknown command: ksdssp #130  

> kdssp #130

Unknown command: kdssp #130  

> dssp #130

> isolde start

> set selectionWidth 4

Forcefield cache not found or out of date. Regenerating from ffXML files. This
is normal if running ISOLDE for the first time, or after upgrading OpenMM.  

Done loading forcefield  

> isolde set simFidelityMode Medium/Medium

ISOLDE: setting sim fidelity mode to Medium/Medium  
nonbonded_cutoff_distance = 0.900000  
use_gbsa = True  
gbsa_cutoff = 1.100000  

> clipper associate #8 toModel #2

Opened postprocess_masked330_onepf.mrc as #2.1.1.2, grid size 274,274,274,
pixel 1.51, shown at step 1, values float32  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 8 residues in model #130 to IUPAC-IUB
standards.  
Chain information for Fit14-27-1-stitchedtemp3-lightrefine4-newrefinedpf-
alsoneighbour-2.pdb  
---  
Chain | Description  
8.2/6 | No description available  
8.2/9 8.2/E 8.2/M | No description available  
8.2/D | No description available  
8.2/I | No description available  
8.2/N 8.2/O 8.2/T | No description available  
  

> open "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/postprocess_masked330_onepf.mrc"

Opened postprocess_masked330_onepf.mrc as #130, grid size 274,274,274, pixel
1.51, shown at level 9.42e-06, step 2, values float32  

> clipper associate #130 toModel #8

Opened postprocess_masked330_onepf.mrc as #8.1.1.1, grid size 274,274,274,
pixel 1.51, shown at step 1, values float32  

> isolde restrain distances "#8.2/6", #8.2/9", #8.2/E", "#8.2/M", "#8.2/D",
> "#8.2/I", "#8.2/N", "#8.2/O", "#8.2/T" templateAtoms "#8.2/6", #8.2/9",
> #8.2/E", "#8.2/M", "#8.2/D", "#8.2/I", "#8.2/N", "#8.2/O", "#8.2/T"
> distancecutoff 10

Missing or invalid "atoms" argument: only initial part "#8.2/9"" of atom
specifier valid  

> isolde restrain distances "#8.2/6", "#8.2/9", #8.2/E", "#8.2/M", "#8.2/D",
> "#8.2/I", "#8.2/N", "#8.2/O", "#8.2/T" templateAtoms "#8.2/6", "#8.2/9",
> #8.2/E", "#8.2/M", "#8.2/D", "#8.2/I", "#8.2/N", "#8.2/O", "#8.2/T"
> distanceCutoff 10

Each atom selection should be from a single chain!  

> isolde restrain distances "#8.2/6", "#8.2/9", #8.2/E", "#8.2/M", "#8.2/D",
> "#8.2/I", "#8.2/N", "#8.2/O", "#8.2/T" templateAtoms "#8.2/6", "#8.2/9",
> #8.2/E", "#8.2/M", "#8.2/D", "#8.2/I", "#8.2/N", "#8.2/O", "#8.2/T"
> distanceCutoff 10

Each atom selection should be from a single chain!  

> isolde restrain distances "#8/6", "#8/9", #8/E", "#8/M", "#8/D", "#8/I",
> "#8/N", "#8/O", "#8/T" templateAtoms "#8/6", "#8/9", #8/E", "#8/M", "#8/D",
> "#8/I", "#8/N", "#8/O", "#8/T" distanceCutoff 10

Each atom selection should be from a single chain!  

> hide #!8.2 models

> show #!8.2 models

> isolde restrain distances "#8.2/6", "#8.2/9", "#8.2/E", "#8.2/M", "#8.2/D",
> "#8.2/I", "#8.2/N", "#8.2/O", "#8.2/T" templateAtoms "#8.2/6", "#8.2/9",
> "#8.2/E", "#8.2/M", "#8.2/D", "#8.2/I", "#8.2/N", "#8.2/O", "#8.2/T"
> distanceCutoff 10

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  

> isolde sim start #8.2/D,I-T,9,E,6

Sim termination reason: None  
ISOLDE: stopped sim  

> addh #8.2

Summary of feedback from adding hydrogens to
Fit14-27-1-stitchedtemp3-lightrefine4-newrefinedpf-alsoneighbour-2.pdb #8.2  
---  
notes | No usable SEQRES records for
Fit14-27-1-stitchedtemp3-lightrefine4-newrefinedpf-alsoneighbour-2.pdb (#8.2)
chain 6; guessing termini instead  
No usable SEQRES records for
Fit14-27-1-stitchedtemp3-lightrefine4-newrefinedpf-alsoneighbour-2.pdb (#8.2)
chain 9; guessing termini instead  
No usable SEQRES records for
Fit14-27-1-stitchedtemp3-lightrefine4-newrefinedpf-alsoneighbour-2.pdb (#8.2)
chain D; guessing termini instead  
No usable SEQRES records for
Fit14-27-1-stitchedtemp3-lightrefine4-newrefinedpf-alsoneighbour-2.pdb (#8.2)
chain E; guessing termini instead  
Termini for Fit14-27-1-stitchedtemp3-lightrefine4-newrefinedpf-
alsoneighbour-2.pdb (#8.2) chain I determined from SEQRES records  
No usable SEQRES records for
Fit14-27-1-stitchedtemp3-lightrefine4-newrefinedpf-alsoneighbour-2.pdb (#8.2)
chain M; guessing termini instead  
No usable SEQRES records for
Fit14-27-1-stitchedtemp3-lightrefine4-newrefinedpf-alsoneighbour-2.pdb (#8.2)
chain N; guessing termini instead  
No usable SEQRES records for
Fit14-27-1-stitchedtemp3-lightrefine4-newrefinedpf-alsoneighbour-2.pdb (#8.2)
chain O; guessing termini instead  
No usable SEQRES records for
Fit14-27-1-stitchedtemp3-lightrefine4-newrefinedpf-alsoneighbour-2.pdb (#8.2)
chain T; guessing termini instead  
Chain-initial residues that are actual N termini:
Fit14-27-1-stitchedtemp3-lightrefine4-newrefinedpf-alsoneighbour-2.pdb #8.2/6
LYS 3, Fit14-27-1-stitchedtemp3-lightrefine4-newrefinedpf-alsoneighbour-2.pdb
#8.2/9 LYS 3, Fit14-27-1-stitchedtemp3-lightrefine4-newrefinedpf-
alsoneighbour-2.pdb #8.2/D LYS 3,
Fit14-27-1-stitchedtemp3-lightrefine4-newrefinedpf-alsoneighbour-2.pdb #8.2/E
LYS 3, Fit14-27-1-stitchedtemp3-lightrefine4-newrefinedpf-alsoneighbour-2.pdb
#8.2/M LYS 3, Fit14-27-1-stitchedtemp3-lightrefine4-newrefinedpf-
alsoneighbour-2.pdb #8.2/N SER 117,
Fit14-27-1-stitchedtemp3-lightrefine4-newrefinedpf-alsoneighbour-2.pdb #8.2/O
SER 117, Fit14-27-1-stitchedtemp3-lightrefine4-newrefinedpf-
alsoneighbour-2.pdb #8.2/T SER 117,
Fit14-27-1-stitchedtemp3-lightrefine4-newrefinedpf-alsoneighbour-2.pdb #8.2/D
LYS 3, Fit14-27-1-stitchedtemp3-lightrefine4-newrefinedpf-alsoneighbour-2.pdb
#8.2/D GLY 53, Fit14-27-1-stitchedtemp3-lightrefine4-newrefinedpf-
alsoneighbour-2.pdb #8.2/M LYS 3,
Fit14-27-1-stitchedtemp3-lightrefine4-newrefinedpf-alsoneighbour-2.pdb #8.2/M
GLY 53, Fit14-27-1-stitchedtemp3-lightrefine4-newrefinedpf-alsoneighbour-2.pdb
#8.2/N SER 117, Fit14-27-1-stitchedtemp3-lightrefine4-newrefinedpf-
alsoneighbour-2.pdb #8.2/O SER 117,
Fit14-27-1-stitchedtemp3-lightrefine4-newrefinedpf-alsoneighbour-2.pdb #8.2/T
SER 117, Fit14-27-1-stitchedtemp3-lightrefine4-newrefinedpf-
alsoneighbour-2.pdb #8.2/9 LYS 3,
Fit14-27-1-stitchedtemp3-lightrefine4-newrefinedpf-alsoneighbour-2.pdb #8.2/9
GLY 53, Fit14-27-1-stitchedtemp3-lightrefine4-newrefinedpf-alsoneighbour-2.pdb
#8.2/E LYS 3, Fit14-27-1-stitchedtemp3-lightrefine4-newrefinedpf-
alsoneighbour-2.pdb #8.2/E GLY 53,
Fit14-27-1-stitchedtemp3-lightrefine4-newrefinedpf-alsoneighbour-2.pdb #8.2/6
LYS 3, Fit14-27-1-stitchedtemp3-lightrefine4-newrefinedpf-alsoneighbour-2.pdb
#8.2/6 GLY 53  
Chain-initial residues that are not actual N termini:
Fit14-27-1-stitchedtemp3-lightrefine4-newrefinedpf-alsoneighbour-2.pdb #8.2/6
GLY 53, Fit14-27-1-stitchedtemp3-lightrefine4-newrefinedpf-alsoneighbour-2.pdb
#8.2/9 GLY 53, Fit14-27-1-stitchedtemp3-lightrefine4-newrefinedpf-
alsoneighbour-2.pdb #8.2/D GLY 53,
Fit14-27-1-stitchedtemp3-lightrefine4-newrefinedpf-alsoneighbour-2.pdb #8.2/E
GLY 53, Fit14-27-1-stitchedtemp3-lightrefine4-newrefinedpf-alsoneighbour-2.pdb
#8.2/I GLU 155, Fit14-27-1-stitchedtemp3-lightrefine4-newrefinedpf-
alsoneighbour-2.pdb #8.2/M GLY 53  
Chain-final residues that are actual C termini:
Fit14-27-1-stitchedtemp3-lightrefine4-newrefinedpf-alsoneighbour-2.pdb #8.2/I
GLU 170, Fit14-27-1-stitchedtemp3-lightrefine4-newrefinedpf-
alsoneighbour-2.pdb #8.2/D MET 49,
Fit14-27-1-stitchedtemp3-lightrefine4-newrefinedpf-alsoneighbour-2.pdb #8.2/D
GLU 170, Fit14-27-1-stitchedtemp3-lightrefine4-newrefinedpf-
alsoneighbour-2.pdb #8.2/M MET 49,
Fit14-27-1-stitchedtemp3-lightrefine4-newrefinedpf-alsoneighbour-2.pdb #8.2/M
VAL 116, Fit14-27-1-stitchedtemp3-lightrefine4-newrefinedpf-
alsoneighbour-2.pdb #8.2/N GLU 170,
Fit14-27-1-stitchedtemp3-lightrefine4-newrefinedpf-alsoneighbour-2.pdb #8.2/O
GLU 170, Fit14-27-1-stitchedtemp3-lightrefine4-newrefinedpf-
alsoneighbour-2.pdb #8.2/T GLU 170,
Fit14-27-1-stitchedtemp3-lightrefine4-newrefinedpf-alsoneighbour-2.pdb #8.2/9
MET 49, Fit14-27-1-stitchedtemp3-lightrefine4-newrefinedpf-alsoneighbour-2.pdb
#8.2/9 VAL 116, Fit14-27-1-stitchedtemp3-lightrefine4-newrefinedpf-
alsoneighbour-2.pdb #8.2/E MET 49,
Fit14-27-1-stitchedtemp3-lightrefine4-newrefinedpf-alsoneighbour-2.pdb #8.2/E
VAL 116, Fit14-27-1-stitchedtemp3-lightrefine4-newrefinedpf-
alsoneighbour-2.pdb #8.2/6 MET 49,
Fit14-27-1-stitchedtemp3-lightrefine4-newrefinedpf-alsoneighbour-2.pdb #8.2/6
GLU 149  
Chain-final residues that are not actual C termini:
Fit14-27-1-stitchedtemp3-lightrefine4-newrefinedpf-alsoneighbour-2.pdb #8.2/6
GLU 149, Fit14-27-1-stitchedtemp3-lightrefine4-newrefinedpf-
alsoneighbour-2.pdb #8.2/6 MET 49,
Fit14-27-1-stitchedtemp3-lightrefine4-newrefinedpf-alsoneighbour-2.pdb #8.2/9
VAL 116, Fit14-27-1-stitchedtemp3-lightrefine4-newrefinedpf-
alsoneighbour-2.pdb #8.2/9 MET 49,
Fit14-27-1-stitchedtemp3-lightrefine4-newrefinedpf-alsoneighbour-2.pdb #8.2/D
GLU 170, Fit14-27-1-stitchedtemp3-lightrefine4-newrefinedpf-
alsoneighbour-2.pdb #8.2/D MET 49,
Fit14-27-1-stitchedtemp3-lightrefine4-newrefinedpf-alsoneighbour-2.pdb #8.2/E
VAL 116, Fit14-27-1-stitchedtemp3-lightrefine4-newrefinedpf-
alsoneighbour-2.pdb #8.2/E MET 49,
Fit14-27-1-stitchedtemp3-lightrefine4-newrefinedpf-alsoneighbour-2.pdb #8.2/M
VAL 116, Fit14-27-1-stitchedtemp3-lightrefine4-newrefinedpf-
alsoneighbour-2.pdb #8.2/M MET 49,
Fit14-27-1-stitchedtemp3-lightrefine4-newrefinedpf-alsoneighbour-2.pdb #8.2/N
GLU 170, Fit14-27-1-stitchedtemp3-lightrefine4-newrefinedpf-
alsoneighbour-2.pdb #8.2/O GLU 170,
Fit14-27-1-stitchedtemp3-lightrefine4-newrefinedpf-alsoneighbour-2.pdb #8.2/T
GLU 170  
Missing OXT added to C-terminal residue
Fit14-27-1-stitchedtemp3-lightrefine4-newrefinedpf-alsoneighbour-2.pdb #8.2/I
GLU 170  
Missing OXT added to C-terminal residue
Fit14-27-1-stitchedtemp3-lightrefine4-newrefinedpf-alsoneighbour-2.pdb #8.2/D
MET 49  
Missing OXT added to C-terminal residue
Fit14-27-1-stitchedtemp3-lightrefine4-newrefinedpf-alsoneighbour-2.pdb #8.2/D
GLU 170  
Missing OXT added to C-terminal residue
Fit14-27-1-stitchedtemp3-lightrefine4-newrefinedpf-alsoneighbour-2.pdb #8.2/M
MET 49  
Missing OXT added to C-terminal residue
Fit14-27-1-stitchedtemp3-lightrefine4-newrefinedpf-alsoneighbour-2.pdb #8.2/M
VAL 116  
9 messages similar to the above omitted  
805 hydrogen bonds  
Adding 'H' to Fit14-27-1-stitchedtemp3-lightrefine4-newrefinedpf-
alsoneighbour-2.pdb #8.2/6 GLY 53  
Adding 'H' to Fit14-27-1-stitchedtemp3-lightrefine4-newrefinedpf-
alsoneighbour-2.pdb #8.2/9 GLY 53  
Adding 'H' to Fit14-27-1-stitchedtemp3-lightrefine4-newrefinedpf-
alsoneighbour-2.pdb #8.2/D GLY 53  
Adding 'H' to Fit14-27-1-stitchedtemp3-lightrefine4-newrefinedpf-
alsoneighbour-2.pdb #8.2/E GLY 53  
Adding 'H' to Fit14-27-1-stitchedtemp3-lightrefine4-newrefinedpf-
alsoneighbour-2.pdb #8.2/I GLU 155  
1 messages similar to the above omitted  
6498 hydrogens added  
  

> isolde sim start #8.2/D,I-T,9,E,6

ISOLDE: started sim  

> hide sel atoms

> show sel cartoons

> ui windowfill toggle

> isolde sim stop discardTo start

Sim termination reason: None  
reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde restrain distances "#8.2/6", "#8.2/9", "#8.2/E", "#8.2/M", "#8.2/D",
> "#8.2/I", "#8.2/N", "#8.2/O", "#8.2/T" templateAtoms "#8.2/6", "#8.2/9",
> "#8.2/E", "#8.2/M", "#8.2/D", "#8.2/I", "#8.2/N", "#8.2/O", "#8.2/T"
> distanceCutoff 5

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  

> close #8.2.8

> isolde restrain distances "#8.2/6", "#8.2/9", "#8.2/E", "#8.2/M", "#8.2/D",
> "#8.2/I", "#8.2/N", "#8.2/O", "#8.2/T" templateAtoms "#8.2/6", "#8.2/9",
> "#8.2/E", "#8.2/M", "#8.2/D", "#8.2/I", "#8.2/N", "#8.2/O", "#8.2/T"
> distanceCutoff 5

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  

> isolde sim start #8.2/D,I-T,9,E,6

ISOLDE: started sim  

> hide sel atoms

> show sel cartoons

> isolde sim stop discardTo start

Sim termination reason: None  
reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> select subtract #8.2/N:117-143

12478 atoms, 12502 bonds, 793 residues, 2 models selected  

> isolde sim start #8.2/D,I-M,O-T,9,E,6/N:144-170

ISOLDE: started sim  

> hide sel atoms

> show sel cartoons

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 11 residues in model #8.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> select clear

> hide #!8.2 atoms

> show #!8.2 cartoons

[Repeated 1 time(s)]

> open "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Fit14-27-1-stitchedtemp3-lightrefine4-newrefinedpf-
> alsoneighbour-2.pdb"

Summary of feedback from opening /Users/chaaban/Library/CloudStorage/OneDrive-
MRCLaboratoryofMolecularBiology/Documents/Carter
Lab/Diorge/Membranes/Fit14-27-1-stitchedtemp3-lightrefine4-newrefinedpf-
alsoneighbour-2.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 PRO 0 118
LEU 0 142 1 25  
Start residue of secondary structure not found: HELIX 2 2 PRO 0 145 GLU 0 149
1 5  
PDB SEQRES record for chain D is incomplete. Ignoring input sequence records
as basis for sequence.  
  
Chain information for Fit14-27-1-stitchedtemp3-lightrefine4-newrefinedpf-
alsoneighbour-2.pdb #130  
---  
Chain | Description  
6 | No description available  
9 E M | No description available  
D | No description available  
I | No description available  
N O T | No description available  
  

> hide #!130#!8.2 atoms

> hide #!130#!8.2 cartoons

> show #!130#!8.2 cartoons

> ui windowfill toggle

> open "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/postprocess_masked330_onepf.mrc"

Opened postprocess_masked330_onepf.mrc as #131, grid size 274,274,274, pixel
1.51, shown at level 9.42e-06, step 2, values float32  

> volume #131 level 0.01334

> volume #131 step 1

> select clear

[Repeated 1 time(s)]

> select add #131

2 models selected  

> transparency #131.1 50

> select subtract #131

Nothing selected  

> ui windowfill toggle

[Repeated 1 time(s)]

> volume #131 level 0.02878

> volume #131 level 0.02026

> volume #131 level 0.01813

> hide #!130 models

> hide #!131 models

> show #!7 models

> volume #7 level 0.01481

> hide #!7 models

> show #!131 models

> volume #131 level 0.006285

> volume #131 level 0.01414

> hide #!131 models

> show #!131 models

> volume #131 level 0.005486

> hide #!131 models

> show #!131 models

> volume #131 level 0.01148

> volume #131 level 0.01574

> ui windowfill toggle

[Repeated 1 time(s)]

> open "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Fit14-27-1-stitchedtemp3-lightrefine4-newrefinedpf-
> alsoneighbour-2-refined-2-fixcrosshelix-3-refined.pdb"

Summary of feedback from opening /Users/chaaban/Library/CloudStorage/OneDrive-
MRCLaboratoryofMolecularBiology/Documents/Carter
Lab/Diorge/Membranes/Fit14-27-1-stitchedtemp3-lightrefine4-newrefinedpf-
alsoneighbour-2-refined-2-fixcrosshelix-3-refined.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 PRO 0 118
LEU 0 142 1 25  
Start residue of secondary structure not found: HELIX 2 2 PRO 0 145 GLU 0 149
1 5  
PDB SEQRES record for chain D is incomplete. Ignoring input sequence records
as basis for sequence.  
  
Chain information for Fit14-27-1-stitchedtemp3-lightrefine4-newrefinedpf-
alsoneighbour-2-refined-2-fixcrosshelix-3-refined.pdb #132  
---  
Chain | Description  
6 | No description available  
9 M | No description available  
D | No description available  
E | No description available  
I | No description available  
N O T | No description available  
  

> hide #!132#!8.2 atoms

> show #!132#!8.2 cartoons

> open "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Fit14-27-1-stitchedtemp3-lightrefine4-newrefinedpf-
> alsoneighbour-2-refined-2-fixcrosshelix-3-refined-2.pdb"

Summary of feedback from opening /Users/chaaban/Library/CloudStorage/OneDrive-
MRCLaboratoryofMolecularBiology/Documents/Carter
Lab/Diorge/Membranes/Fit14-27-1-stitchedtemp3-lightrefine4-newrefinedpf-
alsoneighbour-2-refined-2-fixcrosshelix-3-refined-2.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 PRO 0 118
LEU 0 142 1 25  
Start residue of secondary structure not found: HELIX 2 2 PRO 0 145 GLU 0 149
1 5  
PDB SEQRES record for chain D is incomplete. Ignoring input sequence records
as basis for sequence.  
  
Chain information for Fit14-27-1-stitchedtemp3-lightrefine4-newrefinedpf-
alsoneighbour-2-refined-2-fixcrosshelix-3-refined-2.pdb #133  
---  
Chain | Description  
6 | No description available  
9 M | No description available  
D | No description available  
E | No description available  
I | No description available  
N O T | No description available  
  

> hide #!132-133#!8.2 atoms

> show #!132-133#!8.2 cartoons

> hide #!131 models

> show #!131 models

> hide #!132 models

> show #!132 models

> hide #!133 models

> open "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Fit14-27-1-stitchedtemp3-lightrefine4-newrefinedpf-
> alsoneighbour-2-refined-2-fixcrosshelix-3-refined-2.pdb"

Summary of feedback from opening /Users/chaaban/Library/CloudStorage/OneDrive-
MRCLaboratoryofMolecularBiology/Documents/Carter
Lab/Diorge/Membranes/Fit14-27-1-stitchedtemp3-lightrefine4-newrefinedpf-
alsoneighbour-2-refined-2-fixcrosshelix-3-refined-2.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 PRO 0 118
LEU 0 142 1 25  
Start residue of secondary structure not found: HELIX 2 2 PRO 0 145 GLU 0 149
1 5  
PDB SEQRES record for chain D is incomplete. Ignoring input sequence records
as basis for sequence.  
  
Chain information for Fit14-27-1-stitchedtemp3-lightrefine4-newrefinedpf-
alsoneighbour-2-refined-2-fixcrosshelix-3-refined-2.pdb #134  
---  
Chain | Description  
6 | No description available  
9 M | No description available  
D | No description available  
E | No description available  
I | No description available  
N O T | No description available  
  

> hide #!132,134#!8.2 atoms

> show #!132,134#!8.2 cartoons

> hide #!132 models

> hide #!131 models

> show #!131 models

> open "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Fit14-27-1-stitchedtemp3-lightrefine4-newrefinedpf-
> alsoneighbour-2-refined-2-fixcrosshelix-3-refined-3.pdb"

Summary of feedback from opening /Users/chaaban/Library/CloudStorage/OneDrive-
MRCLaboratoryofMolecularBiology/Documents/Carter
Lab/Diorge/Membranes/Fit14-27-1-stitchedtemp3-lightrefine4-newrefinedpf-
alsoneighbour-2-refined-2-fixcrosshelix-3-refined-3.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 PRO 0 118
LEU 0 142 1 25  
Start residue of secondary structure not found: HELIX 2 2 PRO 0 145 GLU 0 149
1 5  
PDB SEQRES record for chain D is incomplete. Ignoring input sequence records
as basis for sequence.  
  
Chain information for Fit14-27-1-stitchedtemp3-lightrefine4-newrefinedpf-
alsoneighbour-2-refined-2-fixcrosshelix-3-refined-3.pdb #135  
---  
Chain | Description  
6 | No description available  
9 M | No description available  
A | No description available  
D | No description available  
E | No description available  
N O T | No description available  
  

> hide #!134-135#!8.2 atoms

> show #!134-135#!8.2 cartoons

[Repeated 1 time(s)]

> hide #!134 models

> ui windowfill toggle

> open "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Fit14-27-1-stitchedtemp3-lightrefine4-newrefinedpf-
> alsoneighbour-2-refined-2-fixcrosshelix-3-refined-3.pdb"

Summary of feedback from opening /Users/chaaban/Library/CloudStorage/OneDrive-
MRCLaboratoryofMolecularBiology/Documents/Carter
Lab/Diorge/Membranes/Fit14-27-1-stitchedtemp3-lightrefine4-newrefinedpf-
alsoneighbour-2-refined-2-fixcrosshelix-3-refined-3.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 PRO 0 118
LEU 0 142 1 25  
Start residue of secondary structure not found: HELIX 2 2 PRO 0 145 GLU 0 149
1 5  
PDB SEQRES record for chain D is incomplete. Ignoring input sequence records
as basis for sequence.  
  
Chain information for Fit14-27-1-stitchedtemp3-lightrefine4-newrefinedpf-
alsoneighbour-2-refined-2-fixcrosshelix-3-refined-3.pdb #136  
---  
Chain | Description  
6 | No description available  
9 M | No description available  
D | No description available  
E | No description available  
I | No description available  
N O T | No description available  
  

> hide #!135-136#!8.2 atoms

> show #!135-136#!8.2 cartoons

> ui windowfill toggle

> hide #!135 models

> show #!135 models

> hide #!135 models

> show #!135 models

> hide #!135 models

> show #!135 models

> hide #!135 models

> show #!135 models

> hide #!135 models

> open "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Fit14-27-1-stitchedtemp3-lightrefine4-newrefinedpf-
> alsoneighbour-2-refined-2-fixcrosshelix-3-refined-4.pdb"

Summary of feedback from opening /Users/chaaban/Library/CloudStorage/OneDrive-
MRCLaboratoryofMolecularBiology/Documents/Carter
Lab/Diorge/Membranes/Fit14-27-1-stitchedtemp3-lightrefine4-newrefinedpf-
alsoneighbour-2-refined-2-fixcrosshelix-3-refined-4.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 PRO 0 118
LEU 0 142 1 25  
Start residue of secondary structure not found: HELIX 2 2 PRO 0 145 GLU 0 149
1 5  
PDB SEQRES record for chain D is incomplete. Ignoring input sequence records
as basis for sequence.  
  
Chain information for Fit14-27-1-stitchedtemp3-lightrefine4-newrefinedpf-
alsoneighbour-2-refined-2-fixcrosshelix-3-refined-4.pdb #137  
---  
Chain | Description  
6 | No description available  
9 M | No description available  
D | No description available  
E | No description available  
I | No description available  
N O T | No description available  
  

> hide #!136-137#!8.2 atoms

> show #!136-137#!8.2 cartoons

> open "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Fit14-27-1-stitchedtemp3-lightrefine4-newrefinedpf-
> alsoneighbour-2-refined-2-fixcrosshelix-3-refined-4-replacefirst-
> rechained.pdb"

Summary of feedback from opening /Users/chaaban/Library/CloudStorage/OneDrive-
MRCLaboratoryofMolecularBiology/Documents/Carter
Lab/Diorge/Membranes/Fit14-27-1-stitchedtemp3-lightrefine4-newrefinedpf-
alsoneighbour-2-refined-2-fixcrosshelix-3-refined-4-replacefirst-rechained.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 PRO 0 118
LEU 0 142 1 25  
Start residue of secondary structure not found: HELIX 2 2 PRO 0 145 GLU 0 149
1 5  
PDB SEQRES record for chain E is incomplete. Ignoring input sequence records
as basis for sequence.  
  
Chain information for Fit14-27-1-stitchedtemp3-lightrefine4-newrefinedpf-
alsoneighbour-2-refined-2-fixcrosshelix-3-refined-4-replacefirst-rechained.pdb
#138  
---  
Chain | Description  
A | No description available  
B C D | No description available  
E | No description available  
F | No description available  
G H | No description available  
I | No description available  
  

> hide #!136-138#!8.2 atoms

> show #!136-138#!8.2 cartoons

> hide #!137 models

> hide #!136 models

> close session

> open "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Fit14-27-1-stitchedtemp3-lightrefine4-newrefinedpf-
> alsoneighbour-2-refined-2-fixcrosshelix-3-refined-4-replacefirst-
> rechained.pdb" format pdb

Summary of feedback from opening /Users/chaaban/Library/CloudStorage/OneDrive-
MRCLaboratoryofMolecularBiology/Documents/Carter
Lab/Diorge/Membranes/Fit14-27-1-stitchedtemp3-lightrefine4-newrefinedpf-
alsoneighbour-2-refined-2-fixcrosshelix-3-refined-4-replacefirst-rechained.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 PRO 0 118
LEU 0 142 1 25  
Start residue of secondary structure not found: HELIX 2 2 PRO 0 145 GLU 0 149
1 5  
PDB SEQRES record for chain E is incomplete. Ignoring input sequence records
as basis for sequence.  
  
Chain information for Fit14-27-1-stitchedtemp3-lightrefine4-newrefinedpf-
alsoneighbour-2-refined-2-fixcrosshelix-3-refined-4-replacefirst-rechained.pdb
#1  
---  
Chain | Description  
A | No description available  
B C D | No description available  
E | No description available  
F | No description available  
G H | No description available  
I | No description available  
  

> hide atoms

> show cartoons

> lighting soft

[Repeated 1 time(s)]

> preset custom clean-chain

Using preset: Custom / Clean-chain  

> set bgColor #ffffff00

Preset expands to these ChimeraX commands:

    
    
    lighting soft
    set bgColor white
    cartoon style coil width 1.5 thickness 0.8
    cartoon style helix xsection round width 3 thickness 0.8
    cartoon style strand xsection round width 3 thickness 0.8
    cartoon style strand arrowscale 1
    cartoon style helix xsection oval sides 10
    graphics silhouettes true
    graphics silhouettes width 1.5
    graphics silhouettes depthJump 0.003
    lighting msDepthBias 0.004
    lighting shadows true intensity 0.06
    lighting depthCueColor #000000
    color bychain
    ui windowfill true

  

> ui windowfill toggle

> open "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/pointy-1pf.pdb"

Chain information for pointy-1pf.pdb #2  
---  
Chain | Description  
0 6 o r x | No description available  
W | No description available  
Z | No description available  
c | No description available  
f | No description available  
u | No description available  
  

> hide atoms

> show cartoons

> show atoms

> delete atoms sel

> delete bonds sel

> preset custom pretty-chain

Using preset: Custom / Pretty-chain  
Preset expands to these ChimeraX commands:

    
    
    lighting soft
    set bgColor white
    cartoon style coil width 1.5 thickness 0.8
    cartoon style helix xsection round width 3 thickness 0.8
    cartoon style strand xsection round width 3 thickness 0.8
    cartoon style strand arrowscale 1
    cartoon style helix xsection oval sides 10
    graphics silhouettes true
    graphics silhouettes width 1.5
    graphics silhouettes depthJump 0.003
    lighting msDepthBias 0.004
    lighting shadows true intensity 0.06
    lighting depthCueColor #000000
    color bychain

  

> hide atoms

> show cartoons

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> close #2

> open "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/pointy-1pf-relative-rechained.pdb"

Summary of feedback from opening /Users/chaaban/Library/CloudStorage/OneDrive-
MRCLaboratoryofMolecularBiology/Documents/Carter
Lab/Diorge/Membranes/pointy-1pf-relative-rechained.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 TRP W 5
LYS W 48 1 44  
Start residue of secondary structure not found: HELIX 2 2 LYS W 55 SER W 88 1
34  
Start residue of secondary structure not found: HELIX 3 3 TRP Z 5 LYS Z 48 1
44  
Start residue of secondary structure not found: HELIX 4 4 LYS Z 55 THR Z 115 1
61  
Start residue of secondary structure not found: HELIX 5 5 TRP c 5 LYS c 48 1
44  
27 messages similar to the above omitted  
  
Chain information for pointy-1pf-relative-rechained.pdb #2  
---  
Chain | Description  
A B D E F | No description available  
C | No description available  
G | No description available  
H | No description available  
I | No description available  
  

> hide atoms

> preset custom clean-chain

Using preset: Custom / Clean-chain  
Preset expands to these ChimeraX commands:

    
    
    lighting soft
    set bgColor white
    cartoon style coil width 1.5 thickness 0.8
    cartoon style helix xsection round width 3 thickness 0.8
    cartoon style strand xsection round width 3 thickness 0.8
    cartoon style strand arrowscale 1
    cartoon style helix xsection oval sides 10
    graphics silhouettes true
    graphics silhouettes width 1.5
    graphics silhouettes depthJump 0.003
    lighting msDepthBias 0.004
    lighting shadows true intensity 0.06
    lighting depthCueColor #000000
    color bychain
    ui windowfill true

  

> ui windowfill toggle

> hide #!2 models

> show #!2 models

> select add #2

13873 atoms, 13870 bonds, 895 residues, 1 model selected  

> view sel

No displayed objects specified.  

> close #2

> open "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/pointy-1pf-relative-rechained.pdb"

Summary of feedback from opening /Users/chaaban/Library/CloudStorage/OneDrive-
MRCLaboratoryofMolecularBiology/Documents/Carter
Lab/Diorge/Membranes/pointy-1pf-relative-rechained.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 TRP W 5
LYS W 48 1 44  
Start residue of secondary structure not found: HELIX 2 2 LYS W 55 SER W 88 1
34  
Start residue of secondary structure not found: HELIX 3 3 TRP Z 5 LYS Z 48 1
44  
Start residue of secondary structure not found: HELIX 4 4 LYS Z 55 THR Z 115 1
61  
Start residue of secondary structure not found: HELIX 5 5 TRP c 5 LYS c 48 1
44  
27 messages similar to the above omitted  
  
Chain information for pointy-1pf-relative-rechained.pdb #2  
---  
Chain | Description  
A B D E F | No description available  
C | No description available  
G | No description available  
H | No description available  
I | No description available  
  

> hide atoms

> show cartoons

> show atoms

> delete atoms sel

> delete bonds sel

> delete atoms sel

> delete bonds sel

> hide atoms

> hide cartoons

> show cartoons

> preset custom pretty-chain

Using preset: Custom / Pretty-chain  
Preset expands to these ChimeraX commands:

    
    
    lighting soft
    set bgColor white
    cartoon style coil width 1.5 thickness 0.8
    cartoon style helix xsection round width 3 thickness 0.8
    cartoon style strand xsection round width 3 thickness 0.8
    cartoon style strand arrowscale 1
    cartoon style helix xsection oval sides 10
    graphics silhouettes true
    graphics silhouettes width 1.5
    graphics silhouettes depthJump 0.003
    lighting msDepthBias 0.004
    lighting shadows true intensity 0.06
    lighting depthCueColor #000000
    color bychain

  

> ui tool show Matchmaker

> hide #!2 models

> matchmaker #2/G to #1/G pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker Fit14-27-1-stitchedtemp3-lightrefine4-newrefinedpf-
alsoneighbour-2-refined-2-fixcrosshelix-3-refined-4-replacefirst-
rechained.pdb, chain G (#1) with pointy-1pf-relative-rechained.pdb, chain G
(#2), sequence alignment score = 573.4  
RMSD between 71 pruned atom pairs is 0.804 angstroms; (across all 111 pairs:
3.894)  
  

> show #!2 models

> morph

Missing or invalid "structures" argument: empty atom specifier  

> morph #1.2

Require at least 2 structures for morph  

> morph #1 #2

Computed 51 frame morph #3  

> coordset #3 1,51

> preset custom pretty-chain

Using preset: Custom / Pretty-chain  
Preset expands to these ChimeraX commands:

    
    
    lighting soft
    set bgColor white
    cartoon style coil width 1.5 thickness 0.8
    cartoon style helix xsection round width 3 thickness 0.8
    cartoon style strand xsection round width 3 thickness 0.8
    cartoon style strand arrowscale 1
    cartoon style helix xsection oval sides 10
    graphics silhouettes true
    graphics silhouettes width 1.5
    graphics silhouettes depthJump 0.003
    lighting msDepthBias 0.004
    lighting shadows true intensity 0.06
    lighting depthCueColor #000000
    color bychain

  

> morph #2 #1

Computed 51 frame morph #4  

> coordset #4 1,51

> hide #!3 models

> preset custom pretty-chain

Using preset: Custom / Pretty-chain  
Preset expands to these ChimeraX commands:

    
    
    lighting soft
    set bgColor white
    cartoon style coil width 1.5 thickness 0.8
    cartoon style helix xsection round width 3 thickness 0.8
    cartoon style strand xsection round width 3 thickness 0.8
    cartoon style strand arrowscale 1
    cartoon style helix xsection oval sides 10
    graphics silhouettes true
    graphics silhouettes width 1.5
    graphics silhouettes depthJump 0.003
    lighting msDepthBias 0.004
    lighting shadows true intensity 0.06
    lighting depthCueColor #000000
    color bychain

  

> select #2/A

265 atoms, 264 bonds, 19 residues, 1 model selected  

> color #2/A corflower blue

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  

> color #2/A bychain corflower blue

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> color

> color /A blue

> color /A cornflower blue

[Repeated 1 time(s)]

> color /B medium turquoise

> color /A cornflower blue

> color /B medium turquoise

> color /C medium sea green

> color /D pale goldenrod

> color /E peach puff

> color /F plum

> color /G medium orchid

> color /A cornflower blue

> color /B medium turquoise

> color /C medium sea green

> color /D pale goldenrod

> color /E peach puff

> color /F plum

> color /G slate blue

> color /A cornflower blue

> color /B medium turquoise

> color /C medium sea green

> color /D pale goldenrod

> color /E peach puff

> color /F plum

> color /G slate blue

> color /H lavender

> color /A cornflower blue

> color /B medium turquoise

> color /C medium sea green

> color /D pale goldenrod

> color /E peach puff

> color /F plum

> color /G slate blue

> color /H lavender

> color /I salmon

> color /A cornflower blue

> color /B medium turquoise

> color /C medium sea green

> color /D pale goldenrod

> color /E goldenrod

> color /F plum

> color /G slate blue

> color /H lavender

> color /I salmon

> color /A cornflower blue

> color /B medium turquoise

> color /C medium sea green

> color /D pale goldenrod

> color /E goldenrod

> color /F plum

> color /G dark cyan

> color /H lavender

> color /I salmon

> color /A cornflower blue

> color /B medium turquoise

> color /C medium sea green

> color /D pale goldenrod

> color /E goldenrod

> color /F plum

> color /G hot pink

> color /H lavender

> color /I salmon

> morph

Missing or invalid "structures" argument: empty atom specifier  

> morph #2 #1 wrap true

Computed 101 frame morph #5  

> coordset #5 1,101

> hide #!4 models

> lighting soft

> set bgColor white

> cartoon style coil width 1.5 thickness 0.8

> cartoon style helix xsection round width 3 thickness 0.8

> cartoon style strand xsection round width 3 thickness 0.8

> cartoon style strand arrowScale 1

> cartoon style helix xsection oval sides 10

> graphics silhouettes true

> graphics silhouettes width 1.5

> graphics silhouettes depthJump 0.003

> lighting msDepthBias 0.004

> lighting shadows true intensity 0.06

> lighting depthCueColor #000000

> movie record

> movie encode /Users/chaaban/Desktop/movie.mp4 framerate 25.0

Movie saved to /Users/chaaban/Desktop/movie.mp4  
  

> open "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/postprocess_masked330_onepf.mrc"

Opened postprocess_masked330_onepf.mrc as #6, grid size 274,274,274, pixel
1.51, shown at level 9.42e-06, step 2, values float32  

> volume #6 level 0.01241

> hide #!6 models

> hide #!5 models

> show #!6 models

> show #!1 models

> hide #!1 models

> show #!1 models

> ui tool show "Fit in Map"

> fitmap #1 inMap #6

Fit molecule Fit14-27-1-stitchedtemp3-lightrefine4-newrefinedpf-
alsoneighbour-2-refined-2-fixcrosshelix-3-refined-4-replacefirst-rechained.pdb
(#1) to map postprocess_masked330_onepf.mrc (#6) using 6218 atoms  
average map value = 0.01328, steps = 40  
shifted from previous position = 0.162  
rotated from previous position = 0.147 degrees  
atoms outside contour = 3565, contour level = 0.012408  
  
Position of Fit14-27-1-stitchedtemp3-lightrefine4-newrefinedpf-
alsoneighbour-2-refined-2-fixcrosshelix-3-refined-4-replacefirst-rechained.pdb
(#1) relative to postprocess_masked330_onepf.mrc (#6) coordinates:  
Matrix rotation and translation  
0.99999701 -0.00172986 0.00172963 0.05739393  
0.00173119 0.99999820 -0.00077010 -0.06466265  
-0.00172830 0.00077310 0.99999821 0.15764343  
Axis 0.30081486 0.67405099 0.67465968  
Axis point 68.53340975 19.14218260 0.00000000  
Rotation angle (degrees) 0.14696576  
Shift along axis 0.08003468  
  

> transparency #1,6 50

> ui tool show "Hide Dust"

> surface dust #6 size 9.04

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Fit-240114.cxs"

——— End of log from Sun Jan 14 14:18:05 2024 ———

opened ChimeraX session  

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Fit-240114-back.png" width 1600 transparentBackground
> true

> open "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/188.cif"

Summary of feedback from opening /Users/chaaban/Library/CloudStorage/OneDrive-
MRCLaboratoryofMolecularBiology/Documents/Carter Lab/Diorge/Membranes/188.cif  
---  
warnings | Missing entity information. Treating each chain as a separate
entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for 188.cif #7  
---  
Chain | Description  
A0 | No description available  
A1 | No description available  
A2 | No description available  
A3 | No description available  
A4 | No description available  
A5 | No description available  
A6 | No description available  
A7 | No description available  
A8 | No description available  
A9 | No description available  
Aa | No description available  
Aaa | No description available  
Aab | No description available  
Ab | No description available  
Ac | No description available  
Ad | No description available  
Ae | No description available  
Af | No description available  
Ag | No description available  
Ah | No description available  
Ai | No description available  
Aj | No description available  
Ak | No description available  
Al | No description available  
Am | No description available  
An | No description available  
Ao | No description available  
Ap | No description available  
Aq | No description available  
Ar | No description available  
As | No description available  
At | No description available  
Au | No description available  
Av | No description available  
Aw | No description available  
Ax | No description available  
Ay | No description available  
Az | No description available  
  

> hide #!6 models

> hide #!1 models

> show #!1 models

> close session

> open "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/188.cif" format mmcif

Summary of feedback from opening /Users/chaaban/Library/CloudStorage/OneDrive-
MRCLaboratoryofMolecularBiology/Documents/Carter Lab/Diorge/Membranes/188.cif  
---  
warnings | Missing entity information. Treating each chain as a separate
entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for 188.cif #1  
---  
Chain | Description  
A0 | No description available  
A1 | No description available  
A2 | No description available  
A3 | No description available  
A4 | No description available  
A5 | No description available  
A6 | No description available  
A7 | No description available  
A8 | No description available  
A9 | No description available  
Aa | No description available  
Aaa | No description available  
Aab | No description available  
Ab | No description available  
Ac | No description available  
Ad | No description available  
Ae | No description available  
Af | No description available  
Ag | No description available  
Ah | No description available  
Ai | No description available  
Aj | No description available  
Ak | No description available  
Al | No description available  
Am | No description available  
An | No description available  
Ao | No description available  
Ap | No description available  
Aq | No description available  
Ar | No description available  
As | No description available  
At | No description available  
Au | No description available  
Av | No description available  
Aw | No description available  
Ax | No description available  
Ay | No description available  
Az | No description available  
  

> hide atoms

> show cartoons

> preset custom clean-chain

Using preset: Custom / Clean-chain  
Preset expands to these ChimeraX commands:

    
    
    lighting soft
    set bgColor white
    cartoon style coil width 1.5 thickness 0.8
    cartoon style helix xsection round width 3 thickness 0.8
    cartoon style strand xsection round width 3 thickness 0.8
    cartoon style strand arrowscale 1
    cartoon style helix xsection oval sides 10
    graphics silhouettes true
    graphics silhouettes width 1.5
    graphics silhouettes depthJump 0.003
    lighting msDepthBias 0.004
    lighting shadows true intensity 0.06
    lighting depthCueColor #000000
    color bychain
    ui windowfill true

  

> ui windowfill toggle

> open "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/188_b250.mrc"

Opened 188_b250.mrc as #2, grid size 250,250,250, pixel 0.826, shown at level
0.00707, step 1, values float32  

> hide cartoons

> show atoms

> style stick

Changed 20272 atom styles  

> transparency 50

> ui mousemode right zoom

> ui mousemode right "rotate selected models"

> ui mousemode right zoom

> ui tool show "Color Zone"

> color zone #2 near #1 distance 4.96

> transparency 50

> select clear

> lighting depthCueColor #999999

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Filament-240114.csx"

No known data format for file suffix '.csx'  

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Filament-240114.cxs"

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Filament-240114-fitmap.png" width 1600
> transparentBackground true

> hide #!1 models

> transparency #2 0

> view

> ui tool show "Hide Dust"

> surface dust #2 size 4.96

> volume #2 level 0.006833

> volume #2 level 0.006236

> surface dust #2 size 4.96

> transparency #2 50

> select clear

> transparency #2 0

> color zone #2 near #1 distance 4.96

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Filament-240114-map.png" width 1600
> transparentBackground true

> show #!1 models

> transparency 50

> select ~sel & ##selected

Nothing selected  

> select ~sel & ##selected

Nothing selected  

> select clear

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Filament-240114-map-withfit.png" width 1600
> transparentBackground true

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Filament-240114.cxs"

> color byhetero

> hide #!1 models

> show #!1 models

> hide #!2 models

> show cartoons

> view sel

> show #!2 models

> select clear

> volume #2 level 0.004206

> transparency 50

> view

> color zone #2 near #1 distance 4.96

> select clear

> preset custom pretty-chain

Using preset: Custom / Pretty-chain  
Preset expands to these ChimeraX commands:

    
    
    lighting soft
    set bgColor white
    cartoon style coil width 1.5 thickness 0.8
    cartoon style helix xsection round width 3 thickness 0.8
    cartoon style strand xsection round width 3 thickness 0.8
    cartoon style strand arrowscale 1
    cartoon style helix xsection oval sides 10
    graphics silhouettes true
    graphics silhouettes width 1.5
    graphics silhouettes depthJump 0.003
    lighting msDepthBias 0.004
    lighting shadows true intensity 0.06
    lighting depthCueColor #000000
    color bychain

  

> color zone #2 near #1 distance 4.96

> volume splitbyzone #2

Opened 188_b250.mrc 0 as #3.1, grid size 250,250,250, pixel 0.826, shown at
level 0.00421, step 1, values float32  
Opened 188_b250.mrc 1 as #3.2, grid size 250,250,250, pixel 0.826, shown at
level 0.00421, step 1, values float32  
Opened 188_b250.mrc 2 as #3.3, grid size 250,250,250, pixel 0.826, shown at
level 0.00421, step 1, values float32  
Opened 188_b250.mrc 3 as #3.4, grid size 250,250,250, pixel 0.826, shown at
level 0.00421, step 1, values float32  
Opened 188_b250.mrc 4 as #3.5, grid size 250,250,250, pixel 0.826, shown at
level 0.00421, step 1, values float32  
Opened 188_b250.mrc 5 as #3.6, grid size 250,250,250, pixel 0.826, shown at
level 0.00421, step 1, values float32  
Opened 188_b250.mrc 6 as #3.7, grid size 250,250,250, pixel 0.826, shown at
level 0.00421, step 1, values float32  
Opened 188_b250.mrc 7 as #3.8, grid size 250,250,250, pixel 0.826, shown at
level 0.00421, step 1, values float32  
Opened 188_b250.mrc 8 as #3.9, grid size 250,250,250, pixel 0.826, shown at
level 0.00421, step 1, values float32  
Opened 188_b250.mrc 9 as #3.10, grid size 250,250,250, pixel 0.826, shown at
level 0.00421, step 1, values float32  
Opened 188_b250.mrc 10 as #3.11, grid size 250,250,250, pixel 0.826, shown at
level 0.00421, step 1, values float32  
Opened 188_b250.mrc 11 as #3.12, grid size 250,250,250, pixel 0.826, shown at
level 0.00421, step 1, values float32  
Opened 188_b250.mrc 12 as #3.13, grid size 250,250,250, pixel 0.826, shown at
level 0.00421, step 1, values float32  
Opened 188_b250.mrc 13 as #3.14, grid size 250,250,250, pixel 0.826, shown at
level 0.00421, step 1, values float32  
Opened 188_b250.mrc 14 as #3.15, grid size 250,250,250, pixel 0.826, shown at
level 0.00421, step 1, values float32  
Opened 188_b250.mrc 15 as #3.16, grid size 250,250,250, pixel 0.826, shown at
level 0.00421, step 1, values float32  
Opened 188_b250.mrc 16 as #3.17, grid size 250,250,250, pixel 0.826, shown at
level 0.00421, step 1, values float32  
Opened 188_b250.mrc 17 as #3.18, grid size 250,250,250, pixel 0.826, shown at
level 0.00421, step 1, values float32  
Opened 188_b250.mrc 18 as #3.19, grid size 250,250,250, pixel 0.826, shown at
level 0.00421, step 1, values float32  
Opened 188_b250.mrc 19 as #3.20, grid size 250,250,250, pixel 0.826, shown at
level 0.00421, step 1, values float32  
Opened 188_b250.mrc 20 as #3.21, grid size 250,250,250, pixel 0.826, shown at
level 0.00421, step 1, values float32  
Opened 188_b250.mrc 21 as #3.22, grid size 250,250,250, pixel 0.826, shown at
level 0.00421, step 1, values float32  
Opened 188_b250.mrc 22 as #3.23, grid size 250,250,250, pixel 0.826, shown at
level 0.00421, step 1, values float32  
Opened 188_b250.mrc 23 as #3.24, grid size 250,250,250, pixel 0.826, shown at
level 0.00421, step 1, values float32  
Opened 188_b250.mrc 24 as #3.25, grid size 250,250,250, pixel 0.826, shown at
level 0.00421, step 1, values float32  
Opened 188_b250.mrc 25 as #3.26, grid size 250,250,250, pixel 0.826, shown at
level 0.00421, step 1, values float32  
Opened 188_b250.mrc 26 as #3.27, grid size 250,250,250, pixel 0.826, shown at
level 0.00421, step 1, values float32  
Opened 188_b250.mrc 27 as #3.28, grid size 250,250,250, pixel 0.826, shown at
level 0.00421, step 1, values float32  
Opened 188_b250.mrc 28 as #3.29, grid size 250,250,250, pixel 0.826, shown at
level 0.00421, step 1, values float32  
Opened 188_b250.mrc 29 as #3.30, grid size 250,250,250, pixel 0.826, shown at
level 0.00421, step 1, values float32  
Opened 188_b250.mrc 30 as #3.31, grid size 250,250,250, pixel 0.826, shown at
level 0.00421, step 1, values float32  
Opened 188_b250.mrc 31 as #3.32, grid size 250,250,250, pixel 0.826, shown at
level 0.00421, step 1, values float32  
Opened 188_b250.mrc 32 as #3.33, grid size 250,250,250, pixel 0.826, shown at
level 0.00421, step 1, values float32  
Opened 188_b250.mrc 33 as #3.34, grid size 250,250,250, pixel 0.826, shown at
level 0.00421, step 1, values float32  
Opened 188_b250.mrc 34 as #3.35, grid size 250,250,250, pixel 0.826, shown at
level 0.00421, step 1, values float32  
Opened 188_b250.mrc 35 as #3.36, grid size 250,250,250, pixel 0.826, shown at
level 0.00421, step 1, values float32  
Opened 188_b250.mrc 36 as #3.37, grid size 250,250,250, pixel 0.826, shown at
level 0.00421, step 1, values float32  
Opened 188_b250.mrc 37 as #3.38, grid size 250,250,250, pixel 0.826, shown at
level 0.00421, step 1, values float32  
Opened 188_b250.mrc 38 as #3.39, grid size 250,250,250, pixel 0.826, shown at
level 0.00421, step 1, values float32  

> hide #!3.1-36 target m

> hide #!1 models

> hide #!3.37 models

> hide #!3.38 models

> hide #!3.39 models

> show #!3.37 models

> hide #!3.37 models

> show #!3.36 models

> hide #!3.36 models

> show #!3.35 models

> hide #!3.35 models

> show #!3.34 models

> hide #!3.34 models

> show #!3.33 models

> hide #!3.33 models

> show #!3.32 models

> hide #!3.32 models

> show #!3.31 models

> hide #!3.31 models

> show #!3.30 models

> hide #!3.30 models

> show #!3.29 models

> hide #!3.29 models

> show #!3.28 models

> hide #!3.28 models

> show #!3.27 models

> hide #!3.27 models

> show #!3.26 models

> hide #!3.26 models

> show #!3.25 models

> hide #!3.25 models

> show #!3.24 models

> hide #!3.24 models

> show #!3.23 models

> hide #!3.23 models

> show #!3.22 models

> hide #!3.22 models

> show #!3.21 models

> hide #!3.21 models

> show #!3.20 models

> hide #!3.20 models

> show #!3.19 models

> hide #!3.19 models

> show #!3.18 models

> hide #!3.18 models

> show #!3.17 models

> hide #!3.17 models

> show #!3.16 models

> hide #!3.16 models

> show #!3.15 models

> hide #!3.15 models

> show #!3.14 models

> hide #!3.14 models

> show #!3.13 models

> hide #!3.13 models

> show #!3.12 models

> hide #!3.12 models

> show #!3.11 models

> hide #!3.11 models

> show #!3.10 models

> hide #!3.10 models

> show #!3.9 models

> hide #!3.9 models

> show #!3.8 models

> hide #!3.8 models

> show #!3.7 models

> hide #!3.7 models

> show #!3.7 models

> hide #!3.7 models

> show #!3.6 models

> hide #!3.6 models

> show #!3.5 models

> hide #!3.5 models

> show #!3.4 models

> hide #!3.4 models

> show #!3.3 models

> hide #!3.3 models

> show #!3.2 models

> hide #!3.2 models

> show #!3.1 models

> hide #!3.1 models

> show #!3.2 models

> hide #!3.2 models

> show #!3.3 models

> hide #!3.3 models

> show #!3.4 models

> hide #!3.4 models

> show #!3.5 models

> hide #!3.5 models

> show #!1 models

> close #3

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> volume #2 level 0.003848

> volume #2 level 0.003729

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> select add #1

20272 atoms, 20308 bonds, 2600 residues, 1 model selected  

> color sel bypolymer

> select subtract #1

Nothing selected  

> color bychain

> hide atoms

> show cartoons

> color sel light sea green

> ui tool show "Color Actions"

> color sel lavender

> color sel pale goldenrod

> color sel alice blue

> color sel azure

> color sel light steel blue

> color sel aquamarine

> color sel sky blue

> select ~sel

10240 atoms, 10261 bonds, 1314 residues, 3 models selected  

> color sel violet

> select clear

> undo

> select clear

[Repeated 2 time(s)]

> color sel pale turquoise

> color sel light sky blue

> select ~sel

9985 atoms, 10001 bonds, 1278 residues, 3 models selected  

> color sel violet

> color sel plum

> color sel violet

> color sel cornsilk

> color sel lemon chiffon

> color sel navajo white

> color sel peach puff

[Repeated 1 time(s)]

> color sel pink

> color sel misty rose

> color sel bisque

> color sel light pink

> color sel light coral

> color sel magenta

> color sel pale violet red

> color sel light coral

> color sel wheat

> color sel honeydew

> color sel pale goldenrod

> color sel violet

> color sel pale goldenrod

> select clear

> color sel light blue

> color sel light sky blue

> select clear

> show cartoons

> redo

> undo

> combine sel

> select ~sel

30573 atoms, 30625 bonds, 3924 residues, 2 models selected  

> select subtract #3

10301 atoms, 10317 bonds, 1324 residues, 1 model selected  

> combine sel

> hide #!1 models

> select add #1

20272 atoms, 20308 bonds, 2600 residues, 1 model selected  

> select subtract #1

Nothing selected  

> select add #4

20272 atoms, 20308 bonds, 2600 residues, 1 model selected  

> hide #!4 models

> show #!4 models

> hide sel cartoons

> hide #!4 models

> hide #!3 models

> color sel wheat

> color sel khaki

> color sel pale goldenrod

> color sel light goldenrod yellow

> color sel yellow

> color sel khaki

> color sel antique white

> color sel old lace

> color sel light pink

> color sel lemon chiffon

> color sel ivory

> color sel white

> select clear

> undo

> color sel light yellow

> select clear

> select ~sel

50845 atoms, 50933 bonds, 6524 residues, 5 models selected  

> select subtract #4

30573 atoms, 30625 bonds, 3924 residues, 4 models selected  

> select subtract #3

10301 atoms, 10317 bonds, 1324 residues, 3 models selected  

> select subtract #2

10301 atoms, 10317 bonds, 1324 residues, 1 model selected  

> show sel cartoons

> select ~sel

50515 atoms, 50605 bonds, 6476 residues, 5 models selected  

> hide sel & #!1 cartoons

> select clear

> color sel cornflower blue

> select clear

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Filament-240114-individuals.cxs"

——— End of log from Sun Jan 14 14:55:25 2024 ———

opened ChimeraX session  

> close #3-4

> select clear

> show cartoons

> combine #1

> select #3/Ad

985 atoms, 990 bonds, 126 residues, 1 model selected  

> select ~sel

39559 atoms, 39626 bonds, 5074 residues, 4 models selected  

> select subtract #1

19287 atoms, 19318 bonds, 2474 residues, 3 models selected  

> select subtract #2

19287 atoms, 19318 bonds, 2474 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select #1/Aj

482 atoms, 483 bonds, 63 residues, 1 model selected  

> select ~sel

20775 atoms, 20815 bonds, 2663 residues, 4 models selected  

> select subtract #3

19790 atoms, 19825 bonds, 2537 residues, 3 models selected  

> select subtract #2

19790 atoms, 19825 bonds, 2537 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> ui tool show Matchmaker

> matchmaker #1/Aj to #3/Ad pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker copy of 188.cif, chain Ad (#3) with 188.cif, chain Aj (#1),
sequence alignment score = 122  
RMSD between 25 pruned atom pairs is 0.122 angstroms; (across all 25 pairs:
0.122)  
  

> select clear

> delete atoms sel

> delete bonds sel

> delete atoms sel

> delete bonds sel

> delete atoms sel

> delete bonds sel

> color sel cornflower blue

> select clear

> select ~sel & ##selected

Nothing selected  

> select ~sel & ##selected

Nothing selected  

> select ~sel & ##selected

Nothing selected  

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Filament-240114-onesubunit.cxs"

> open "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/188.cif"

Summary of feedback from opening /Users/chaaban/Library/CloudStorage/OneDrive-
MRCLaboratoryofMolecularBiology/Documents/Carter Lab/Diorge/Membranes/188.cif  
---  
warnings | Missing entity information. Treating each chain as a separate
entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for 188.cif #4  
---  
Chain | Description  
A0 | No description available  
A1 | No description available  
A2 | No description available  
A3 | No description available  
A4 | No description available  
A5 | No description available  
A6 | No description available  
A7 | No description available  
A8 | No description available  
A9 | No description available  
Aa | No description available  
Aaa | No description available  
Aab | No description available  
Ab | No description available  
Ac | No description available  
Ad | No description available  
Ae | No description available  
Af | No description available  
Ag | No description available  
Ah | No description available  
Ai | No description available  
Aj | No description available  
Ak | No description available  
Al | No description available  
Am | No description available  
An | No description available  
Ao | No description available  
Ap | No description available  
Aq | No description available  
Ar | No description available  
As | No description available  
At | No description available  
Au | No description available  
Av | No description available  
Aw | No description available  
Ax | No description available  
Ay | No description available  
Az | No description available  
  

> hide atoms

> show cartoons

> combine #1,3

[Repeated 5 time(s)]

> hide #!5-10 target m

> hide #!1 models

> hide #!4 models

> hide #!3 models

> show #!4 models

> show #!5 models

> hide #!4 models

> mmaker #5/Ad to #4/A[

No 'to' model specified  

> mmaker #5/Ad to #4/Ap

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 188.cif, chain Ap (#4) with combination, chain Ad (#5), sequence
alignment score = 65.8  
RMSD between 15 pruned atom pairs is 0.182 angstroms; (across all 15 pairs:
0.182)  
  

> show #!4 models

> mmaker #6/Ad to #4/Af

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 188.cif, chain Af (#4) with combination, chain Ad (#6), sequence
alignment score = 168.3  
RMSD between 35 pruned atom pairs is 0.095 angstroms; (across all 35 pairs:
0.095)  
  

> show #!6 models

> select ~sel & ##selected

Nothing selected  

> select ~sel & ##selected

Nothing selected  

> select ~sel & ##selected

Nothing selected  

> select ~sel & ##selected

Nothing selected  

> mmaker #7/Ad to #4/Ae

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 188.cif, chain Ae (#4) with combination, chain Ad (#7), sequence
alignment score = 601.3  
RMSD between 115 pruned atom pairs is 0.134 angstroms; (across all 121 pairs:
1.198)  
  

> show #!7 models

> mmaker #7/Ad to #4/At

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 188.cif, chain At (#4) with combination, chain Ad (#7), sequence
alignment score = 283.5  
RMSD between 57 pruned atom pairs is 0.084 angstroms; (across all 57 pairs:
0.084)  
  

> mmaker #8/Ad to #4/Ae

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 188.cif, chain Ae (#4) with combination, chain Ad (#8), sequence
alignment score = 601.3  
RMSD between 115 pruned atom pairs is 0.134 angstroms; (across all 121 pairs:
1.198)  
  

> show #!8 models

> mmaker #9/Ad to #4/Ad

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 188.cif, chain Ad (#4) with combination, chain Ad (#9), sequence
alignment score = 646.7  
RMSD between 126 pruned atom pairs is 0.000 angstroms; (across all 126 pairs:
0.000)  
  

> show #!9 models

> mmaker #10/Ad to #4/Ab

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 188.cif, chain Ab (#4) with combination, chain Ad (#10), sequence
alignment score = 505.8  
RMSD between 100 pruned atom pairs is 0.246 angstroms; (across all 103 pairs:
0.930)  
  

> show #!10 models

> hide #!4 models

> lighting soft

> set bgColor white

> cartoon style coil width 1.5 thickness 0.8

> cartoon style helix xsection round width 3 thickness 0.8

> cartoon style strand xsection round width 3 thickness 0.8

> cartoon style strand arrowScale 1

> cartoon style helix xsection oval sides 10

> graphics silhouettes true

> graphics silhouettes width 1.5

> graphics silhouettes depthJump 0.003

> lighting msDepthBias 0.004

> lighting shadows true intensity 0.06

> lighting depthCueColor #000000

> color sel bychain

> color #5 #8efa00ff

> color #5 #0096ffff

> color #6 #d783ffff

> color #7 #ff2f92ff

> color #8 #942193ff

> color #9 #00fa92ff

> color #9 #009193ff

> color #9 #8efa00ff

> color #9 #008f00ff

> color #9 #4f8f00ff

> color #9 #009051ff

> color #9 #009193ff

> color #10 #00f900ff

> color #10 #008f00ff

> color #10 #929000ff

> color #10 #4f8f00ff

> color #10 #008f00ff

> color #10 #009051ff

> select clear

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Filament-240114-onepf.cxs"

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Filament-240114-onepf.png" width 1600
> transparentBackground true

> show #!4 models

> hide #!4 models

> combine #1,3

> show #!4 models

> mmaker #11/Ad to #4/Ao

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 188.cif, chain Ao (#4) with combination, chain Ad (#11), sequence
alignment score = 287.7  
RMSD between 60 pruned atom pairs is 0.275 angstroms; (across all 63 pairs:
1.143)  
  

> hide #!4 models

> color #11 #73fcd6ff

> color #11 #73fa79ff

> mmaker #11/Ad to #4/Ao

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 188.cif, chain Ao (#4) with combination, chain Ad (#11), sequence
alignment score = 287.7  
RMSD between 60 pruned atom pairs is 0.275 angstroms; (across all 63 pairs:
1.143)  
  

> lighting soft

> set bgColor white

> cartoon style coil width 1.5 thickness 0.8

> cartoon style helix xsection round width 3 thickness 0.8

> cartoon style strand xsection round width 3 thickness 0.8

> cartoon style strand arrowScale 1

> cartoon style helix xsection oval sides 10

> graphics silhouettes true

> graphics silhouettes width 1.5

> graphics silhouettes depthJump 0.003

> lighting msDepthBias 0.004

> lighting shadows true intensity 0.06

> lighting depthCueColor #000000

> select clear

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Filament-240114-onepf.cxs"

——— End of log from Sun Jan 14 15:43:04 2024 ———

opened ChimeraX session  

> ui tool show "Show Sequence Viewer"

> sequence chain #1/Aj #4/Aj #5/Aj #6/Aj #7/Aj #8/Aj #9/Aj #10/Aj #11/Aj

Alignment identifier is 1  

> select #7/Aj:147

8 atoms, 7 bonds, 1 residue, 1 model selected  

> open "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Filament-240114-individuals.cxs"


===== Log before crash end =====

Log:
UCSF ChimeraX version: 1.7 (2023-12-19)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.1 Metal - 88
OpenGL renderer: Apple M2 Max
OpenGL vendor: Apple

Python: 3.11.2
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: Mac
      Model Identifier: Mac14,5
      Model Number: Z17J0018AB/A
      Chip: Unknown
      Total Number of Cores: 12 (8 performance and 4 efficiency)
      Memory: 64 GB
      System Firmware Version: 10151.61.4
      OS Loader Version: 10151.61.4

Software:

    System Software Overview:

      System Version: macOS 14.2.1 (23C71)
      Kernel Version: Darwin 23.2.0
      Time since boot: 10 days, 14 hours, 40 minutes

Graphics/Displays:

    Apple M2 Max:

      Chipset Model: Apple M2 Max
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 30
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3024 x 1964 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal


Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.4.1
    Babel: 2.14.0
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 0.10.0
    certifi: 2022.12.7
    cftime: 1.6.3
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.13
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.4.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.1
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.49.1
    ChimeraX-AtomicLibrary: 12.1.3
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.10.5
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.3.2
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-Clipper: 0.22.3
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.5
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.7
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.7
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.8
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.1.4
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.13
    ChimeraX-ModelPanel: 1.4
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.1
    ChimeraX-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.1
    ChimeraX-PDB: 2.7.3
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.3
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.2
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.12.3
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.33.2
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.3.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.3
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.0
    contourpy: 1.2.0
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 0.29.33
    debugpy: 1.8.0
    decorator: 5.1.1
    docutils: 0.19
    executing: 2.0.1
    filelock: 3.9.0
    fonttools: 4.47.0
    funcparserlib: 2.0.0a0
    glfw: 2.6.4
    grako: 3.16.5
    h5py: 3.10.0
    html2text: 2020.1.16
    idna: 3.6
    ihm: 0.38
    imagecodecs: 2023.9.18
    imagesize: 1.4.1
    ipykernel: 6.23.2
    ipython: 8.14.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.1.1
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.2.0
    jupyter-core: 5.5.1
    jupyterlab-widgets: 3.0.9
    kiwisolver: 1.4.5
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.3
    matplotlib: 3.7.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.8
    netCDF4: 1.6.2
    networkx: 3.1
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.8
    numpy: 1.25.1
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.9.0
    pickleshare: 0.7.5
    Pillow: 10.0.1
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 4.1.0
    prompt-toolkit: 3.0.43
    psutil: 5.9.5
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.16.1
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.2801
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2023.3.post1
    pyzmq: 25.1.2
    qtconsole: 5.4.3
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.11.1
    setuptools: 67.4.0
    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.7
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.5
    sphinxcontrib-htmlhelp: 2.0.4
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.6
    sphinxcontrib-serializinghtml: 1.1.9
    stack-data: 0.6.3
    superqt: 0.5.0
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2023.7.18
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.4
    traitlets: 5.9.0
    typing-extensions: 4.9.0
    tzdata: 2023.3
    urllib3: 2.1.0
    wcwidth: 0.2.12
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.9