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Opened 5 hours ago
#20870 new defect
ChimeraX bug report submission
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Unassigned | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | ||
| Project: |
Description
The following bug report has been submitted:
Platform: macOS-15.6.1-arm64-arm-64bit
ChimeraX Version: 1.10 (2025-06-26 08:57:52 UTC)
Description
Last time you used ChimeraX it crashed.
This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX.
Fatal Python error: Segmentation fault
Thread 0x0000000332eeb000 (most recent call first):
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 579 in _handle_results
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000331edf000 (most recent call first):
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 531 in _handle_tasks
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000330ed3000 (most recent call first):
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py", line 415 in select
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py", line 930 in wait
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 502 in _wait_for_updates
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 522 in _handle_workers
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000032fec7000 (most recent call first):
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000032eebb000 (most recent call first):
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000032deaf000 (most recent call first):
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000032cea3000 (most recent call first):
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000032be97000 (most recent call first):
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000032ae8b000 (most recent call first):
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000329e7f000 (most recent call first):
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000328e73000 (most recent call first):
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000327e67000 (most recent call first):
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000326e5b000 (most recent call first):
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Current thread 0x000000020cdfa0c0 (most recent call first):
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 368 in event_loop
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1057 in init
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1220 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.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, psutil._psutil_osx, psutil._psutil_posix, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.pdb_lib._load_libs, chimerax.map._map, chimerax.surface._surface, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, PIL._imaging, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree, PIL._imagingmath (total: 56)
{"app_name":"ChimeraX","timestamp":"2026-08-24 21:13:07.00 -0700","app_version":"1.10.0","slice_uuid":"9cf8124a-d876-34ad-b7ee-c011183ebc15","build_version":"1.10.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 15.6.1 (24G90)","roots_installed":0,"name":"ChimeraX","incident_id":"96E8A6BB-A8E9-43E9-A28F-EBFD150B13C5"}
{
"uptime" : 1300000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "Mac16,1",
"coalitionID" : 24261,
"osVersion" : {
"train" : "macOS 15.6.1",
"build" : "24G90",
"releaseType" : "User"
},
"captureTime" : "2026-08-24 21:12:58.6560 -0700",
"codeSigningMonitor" : 2,
"incident" : "96E8A6BB-A8E9-43E9-A28F-EBFD150B13C5",
"pid" : 24585,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2026-08-23 20:07:56.9558 -0700",
"procStartAbsTime" : 30557694964430,
"procExitAbsTime" : 31908189942983,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.10.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.10.0","CFBundleVersion":"1.10.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"E6935CCC-00FB-5F34-AAAE-1134439CDC45","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "02617790-4175-61F6-64D0-37DD1CBDFEA0",
"appleIntelligenceStatus" : {"state":"unavailable","reasons":["siriAssetIsNotReady","notOptedIn","assetIsNotReady"]},
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"codeSigningAuxiliaryInfo" : 0,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRm+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkZDg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"bootSessionUUID" : "95C29F80-F3BB-4CD4-8E61-3CBD8ACD7366",
"wakeTime" : 8234,
"sleepWakeUUID" : "38904F2E-8AB3-4C6B-A732-06A5D0AD7EBE",
"sip" : "enabled",
"vmRegionInfo" : "0x817678acfb0 is not in any region. Bytes after previous region: 8415578083249 Bytes before following region: 96656501846096\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL reserved VM address space (unallocated)\n---> GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV ",
"exception" : {"codes":"0x0000000000000001, 0x00008817678acfb0","rawCodes":[1,149634102775728],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x00008817678acfb0 -> 0x00000817678acfb0 (possible pointer authentication failure)"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":24585},
"ktriageinfo" : "CL - (arg = 0x0) cluster_pagein past EOF\nAPFS - (arg = 0x3bcc001600200040) cluster_pagein() failed\nVM - (arg = 0x1900000016) Filesystem pagein returned an error in vnode_pagein\nVM - (arg = 0x0) Page has error bit set\nCL - (arg = 0x0) cluster_pagein past EOF\n",
"vmregioninfo" : "0x817678acfb0 is not in any region. Bytes after previous region: 8415578083249 Bytes before following region: 96656501846096\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL reserved VM address space (unallocated)\n---> GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV ",
"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" : [{"threadState":{"x":[{"value":0},{"value":0},{"value":1},{"value":4966349464},{"value":80},{"value":95},{"value":2305948562361253792},{"value":4607123745},{"value":10540207878948483797},{"value":10540207887741932053},{"value":14757395258967641293},{"value":4294967286},{"value":4966349394},{"value":0},{"value":53},{"value":4294967280},{"value":328},{"value":8823051608},{"value":0},{"value":11},{"value":259},{"value":8805917088,"symbolLocation":224,"symbol":"_main_thread"},{"value":316},{"value":1},{"value":4332357168,"symbolLocation":0,"symbol":"faulthandler_handlers"},{"value":8767082496,"symbolLocation":0,"symbol":"OBJC_IVAR_$_NSTouchBarInputMethodCandidateList._list"},{"value":8767082496,"symbolLocation":0,"symbol":"OBJC_IVAR_$_NSTouchBarInputMethodCandidateList._list"},{"value":5},{"value":1}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6960871564},"cpsr":{"value":1073741824},"fp":{"value":4966349536},"sp":{"value":4966349504},"esr":{"value":1442840704,"description":" 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===== Log before crash start =====
UCSF ChimeraX version: 1.10 (2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
> open
> /Users/payalpratap/Desktop/Structural_Biology/UCSF_Local_Directory/Fusion4_Tspan12_Bril/Chimera/Tspan12_Fzd4_FEVR_mutants.cxs
Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 as #4, grid
size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32
Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 0 as #5.1,
grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32
Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 1 as #5.2,
grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32
Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 2 as #5.3,
grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32
Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 3 as #5.4,
grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32
Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 4 as #5.5,
grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32
Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 5 as #5.6,
grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32
Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 6 as #5.7,
grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32
Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 7 as #5.8,
grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32
Opened cryosparc_P9_J329_006_volume_map_sharp_deepEMhancer_resampled.mrc as
#7, grid size 480,480,480, pixel 0.819, shown at level 1.09, step 1, values
float32
Log from Wed Aug 12 15:30:28 2026UCSF ChimeraX version: 1.10 (2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
> open
> /Users/payalpratap/Desktop/Structural_Biology/UCSF_Local_Directory/Fusion4_Tspan12_Bril/Chimera/Tspan12_Fzd4_FEVR_mutants.cxs
> format session
Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 as #4, grid
size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32
Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 0 as #5.1,
grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32
Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 1 as #5.2,
grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32
Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 2 as #5.3,
grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32
Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 3 as #5.4,
grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32
Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 4 as #5.5,
grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32
Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 5 as #5.6,
grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32
Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 6 as #5.7,
grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32
Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 7 as #5.8,
grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32
Opened cryosparc_P9_J329_006_volume_map_sharp_deepEMhancer_resampled.mrc as
#7, grid size 480,480,480, pixel 0.819, shown at level 1.09, step 1, values
float32
Log from Tue Aug 4 16:40:37 2026UCSF ChimeraX version: 1.10 (2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
> open
> /Users/payalpratap/Desktop/Structural_Biology/UCSF_Local_Directory/Fusion4_Tspan12_Bril/Chimera/Tspan12_Fzd4_FEVR_mutants.cxs
Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 as #4, grid
size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32
Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 0 as #5.1,
grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32
Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 1 as #5.2,
grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32
Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 2 as #5.3,
grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32
Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 3 as #5.4,
grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32
Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 4 as #5.5,
grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32
Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 5 as #5.6,
grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32
Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 6 as #5.7,
grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32
Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 7 as #5.8,
grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32
Opened cryosparc_P9_J329_006_volume_map_sharp_deepEMhancer_resampled.mrc as
#7, grid size 480,480,480, pixel 0.819, shown at level 1.09, step 1, values
float32
Log from Tue Aug 4 09:23:10 2026UCSF ChimeraX version: 1.10 (2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
> open
> /Users/payalpratap/Desktop/Structural_Biology/UCSF_Local_Directory/Fusion4_Tspan12_Bril/Chimera/Tspan12_Fzd4_FEVR_mutants.cxs
> format session
Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 as #4, grid
size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32
Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 0 as #5.1,
grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32
Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 1 as #5.2,
grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32
Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 2 as #5.3,
grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32
Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 3 as #5.4,
grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32
Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 4 as #5.5,
grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32
Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 5 as #5.6,
grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32
Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 6 as #5.7,
grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32
Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 7 as #5.8,
grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32
Opened cryosparc_P9_J329_006_volume_map_sharp_deepEMhancer_resampled.mrc as
#7, grid size 480,480,480, pixel 0.819, shown at level 1.09, step 1, values
float32
Log from Mon Jul 27 21:06:11 2026UCSF ChimeraX version: 1.10 (2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
> open
> /Users/payalpratap/Desktop/Structural_Biology/UCSF_Local_Directory/Fusion4_Tspan12_Bril/Chimera/Tspan12_Fzd4_Figure4.cxs
> format session
Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 as #4, grid
size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32
Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 0 as #5.1,
grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32
Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 1 as #5.2,
grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32
Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 2 as #5.3,
grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32
Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 3 as #5.4,
grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32
Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 4 as #5.5,
grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32
Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 5 as #5.6,
grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32
Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 6 as #5.7,
grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32
Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 7 as #5.8,
grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32
Opened cryosparc_P9_J329_006_volume_map_sharp_deepEMhancer_resampled.mrc as
#7, grid size 480,480,480, pixel 0.819, shown at level 0.898, step 1, values
float32
Log from Fri Jul 24 01:26:39 2026UCSF ChimeraX version: 1.10 (2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
> open
> /Users/payalpratap/Desktop/Structural_Biology/UCSF_Local_Directory/Fusion4_Tspan12_Bril/Chimera/Tspan12_Fzd4_Figure4.cxs
> format session
Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 as #4, grid
size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32
Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 0 as #5.1,
grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32
Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 1 as #5.2,
grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32
Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 2 as #5.3,
grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32
Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 3 as #5.4,
grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32
Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 4 as #5.5,
grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32
Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 5 as #5.6,
grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32
Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 6 as #5.7,
grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32
Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 7 as #5.8,
grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32
Log from Mon Jul 20 00:02:01 2026UCSF ChimeraX version: 1.10 (2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/payalpratap/Desktop/Structural_Biology/UCSF_Local_Directory/Fusion4_Tspan12_Bril/Phenix/RealSpaceRefine_140/Fusion_BRIL4_real_space_refined_140.pdb
Chain information for Fusion_BRIL4_real_space_refined_140.pdb #1
---
Chain | Description
A | No description available
B | No description available
H | No description available
K | No description available
L | No description available
> show cartoons
> style stick
Changed 17736 atom styles
> hide atoms
> select clear
[Repeated 1 time(s)]
> select /B:219
10 atoms, 9 bonds, 1 residue, 1 model selected
> select up
220 atoms, 219 bonds, 22 residues, 1 model selected
> select up
239 atoms, 238 bonds, 24 residues, 1 model selected
> select clear
> select /B:189
10 atoms, 9 bonds, 1 residue, 1 model selected
> select up
87 atoms, 87 bonds, 6 residues, 1 model selected
> select up
1337 atoms, 1364 bonds, 85 residues, 1 model selected
> color sel red
> select clear
> select /B:226
10 atoms, 9 bonds, 1 residue, 1 model selected
> select up
220 atoms, 219 bonds, 22 residues, 1 model selected
> select up
239 atoms, 238 bonds, 24 residues, 1 model selected
> select up
258 atoms, 256 bonds, 25 residues, 1 model selected
> select down
239 atoms, 238 bonds, 24 residues, 1 model selected
> color sel purple
> color sel hot pink
> color sel magenta
Drag select of 655 residues, 1 pseudobonds
> select up
11190 atoms, 11319 bonds, 1 pseudobond, 735 residues, 2 models selected
> select up
14655 atoms, 14834 bonds, 1 pseudobond, 955 residues, 2 models selected
> select up
17736 atoms, 17959 bonds, 5 pseudobonds, 1163 residues, 2 models selected
> select down
14655 atoms, 14834 bonds, 1 pseudobond, 955 residues, 2 models selected
> hide sel cartoons
> dssp
> undo
> redo
> undo
[Repeated 3 time(s)]
> redo
[Repeated 3 time(s)]
> undo
> dssp
> undo
> open
> /Users/payalpratap/Desktop/Structural_Biology/UCSF_Local_Directory/Fusion4_Tspan12_Bril/Phenix/RealSpaceRefine_140/Fusion_BRIL4_real_space_refined_140_edit.pdb
Chain information for Fusion_BRIL4_real_space_refined_140_edit.pdb #2
---
Chain | Description
A | No description available
B | No description available
H | No description available
K | No description available
L | No description available
> show sel cartoons
> style sel stick
Changed 14655 atom styles
> hide sel atoms
> select add #2
32391 atoms, 32793 bonds, 6 pseudobonds, 2118 residues, 4 models selected
> show sel cartoons
> style sel stick
Changed 32391 atom styles
> hide sel atoms
> hide #!1 models
Drag select of 424 residues, 2 pseudobonds
> select up
8823 atoms, 8926 bonds, 2 pseudobonds, 567 residues, 2 models selected
> select up
14655 atoms, 14834 bonds, 2 pseudobonds, 955 residues, 2 models selected
> select up
17736 atoms, 17959 bonds, 5 pseudobonds, 1163 residues, 2 models selected
> select down
14655 atoms, 14834 bonds, 2 pseudobonds, 955 residues, 2 models selected
> hide sel cartoons
> show #!1 models
Drag select of 181 residues, 2 pseudobonds
> select up
4943 atoms, 5000 bonds, 2 pseudobonds, 315 residues, 2 models selected
> select up
12872 atoms, 13031 bonds, 2 pseudobonds, 835 residues, 2 models selected
> select up
17736 atoms, 17959 bonds, 5 pseudobonds, 1163 residues, 2 models selected
> select down
12872 atoms, 13031 bonds, 2 pseudobonds, 835 residues, 2 models selected
Drag select of 5 residues
> select up
13313 atoms, 13474 bonds, 2 pseudobonds, 867 residues, 2 models selected
> select up
14655 atoms, 14834 bonds, 2 pseudobonds, 955 residues, 2 models selected
> hide sel cartoons
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> dssp
> undo
> close #2
> open
> /Users/payalpratap/Desktop/Structural_Biology/UCSF_Local_Directory/Fusion4_Tspan12_Bril/Phenix/RealSpaceRefine_140/Fusion_BRIL4_real_space_refined_140_edit.pdb
Chain information for Fusion_BRIL4_real_space_refined_140_edit.pdb #2
---
Chain | Description
A | No description available
B | No description available
H | No description available
K | No description available
L | No description available
> show sel cartoons
> style sel stick
Changed 14655 atom styles
> hide sel cartoons
> show sel cartoons
> hide sel atoms
> show sel atoms
> select add #2
32391 atoms, 32793 bonds, 7 pseudobonds, 2118 residues, 4 models selected
> hide sel atoms
> show sel cartoons
> dssp
> hide #!2 models
> undo
[Repeated 1 time(s)]
> hide #!2 models
> hide #!1 models
> show #!1 models
Drag select of 493 residues, 2 pseudobonds
Drag select of 409 residues, 1 pseudobonds
> select up
8640 atoms, 8727 bonds, 1 pseudobond, 569 residues, 2 models selected
> select up
14655 atoms, 14834 bonds, 1 pseudobond, 955 residues, 2 models selected
> hide sel cartoons
> dssp
> undo
> dssp
> undo
> redo
> undo
[Repeated 1 time(s)]
> redo
[Repeated 1 time(s)]
> undo
> hide #!1 models
> show #!2 models
> dssp
> undo
> redo
> undo
> redo
[Repeated 1 time(s)]No redo action is available
> undo
> redo
> undo
Drag select of 464 residues, 1 pseudobonds
> select up
9107 atoms, 9205 bonds, 1 pseudobond, 594 residues, 2 models selected
> select up
14655 atoms, 14834 bonds, 1 pseudobond, 955 residues, 2 models selected
> select up
17736 atoms, 17959 bonds, 5 pseudobonds, 1163 residues, 2 models selected
> select down
14655 atoms, 14834 bonds, 1 pseudobond, 955 residues, 2 models selected
> hide sel cartoons
Drag select of 11 residues
> select up
213 atoms, 219 bonds, 14 residues, 1 model selected
> select up
1337 atoms, 1364 bonds, 85 residues, 1 model selected
> color sel red
> select #2/B:224
10 atoms, 9 bonds, 1 residue, 1 model selected
> select up
220 atoms, 219 bonds, 22 residues, 1 model selected
> select up
239 atoms, 238 bonds, 24 residues, 1 model selected
> select up
258 atoms, 256 bonds, 25 residues, 1 model selected
> select down
239 atoms, 238 bonds, 24 residues, 1 model selected
> color sel magenta
> select clear
[Repeated 1 time(s)]
> select #2/B:36
24 atoms, 23 bonds, 1 residue, 1 model selected
> select add #2/B:59
45 atoms, 44 bonds, 2 residues, 1 model selected
> select up
650 atoms, 659 bonds, 42 residues, 1 model selected
> select down
45 atoms, 44 bonds, 2 residues, 1 model selected
> select add #2/B:58
59 atoms, 57 bonds, 3 residues, 1 model selected
> select add #2/B:56
78 atoms, 75 bonds, 4 residues, 1 model selected
> select add #2/B:55
94 atoms, 90 bonds, 5 residues, 1 model selected
> select add #2/B:57
113 atoms, 108 bonds, 6 residues, 1 model selected
> select add #2/B:54
123 atoms, 117 bonds, 7 residues, 1 model selected
> select add #2/B:53
130 atoms, 123 bonds, 8 residues, 1 model selected
> select add #2/B:52
137 atoms, 129 bonds, 9 residues, 1 model selected
> select add #2/B:51
153 atoms, 144 bonds, 10 residues, 1 model selected
> select add #2/B:47
163 atoms, 153 bonds, 11 residues, 1 model selected
> select add #2/B:48
170 atoms, 159 bonds, 12 residues, 1 model selected
> select add #2/B:49
184 atoms, 172 bonds, 13 residues, 1 model selected
> select add #2/B:50
191 atoms, 178 bonds, 14 residues, 1 model selected
> select add #2/B:46
205 atoms, 191 bonds, 15 residues, 1 model selected
> select add #2/B:45
224 atoms, 209 bonds, 16 residues, 1 model selected
> select add #2/B:44
238 atoms, 222 bonds, 17 residues, 1 model selected
> select add #2/B:42
254 atoms, 237 bonds, 18 residues, 1 model selected
> select add #2/B:43
273 atoms, 255 bonds, 19 residues, 1 model selected
> select add #2/B:41
287 atoms, 268 bonds, 20 residues, 1 model selected
> select add #2/B:40
301 atoms, 281 bonds, 21 residues, 1 model selected
> select add #2/B:39
320 atoms, 299 bonds, 22 residues, 1 model selected
> select add #2/B:37
332 atoms, 310 bonds, 23 residues, 1 model selected
> select add #2/B:38
353 atoms, 331 bonds, 24 residues, 1 model selected
> color sel yellow
> select clear
> select add #2/B:72
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
348 atoms, 350 bonds, 23 residues, 1 model selected
> select add #2/B:64
365 atoms, 367 bonds, 24 residues, 1 model selected
> select add #2/B:63
381 atoms, 382 bonds, 25 residues, 1 model selected
> select add #2/B:61
395 atoms, 396 bonds, 26 residues, 1 model selected
> select add #2/B:62
411 atoms, 411 bonds, 27 residues, 1 model selected
> select add #2/B:60
431 atoms, 431 bonds, 28 residues, 1 model selected
> color sel blue
> color sel #00fdffff
Drag select of 8 residues
Drag select of 5 residues
> select clear
Drag select of 17 residues
> select add #2/B:107
299 atoms, 9 bonds, 18 residues, 1 model selected
> select subtract #2/B:90
280 atoms, 9 bonds, 17 residues, 1 model selected
> select add #2/B:90
299 atoms, 27 bonds, 18 residues, 1 model selected
> color sel lime
> select clear
> select #2/B:26
19 atoms, 18 bonds, 1 residue, 1 model selected
> select up
546 atoms, 552 bonds, 36 residues, 1 model selected
> select clear
> select add #2/B:35
17 atoms, 16 bonds, 1 residue, 1 model selected
> select add #2/B:34
41 atoms, 41 bonds, 2 residues, 1 model selected
> select add #2/B:33
51 atoms, 50 bonds, 3 residues, 1 model selected
> select add #2/B:31
67 atoms, 65 bonds, 4 residues, 1 model selected
> select subtract #2/B:31
51 atoms, 50 bonds, 3 residues, 1 model selected
> select add #2/B:31
67 atoms, 65 bonds, 4 residues, 1 model selected
> select add #2/B:32
78 atoms, 75 bonds, 5 residues, 1 model selected
> select add #2/B:30
88 atoms, 84 bonds, 6 residues, 1 model selected
> select add #2/B:29
107 atoms, 102 bonds, 7 residues, 1 model selected
> select add #2/B:28
123 atoms, 117 bonds, 8 residues, 1 model selected
> select add #2/B:27
134 atoms, 127 bonds, 9 residues, 1 model selected
> select add #2/B:26
153 atoms, 145 bonds, 10 residues, 1 model selected
> select add #2/B:25
164 atoms, 155 bonds, 11 residues, 1 model selected
> select add #2/B:24
181 atoms, 171 bonds, 12 residues, 1 model selected
> select add #2/B:23
200 atoms, 189 bonds, 13 residues, 1 model selected
> select add #2/B:22
224 atoms, 214 bonds, 14 residues, 1 model selected
> select add #2/B:21
244 atoms, 234 bonds, 15 residues, 1 model selected
> select add #2/B:20
251 atoms, 240 bonds, 16 residues, 1 model selected
> select add #2/B:19
258 atoms, 246 bonds, 17 residues, 1 model selected
> select subtract #2/B:19
251 atoms, 240 bonds, 16 residues, 1 model selected
> select add #2/B:19
258 atoms, 246 bonds, 17 residues, 1 model selected
> select add #2/B:18
272 atoms, 259 bonds, 18 residues, 1 model selected
> select add #2/B:17
279 atoms, 265 bonds, 19 residues, 1 model selected
> select add #2/B:16
289 atoms, 274 bonds, 20 residues, 1 model selected
> select add #2/B:15
310 atoms, 295 bonds, 21 residues, 1 model selected
> select add #2/B:13
317 atoms, 301 bonds, 22 residues, 1 model selected
> select add #2/B:14
336 atoms, 319 bonds, 23 residues, 1 model selected
> select add #2/B:12
343 atoms, 325 bonds, 24 residues, 1 model selected
> select add #2/B:11
367 atoms, 348 bonds, 25 residues, 1 model selected
> select add #2/B:9
377 atoms, 357 bonds, 26 residues, 1 model selected
> select add #2/B:10
384 atoms, 363 bonds, 27 residues, 1 model selected
> color sel blue
> select clear
[Repeated 3 time(s)]
> select add #2/B:90
19 atoms, 18 bonds, 1 residue, 1 model selected
> select add #2/B:89
33 atoms, 31 bonds, 2 residues, 1 model selected
> select add #2/B:88
57 atoms, 54 bonds, 3 residues, 1 model selected
> select add #2/B:87
79 atoms, 75 bonds, 4 residues, 1 model selected
> select clear
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 17736 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~worm
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> preset cartoons/nucleotides cylinders/stubs
Using preset: Cartoons/Nucleotides / Cylinders/Stubs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~worm
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh tube rad 2 sides 24 thick 0.6
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides stubs
> preset cartoons/nucleotides licorice/ovals
Using preset: Cartoons/Nucleotides / Licorice/Ovals
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~worm
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh default arrows f x round width 1 thick 1
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides tube/slab shape ellipsoid
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~worm
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> undo
[Repeated 3 time(s)]
> toolshed show
> save /Users/payalpratap/Desktop/image96.png supersample 3
> save
> /Users/payalpratap/Desktop/Structural_Biology/UCSF_Local_Directory/Fusion4_Tspan12_Bril/Chimera/images/Tspan12_1.bmp
> width 878 height 739 supersample 3
> save
> /Users/payalpratap/Desktop/Structural_Biology/UCSF_Local_Directory/Fusion4_Tspan12_Bril/Chimera/images/Tspan12_1.gif
> width 878 height 739 supersample 3
> save
> /Users/payalpratap/Desktop/Structural_Biology/UCSF_Local_Directory/Fusion4_Tspan12_Bril/Chimera/images/Tspan12_1.tif
> width 878 height 739 supersample 3
> save /Users/payalpratap/Desktop/picture.png supersample 3
> transparentBackground true
> lighting flat
> lighting full
> lighting soft
> lighting simple
> graphics silhouettes false
> graphics silhouettes true
> save /Users/payalpratap/Desktop/picture.png supersample 3
> transparentBackground true
[Repeated 1 time(s)]
> graphics silhouettes false
> save /Users/payalpratap/Desktop/picture1.png supersample 3
> transparentBackground true
> open
> /Users/payalpratap/Desktop/Structural_Biology/UCSF_Local_Directory/Fusion4_Tspan12_Bril/cryosparc/DeepEMhancer/cryosparc_P9_J329_006_volume_map_sharp_deepEMhancer_resampled.mrc
Opened cryosparc_P9_J329_006_volume_map_sharp_deepEMhancer_resampled.mrc as
#3, grid size 480,480,480, pixel 0.819, shown at level 0.000616, step 2,
values float32
> volume #3 step 1
> volume #3 level 0.9935
> hide #!3 models
> molmap #2 5
Opened Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 as #4, grid size
52,75,114, pixel 1.67, shown at level 0.114, step 1, values float32
> undo
[Repeated 1 time(s)]
> close #4
> close #3
> show sel cartoons
[Repeated 3 time(s)]
> hide #!2 models
> show #!2 models
> show sel cartoons
[Repeated 2 time(s)]
> select up
675 atoms, 682 bonds, 42 residues, 1 model selected
Drag select of 106 residues, 1 pseudobonds
> select up
1656 atoms, 1672 bonds, 1 pseudobond, 115 residues, 2 models selected
> select up
3081 atoms, 3125 bonds, 1 pseudobond, 208 residues, 2 models selected
> select up
17736 atoms, 17959 bonds, 5 pseudobonds, 1163 residues, 2 models selected
> select up
17736 atoms, 17959 bonds, 5 pseudobonds, 1163 residues, 2 models selected
> select up
35472 atoms, 35918 bonds, 5 pseudobonds, 2326 residues, 3 models selected
> select up
35472 atoms, 35918 bonds, 5 pseudobonds, 2326 residues, 3 models selected
> select up
35472 atoms, 35918 bonds, 5 pseudobonds, 2326 residues, 3 models selected
> show sel & #!2 cartoons
Drag select of 391 residues, 1 pseudobonds
> select up
9198 atoms, 9296 bonds, 1 pseudobond, 601 residues, 2 models selected
> select up
14655 atoms, 14834 bonds, 1 pseudobond, 955 residues, 2 models selected
> select up
17736 atoms, 17959 bonds, 5 pseudobonds, 1163 residues, 2 models selected
> select down
14655 atoms, 14834 bonds, 1 pseudobond, 955 residues, 2 models selected
> combine #2
> hide #!2 models
> hide #!3 models
> show #!3 models
Drag select of 533 residues, 2 pseudobonds
> select up
10789 atoms, 10908 bonds, 2 pseudobonds, 705 residues, 2 models selected
> select up
14655 atoms, 14834 bonds, 2 pseudobonds, 955 residues, 2 models selected
> select up
17736 atoms, 17959 bonds, 5 pseudobonds, 1163 residues, 2 models selected
> select down
14655 atoms, 14834 bonds, 2 pseudobonds, 955 residues, 2 models selected
> delete atoms (#!3 & sel)
> delete bonds (#!3 & sel)
> molmap #2 5
Opened Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 as #4, grid size
52,75,114, pixel 1.67, shown at level 0.114, step 1, values float32
> close #4
> molmap #3 5
Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 as #4, grid
size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32
> color #4 #b2b2b26f models
> ui tool show "Surface Color"
> color radial #4.1 palette #ff0000:#ffffff:#0000ff
> color single #4.1
> ui tool show "Color Zone"
> color zone #4 near #3 distance 10
> color #4 #b2b2b280 models
[Repeated 1 time(s)]
> color zone #4 near #3 distance 10
> volume splitbyzone #4
Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 0 as #5.1,
grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32
Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 1 as #5.2,
grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32
Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 2 as #5.3,
grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32
Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 3 as #5.4,
grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32
Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 4 as #5.5,
grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32
Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 5 as #5.6,
grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32
Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 6 as #5.7,
grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32
Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 7 as #5.8,
grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32
> volume #5.1 level 0.2545
> hide #!5.7 models
> show #!5.7 models
> color #5 #b2b2b2b3 models
> color #5.1 #b2b2b287 models
> ui tool show "Color Zone"
> color zone #5.1 near #3 distance 10
> close #4
> color zone #5.1 near #3 distance 10
[Repeated 1 time(s)]
> close #5
> molmap #3 5
Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 as #4, grid
size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32
> color zone #4 near #3 distance 10
> color #4.1 #b2b2b25b
> color zone #4 near #3 distance 10
[Repeated 1 time(s)]
> volume splitbyzone #4
Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 0 as #5.1,
grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32
Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 1 as #5.2,
grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32
Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 2 as #5.3,
grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32
Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 3 as #5.4,
grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32
Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 4 as #5.5,
grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32
Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 5 as #5.6,
grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32
Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 6 as #5.7,
grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32
Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 7 as #5.8,
grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32
> color #5.2 #0000ff32 models
> color #5.3 #ffff0020 models
> color #5.3 #ffff0034 models
> color #5.4 #00fdff33 models
> color #5.5 #8d81a933 models
> color #5.6 #00ff0033 models
> color #5.7 #ff000033 models
> color #5.7 #fffb00ff models
> undo
[Repeated 1 time(s)]
> color #5.7 #ff2600ff models
> color #5.7 #ff260033 models
> color #5.8 #ff00ff33 models
> select clear
> save /Users/payalpratap/Desktop/picture2.png supersample 3
> transparentBackground true
> color #5.2 #0000ff80 models
> color #5.2 #0000ff66 models
> color #5.1 #b2b2b266 models
> color #5.3 #ffff0066 models
> color #5.4 #00fdff66 models
> color #5.5 #8d81a966 models
> color #5.6 #00ff0066 models
> color #5.7 #ff260066 models
> color #5.8 #ff00ff66 models
> save /Users/payalpratap/Desktop/picture2.png supersample 3
> transparentBackground true
> color #5.2 #0000ff99 models
> color #5.3 #ffff0099 models
> color #5.4 #00fdff99 models
> color #5.5 #8d81a999 models
> color #5.6 #00ff0099 models
> color #5.7 #ff260099 models
> color #5.8 #ff00ff99 models
> save /Users/payalpratap/Desktop/picture2.png supersample 3
> transparentBackground true
[Repeated 1 time(s)]
> save
> /Users/payalpratap/Desktop/Structural_Biology/UCSF_Local_Directory/Fusion4_Tspan12_Bril/Chimera/Tspan12_Fzd4_Figure4.cxs
> includeMaps true
——— End of log from Mon Jul 20 00:02:01 2026 ———
> view name session-start
opened ChimeraX session
> open 8WM9
8wm9 title:
Fzd4/DEP complex [more info...]
Chain information for 8wm9 #6
---
Chain | Description | UniProt
A B | Frizzled-4 | FZD4_HUMAN 1-537
C | Segment polarity protein dishevelled homolog DVL-2 | DVL2_HUMAN 1-736
Non-standard residues in 8wm9 #6
---
Y01 — cholesterol hemisuccinate
> matchmaker #6/A to #3/A
No 'to' model specified
> matchmaker #6/A to #1/A
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 Fusion_BRIL4_real_space_refined_140.pdb, chain A (#1) with 8wm9,
chain A (#6), sequence alignment score = 1322.9
RMSD between 244 pruned atom pairs is 1.063 angstroms; (across all 297 pairs:
5.248)
> hide #!5 models
Drag select of 59 residues
> select up
1284 atoms, 1319 bonds, 161 residues, 1 model selected
> select up
2492 atoms, 2560 bonds, 320 residues, 1 model selected
> select up
2667 atoms, 2750 bonds, 325 residues, 1 model selected
> select up
5879 atoms, 6055 bonds, 729 residues, 1 model selected
> select down
2667 atoms, 2750 bonds, 325 residues, 1 model selected
> select down
2492 atoms, 2560 bonds, 320 residues, 1 model selected
> color sel purple
> select clear
Drag select of 13 residues
> select up
376 atoms, 381 bonds, 49 residues, 1 model selected
> select up
646 atoms, 661 bonds, 84 residues, 1 model selected
> select up
667 atoms, 681 bonds, 87 residues, 1 model selected
> select up
1646 atoms, 1689 bonds, 217 residues, 1 model selected
> select up
1671 atoms, 1714 bonds, 220 residues, 1 model selected
> select up
2283 atoms, 2344 bonds, 298 residues, 1 model selected
> select up
2377 atoms, 2440 bonds, 310 residues, 1 model selected
> select up
2552 atoms, 2630 bonds, 315 residues, 1 model selected
> select up
5879 atoms, 6055 bonds, 729 residues, 1 model selected
> select down
2552 atoms, 2630 bonds, 315 residues, 1 model selected
> select up
5879 atoms, 6055 bonds, 729 residues, 1 model selected
> select down
2552 atoms, 2630 bonds, 315 residues, 1 model selected
> color sel hot pink
> color sel #942193ff
> color sel #531b93ff
> color sel #941751ff
> color sel #942193ff
> color sel #531b93ff
> hide #!3 models
> select ::name="Y01"
350 atoms, 380 bonds, 10 residues, 1 model selected
> color sel #929000ff
> color sel #73fdffff
> color sel #7a81ffff
> color sel #d4fb79ff
> color sel #fffc79ff
> show #!5 models
> hide #!5 models
> show #!3 models
> color sel #8efa00ff
> color sel #00fdffff
> color sel #7a81ffff
> color sel #76d6ffff
> color sel #ff2600ff
> color sel #797979ff
> color sel #5e5e5eff
> color sel #424242ff
> color sel #212121ff
> color sel #4f8f00ff
> show #!4 models
> hide #!4 models
> open
> /Users/payalpratap/Desktop/Structural_Biology/UCSF_Local_Directory/Fusion4_Tspan12_Bril/cryosparc/DeepEMhancer/cryosparc_P9_J329_006_volume_map_sharp_deepEMhancer_resampled.mrc
Opened cryosparc_P9_J329_006_volume_map_sharp_deepEMhancer_resampled.mrc as
#7, grid size 480,480,480, pixel 0.819, shown at level 0.000616, step 2,
values float32
> volume #7 step 1
> volume #7 level 2.117
> volume #7 level 0.8984
> select #6/B:505
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
137 atoms, 140 bonds, 17 residues, 1 model selected
> select up
646 atoms, 661 bonds, 84 residues, 1 model selected
> select up
667 atoms, 681 bonds, 87 residues, 1 model selected
> select up
1646 atoms, 1689 bonds, 217 residues, 1 model selected
> select up
1671 atoms, 1714 bonds, 220 residues, 1 model selected
> select up
2283 atoms, 2344 bonds, 298 residues, 1 model selected
> select up
2377 atoms, 2440 bonds, 310 residues, 1 model selected
> select up
2552 atoms, 2630 bonds, 315 residues, 1 model selected
> select down
2377 atoms, 2440 bonds, 310 residues, 1 model selected
> hide sel cartoons
> color #7 #b2b2b298 models
> hide #!7 models
> show #!7 models
> hide sel atoms
> hide #!3 models
> show #!3 models
> save
> /Users/payalpratap/Desktop/Structural_Biology/UCSF_Local_Directory/Fusion4_Tspan12_Bril/Chimera/Tspan12_Fzd4_Figure4.cxs
> includeMaps true
——— End of log from Fri Jul 24 01:26:39 2026 ———
> view name session-start
opened ChimeraX session
> hide #!6 models
> hide #!7 models
> ui tool show "Show Sequence Viewer"
[Repeated 1 time(s)]
> sequence chain #3/B
Alignment identifier is 3/B
> select #3/B:65
14 atoms, 14 bonds, 1 residue, 1 model selected
> select #3/B:64-65
31 atoms, 32 bonds, 2 residues, 1 model selected
> select #3/B:66
16 atoms, 15 bonds, 1 residue, 1 model selected
> select #3/B:65-66
30 atoms, 30 bonds, 2 residues, 1 model selected
> select #3/B:65-66
30 atoms, 30 bonds, 2 residues, 1 model selected
> select #3/B:65-66
30 atoms, 30 bonds, 2 residues, 1 model selected
> select #3/B:65
14 atoms, 14 bonds, 1 residue, 1 model selected
> select #3/B:65
14 atoms, 14 bonds, 1 residue, 1 model selected
> show sel atoms
> show #!2 models
> style sel stick
Changed 14 atom styles
> select #2/A:300
14 atoms, 13 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 14 atom styles
> style sel stick
Changed 14 atom styles
> color sel byhetero
> select up
502 atoms, 512 bonds, 30 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 502 atom styles
> color sel byhetero
> select H
19035 atoms, 2534 residues, 3 models selected
> delete atoms (#!2-3 & sel)
> delete bonds (#!2-3 & sel)
> select zone #2/B:65 4 #2/A
Selected 3 atoms
> select #3/B:64
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #3/B:64
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #3/B:81
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #3/B:81
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #3/B:84-85
11 atoms, 10 bonds, 2 residues, 1 model selected
> select #3/B:84-85
11 atoms, 10 bonds, 2 residues, 1 model selected
> select #3/B:84-85
11 atoms, 10 bonds, 2 residues, 1 model selected
> select #3/B:84-85
11 atoms, 10 bonds, 2 residues, 1 model selected
> select #3/B:84
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #3/B:84
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #3/B:101
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/B:101
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> show #!7 models
> volume #7 level 0.2571
> volume #7 level 0.706
> volume #7 level 1.54
> ui tool show "Show Sequence Viewer"
> sequence chain #2/A
Alignment identifier is 2/A
> select #2/A:326
7 atoms, 6 bonds, 1 residue, 1 model selected
> hide #!7 models
> select #3/B:190
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #3/B:190
6 atoms, 5 bonds, 1 residue, 1 model selected
> style sel stick
Changed 6 atom styles
> style sel stick
Changed 6 atom styles
> show sel atoms
> select #2/A:326
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/A:223
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:223
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:256
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> select #2/A:347
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #2/A:347
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> show sel atoms
> style sel stick
Changed 11 atom styles
> color sel red
> select #3/B:26
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/B:26
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> show #!7 models
> volume #7 level 0.6419
> hide #!7 models
> color sel red
> select #3/B:49
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3/B:49
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 7 atom styles
> color sel red
> select up
41 atoms, 40 bonds, 7 residues, 1 model selected
> select down
7 atoms, 6 bonds, 1 residue, 1 model selected
> hide #!3 models
> show #!3 models
> hide #!2 models
> hide #!3 models
> show #!3 models
> show #!2 models
> hide #!2 models
> hide #!3 models
> show #!3 models
> show #!2 models
> select #3/B:101
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/B:101
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel red
> show #!7 models
> hide #!7 models
> select #3/B:138
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #3/B:138
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #3/B:138
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 12 atom styles
> color sel yellow
> select #3/B:188
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #3/B:188
4 atoms, 3 bonds, 1 residue, 1 model selected
> color sel yellow
> hide #!3 models
> show #!3 models
> hide #!2 models
> select #3/B:210
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/B:210
8 atoms, 7 bonds, 1 residue, 1 model selected
> show #!2 models
> select #2/A:223
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:223
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel red
> style sel stick
Changed 8 atom styles
> show sel atoms
> color sel byhetero
> select #2/A:256
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:256
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel red
> select
> #2/A:188-190,213-243,250-275,296-298,300-329,341-365,384-390,392-437,445-461,482-499,504-521,523-542,544-566,568-572,578-602
2369 atoms, 2414 bonds, 297 residues, 1 model selected
> select #2/A:342
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:342
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
[Repeated 1 time(s)]
> color sel lime
> style sel stick
Changed 8 atom styles
> color sel red
> color sel byhetero
> show #!7 models
> select #2/A:417
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #2/A:417
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide #!7 models
> show sel atoms
> style sel stick
Changed 11 atom styles
> color sel red
> show #!6 models
> hide #!3 models
> hide #!2 models
> ui tool show "Show Sequence Viewer"
> sequence chain #6/A
Alignment identifier is 6/A
> select #6/A:233
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #6/A:233
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #6/A:335
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #6/A:335
14 atoms, 15 bonds, 1 residue, 1 model selected
> show sel atoms
> select zone #7/A:335 4 #2/A
No atoms or surfaces specified
> select zone #7/A:335 4 #6/C
No atoms or surfaces specified
> select zone #6/A:335 4 #6/C
Selected 2 atoms
> select #6/A:342
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #6/A:342
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> select #6/A:417
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #6/A:417
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #6/A:445
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #6/A:445
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #6/A:488
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #6/A:488
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #6/A:497
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #6/A:497
6 atoms, 5 bonds, 1 residue, 1 model selected
> select ::name="Y01"
350 atoms, 380 bonds, 10 residues, 1 model selected
> select zone #6/Y01 4 #6/A
No atoms or surfaces specified
> select zone Y01 4 #6/A
Missing or invalid "near" argument: invalid objects specifier
> name frozen cholesterol sel
> select zone cholesterol 4 #6/A
Selected 32 atoms
> info selection level residue
residue id #6/A:253 name ARG index 252
residue id #6/A:257 name PHE index 256
residue id #6/A:264 name ILE index 263
residue id #6/A:267 name ILE index 266
residue id #6/A:274 name THR index 273
residue id #6/A:300 name THR index 299
residue id #6/A:304 name ILE index 303
residue id #6/A:307 name LEU index 306
residue id #6/A:311 name PHE index 310
residue id #6/A:312 name PHE index 311
residue id #6/A:344 name SER index 343
residue id #6/A:345 name SER index 344
residue id #6/A:349 name ILE index 348
residue id #6/A:352 name TRP index 351
residue id #6/A:363 name LEU index 362
residue id #6/A:366 name ARG index 365
residue id #6/A:507 name PHE index 506
> ui tool show Log
> select up
154 atoms, 145 bonds, 17 residues, 1 model selected
> color sel yellow
> color sel byhetero
> select ::name="Y01"
350 atoms, 380 bonds, 10 residues, 1 model selected
> color sel byhetero
> select zone cholesterol 5 #6/A
Selected 133 atoms
> show sel atoms
> select up
291 atoms, 276 bonds, 35 residues, 1 model selected
> show sel atoms
> color sel byhetero
> select #6/A:253
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #6/A:253
11 atoms, 10 bonds, 1 residue, 1 model selected
> select
> #3/B:10-45,53-58,65-87,90-106,127-135,145-157,165-171,179-181,189-194,206-213,218-239
1117 atoms, 1134 bonds, 150 residues, 1 model selected
> show #!3 models
> select #3/B:174
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #3/B:174-175
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #3/B:125
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #3/B:107-125
19 atoms, 19 bonds, 1 pseudobond, 2 residues, 2 models selected
> show #!7 models
> ui tool show "Volume Viewer"
> volume #7 level 2.373
> volume #7 level 1.283
> select #3/B:134
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #3/B:134
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide #!6 models
> hide #!7 models
> show #!2 models
> show sel atoms
> style sel stick
Changed 11 atom styles
> select zone #2/B:134 5 #2/A
Selected 1 atoms
> select up
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
159 atoms, 160 bonds, 20 residues, 1 model selected
> select up
2125 atoms, 2175 bonds, 269 residues, 1 model selected
> select down
159 atoms, 160 bonds, 20 residues, 1 model selected
> select down
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
159 atoms, 160 bonds, 20 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 159 atom styles
> color sel byhetero
> select #3/B:22
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #3/B:22
14 atoms, 15 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 14 atom styles
> show #!7 models
> volume #7 level 1.027
> show #!6 models
> hide #!2 models
> hide #!7 models
> select #6/C:444
14 atoms, 15 bonds, 1 residue, 1 model selected
> select up
49 atoms, 50 bonds, 5 residues, 1 model selected
> select up
660 atoms, 675 bonds, 89 residues, 1 model selected
> show sel atoms
> ui tool show "Show Sequence Viewer"
> sequence chain #6/A
Alignment identifier is 6/A
> select #6/A:267
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #6/A:267
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #6/A:267
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #6/A:267
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel cyan
> undo
> show #!2 models
> hide #!6 models
> ui tool show "Show Sequence Viewer"
> sequence chain #2/A
Alignment identifier is 2/A
> select #3/B:73
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #3/B:73
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 11 atom styles
> select #2/A:231
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #2/A:231
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 11 atom styles
> select #2/A:267
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:267
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> select #2/A:264
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:264
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> select #3/B:22
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #3/B:22
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #2/A:231
11 atoms, 11 bonds, 1 residue, 1 model selected
> show #!7 models
> hide #!7 models
> select #3/B:75
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/B:75-76
16 atoms, 15 bonds, 2 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 16 atom styles
> show #!7 models
> hide #!7 models
> select #2/A:267
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:267
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:250
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 12 atom styles
> show #!6 models
> show #!5 models
> show #!4 models
> hide #!4 models
> hide #!5 models
> hide #!2 models
> hide #!6 models
> combine #3
> hide #!3 models
> show #!8 cartoons
[Repeated 4 time(s)]
> close #8
> combine #2
> hide #!8 models
> show #!8 models
Drag select of 56 residues
> select up
761 atoms, 772 bonds, 101 residues, 1 model selected
> select up
921 atoms, 941 bonds, 120 residues, 1 model selected
> select down
761 atoms, 772 bonds, 101 residues, 1 model selected
> select up
921 atoms, 941 bonds, 120 residues, 1 model selected
> select down
761 atoms, 772 bonds, 101 residues, 1 model selected
> select up
921 atoms, 941 bonds, 120 residues, 1 model selected
> select up
8974 atoms, 9197 bonds, 1163 residues, 1 model selected
> select down
921 atoms, 941 bonds, 120 residues, 1 model selected
> color sel #ff2600ff
> color sel #ff7e79ff
Drag select of 35 residues
> select up
340 atoms, 345 bonds, 44 residues, 1 model selected
> select up
1655 atoms, 1692 bonds, 215 residues, 1 model selected
> select up
8974 atoms, 9197 bonds, 1163 residues, 1 model selected
> select down
1655 atoms, 1692 bonds, 215 residues, 1 model selected
> color sel dark gray
Drag select of 16 residues
> select up
363 atoms, 363 bonds, 50 residues, 1 model selected
> select up
1719 atoms, 1770 bonds, 228 residues, 1 model selected
> select up
8974 atoms, 9197 bonds, 1163 residues, 1 model selected
> select down
1719 atoms, 1770 bonds, 228 residues, 1 model selected
> color sel dark gray
> color sel gray
> select clear
Drag select of 46 residues
> select up
555 atoms, 559 bonds, 74 residues, 1 model selected
> select up
1719 atoms, 1770 bonds, 228 residues, 1 model selected
> select up
8974 atoms, 9197 bonds, 1163 residues, 1 model selected
> select down
1719 atoms, 1770 bonds, 228 residues, 1 model selected
> select up
8974 atoms, 9197 bonds, 1163 residues, 1 model selected
> select down
1719 atoms, 1770 bonds, 228 residues, 1 model selected
> color sel #797979ff
> color sel #5e5e5eff
> color sel #424242ff
> color sel #5e5e5eff
> select clear
Drag select of 6 atoms, 6 bonds, 21 residues, 1 pseudobonds
> select up
553 atoms, 557 bonds, 1 pseudobond, 70 residues, 2 models selected
> select up
3109 atoms, 3179 bonds, 1 pseudobond, 392 residues, 2 models selected
> select up
8974 atoms, 9197 bonds, 5 pseudobonds, 1163 residues, 2 models selected
> select up
8974 atoms, 9197 bonds, 5 pseudobonds, 1163 residues, 2 models selected
> select up
43133 atoms, 44022 bonds, 5 pseudobonds, 4426 residues, 11 models selected
> select up
43133 atoms, 44022 bonds, 5 pseudobonds, 4426 residues, 11 models selected
> select down
8974 atoms, 9197 bonds, 5 pseudobonds, 1163 residues, 2 models selected
> select down
5 pseudobonds, 1 model selected
> select down
3109 atoms, 3179 bonds, 1 pseudobond, 392 residues, 2 models selected
> color (#!8 & sel) lime
> select clear
Drag select of 7 residues
> select up
110 atoms, 109 bonds, 22 residues, 1 model selected
> select up
120 atoms, 119 bonds, 24 residues, 1 model selected
> select up
128 atoms, 126 bonds, 25 residues, 1 model selected
> select up
821 atoms, 847 bonds, 109 residues, 1 model selected
> select up
826 atoms, 851 bonds, 110 residues, 1 model selected
> select up
1570 atoms, 1614 bonds, 208 residues, 1 model selected
> select up
8974 atoms, 9197 bonds, 1163 residues, 1 model selected
> select down
1570 atoms, 1614 bonds, 208 residues, 1 model selected
> color sel blue
> select clear
> hide #!8 atoms
> select #3/B:49
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3/B:49
7 atoms, 6 bonds, 1 residue, 1 model selected
> color #8 red
> undo
> ui tool show "Show Sequence Viewer"
> sequence chain #8/B
Alignment identifier is 8/B
> select #8/B:49
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #8/B:49
7 atoms, 6 bonds, 1 residue, 1 model selected
> color sel red
> select #8/B:65
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/B:65
7 atoms, 7 bonds, 1 residue, 1 model selected
> color sel red
> show sel atoms
> style sel stick
Changed 7 atom styles
> color sel byhetero
> color sel orange
> color sel byhetero
> color sel #ff9300ff
> color sel #ff7e79ff
> color sel #ff2600ff
> color sel #d783ffff
> color sel byhetero
> select zone #8/B:64 5 #2/A
Selected 4 atoms
> select zone #8/B:64 5 #8/A
Selected 4 atoms
> show sel atoms
> style sel sphere
Changed 4 atom styles
> show sel atoms
> style sel stick
Changed 4 atom styles
> select up
18 atoms, 16 bonds, 2 residues, 1 model selected
> show sel atoms
> color sel byhetero
> select zone #8/B:64 4 #8/A
Selected 1 atoms
> hide sel atoms
> select up
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
250 atoms, 260 bonds, 30 residues, 1 model selected
> select up
2125 atoms, 2175 bonds, 269 residues, 1 model selected
> hide sel atoms
Drag select of 3 atoms, 4 bonds, 5 residues
> select up
439 atoms, 451 bonds, 55 residues, 1 model selected
> select up
2874 atoms, 2942 bonds, 368 residues, 1 model selected
> select up
2905 atoms, 2974 bonds, 371 residues, 1 model selected
> hide sel atoms
> select #8/B:49
7 atoms, 6 bonds, 1 residue, 1 model selected
> color sel #d783ffff
[Repeated 2 time(s)]
> select #8/B:85
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #8/B:85
7 atoms, 6 bonds, 1 residue, 1 model selected
> color sel #d783ffff
[Repeated 1 time(s)]
> select clear
> select #8/B:101
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/B:101
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel #d783ffff
[Repeated 1 time(s)]
> show #!7 models
> volume #7 level 0.7702
> hide #!7 models
> select #8/B:104
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #8/B:138
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #8/B:138
12 atoms, 12 bonds, 1 residue, 1 model selected
> color sel #d783ffff
[Repeated 1 time(s)]
> select
> #8/B:10-45,53-58,65-87,90-106,127-135,145-157,165-171,179-181,189-194,206-213,218-239
1117 atoms, 1134 bonds, 150 residues, 1 model selected
> select #8/B:188
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #8/B:188
4 atoms, 3 bonds, 1 residue, 1 model selected
> color sel #d783ffff
[Repeated 1 time(s)]
> select
> #8/B:10-45,53-58,65-87,90-106,127-135,145-157,165-171,179-181,189-194,206-213,218-239
1117 atoms, 1134 bonds, 150 residues, 1 model selected
> select #8/B:80
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/B:79-80
16 atoms, 15 bonds, 2 residues, 1 model selected
> select #8/B:79
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/B:79
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel #d783ffff
[Repeated 1 time(s)]
> select #8/B:78
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #8/B:78
4 atoms, 3 bonds, 1 residue, 1 model selected
> color sel #d783ffff
[Repeated 1 time(s)]
> select clear
> select #8/B:210
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/B:210
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/B:210
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel #d783ffff
[Repeated 1 time(s)]
> select #8/B:134
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #8/B:134
11 atoms, 10 bonds, 1 residue, 1 model selected
> color sel #d783ffff
[Repeated 1 time(s)]
> style sel stick
Changed 11 atom styles
> show sel atoms
> color sel byhetero
> select zone #8/B:134 4 #8/A
Nothing selected
> select zone #8/B:134 5 #8/A
Selected 1 atoms
> show sel atoms
[Repeated 1 time(s)]
> style sel stick
Changed 1 atom style
> show sel atoms
> style sel stick
Changed 1 atom style
> select zone #8/B:134 6 #8/A
Selected 3 atoms
> show sel atoms
> select zone #8/B:134 10#8/A
Missing or invalid "range" argument: Expected a number
> show sel atoms
[Repeated 1 time(s)]
> select up
16 atoms, 15 bonds, 2 residues, 1 model selected
> show sel atoms
> hide sel atoms
> select zone #8/B:134 4#8/A
Missing or invalid "range" argument: Expected a number
> select up
159 atoms, 160 bonds, 20 residues, 1 model selected
> select down
16 atoms, 15 bonds, 2 residues, 1 model selected
> select zone #8/B:134 4 #8/A
Nothing selected
> show #!8 atoms
> hide #!8 atoms
> select zone #8/B:134 5 #8/A
Selected 1 atoms
> select up
5 atoms, 4 bonds, 1 residue, 1 model selected
> show sel atoms
> select #8/B:134
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> open 9MAN
9man title:
Structure of Norrin in complex with human Tspan12 large extracellular loop
(Tspan12 LEL) [more info...]
Chain information for 9man #9
---
Chain | Description | UniProt
A B | Maltose/maltodextrin-binding periplasmic protein,Norrin | MALE_ECO57 -355-11, NDP_HUMAN 25-133
C D | Maltose/maltodextrin-binding periplasmic protein,Tetraspanin-12 | MALE_ECO57 -265-101, TSN12_HUMAN 115-224
> matchmaker #9/C to #8/B
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 Fusion_BRIL4_real_space_refined_140_edit.pdb, chain B (#8)
with 9man, chain C (#9), sequence alignment score = 387.9
RMSD between 76 pruned atom pairs is 0.920 angstroms; (across all 85 pairs:
1.671)
> select #8/A:288
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
159 atoms, 160 bonds, 20 residues, 1 model selected
> show sel atoms
> color sel byhetero
> select #8/B:78
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #8/B:78
4 atoms, 3 bonds, 1 residue, 1 model selected
> color sel orange red
> hide #9 models
> select #8/A:253
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 11 atom styles
> color sel byhetero
> show #!7 models
> volume #7 level 1.091
> show #!6 models
> select add #6
5890 atoms, 6065 bonds, 4 pseudobonds, 730 residues, 4 models selected
> hide sel atoms
> select add #7
5890 atoms, 6065 bonds, 4 pseudobonds, 730 residues, 6 models selected
> hide #!6 models
> hide #!7 models
> select #8/A:253
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #8/A:253
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> show #!6 models
> show #!7 models
> select #8/B:18
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/B:18
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/B:23
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide #!7 models
> select #8/B:22
14 atoms, 15 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 14 atom styles
> show #!7 models
> hide #!8 models
> show #!8 models
> hide #!7 models
> select #8/B:147
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #8/B:147
7 atoms, 6 bonds, 1 residue, 1 model selected
> color sel lime
> select clear
> select #8/A:289
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #8/B:142
11 atoms, 10 bonds, 1 residue, 1 model selected
> style sel stick
Changed 11 atom styles
> show sel atoms
> color sel byhetero
> hide #!6 models
> select #8/A:239
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> select #8/B:79
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> select
> #8/B:10-45,53-58,65-87,90-106,127-135,145-157,165-171,179-181,189-194,206-213,218-239
1117 atoms, 1134 bonds, 150 residues, 1 model selected
> select #8/B:148-149
15 atoms, 15 bonds, 2 residues, 1 model selected
> select #8/B:148-149
15 atoms, 15 bonds, 2 residues, 1 model selected
> select #8/B:148
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #8/B:148
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #8/B:147
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #8/B:147
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 7 atom styles
> select #8/B:85
7 atoms, 6 bonds, 1 residue, 1 model selected
> style sel stick
Changed 7 atom styles
> show sel atoms
> select #8/B:95
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #8/B:95
14 atoms, 15 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 14 atom styles
> show #!7 models
> hide #!8 models
> show #!8 models
> hide #!7 models
> ui tool show "Show Sequence Viewer"
> sequence chain #8/A
Alignment identifier is 8/A
> select #8/A:293
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/A:293
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel red
> color sel byhetero
> select #8/A:298-299
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #8/A:298-299
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #8/A:298
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #8/A:298
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel red
> show sel atoms
> style sel stick
Changed 9 atom styles
> select #8/B:65
7 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> show #!1 models
> hide #!8 models
> select #8/B:26
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/B:26
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide #!1 models
> show #!8 models
> show sel atoms
> style sel stick
Changed 8 atom styles
> select #8/A:232
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> select zone #8/B:26 5 #8/A
Nothing selected
> select zone #8/B:26 10 #8/A
Selected 12 atoms
> select zone #8/B:26 5 #8/A
Nothing selected
> show #!8 atoms
> hide #!8 atoms
> select zone #8/B:26 7 #8/A
Nothing selected
> undo
[Repeated 1 time(s)]
> select zone #8/B:26 7 #8/A
Nothing selected
> select zone #8/B:26 8 #8/A
Selected 3 atoms
> show #!7 models
> select #8/B:187
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/B:187
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/B:190
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #8/B:190
6 atoms, 5 bonds, 1 residue, 1 model selected
> hide #!7 models
> color sel red
> show #9 models
> hide #9 models
> select #8/B:81
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #8/B:81
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #8/B:101
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/B:101
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/B:161
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #8/B:161
4 atoms, 3 bonds, 1 residue, 1 model selected
> color sel cyan
> select #8/B:27
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #8/B:27
6 atoms, 5 bonds, 1 residue, 1 model selected
> color sel cyan
> save
> /Users/payalpratap/Desktop/Structural_Biology/UCSF_Local_Directory/Fusion4_Tspan12_Bril/Chimera/Tspan12_Fzd4_FEVR_mutants.cxs
> includeMaps true
——— End of log from Mon Jul 27 21:06:11 2026 ———
> view name session-start
opened ChimeraX session
> select #8/B:101
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/B:101
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/B:210
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/B:210
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/B:44
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #8/B:44
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 7 atom styles
> color sel #ebade7ff
> color sel #fd5af1ff
> color sel #f3d5f3ff
> color sel #ffc2c2ff
> color sel #ebade7ff
> select clear
> color #!8 byhetero
> select #8/B:81
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #8/B:81
4 atoms, 3 bonds, 1 residue, 1 model selected
> color sel hot pink
> color sel magenta
> color sel #ebade7ff
[Repeated 1 time(s)]
> color sel #ff8ad8ff
> select #8/B:44
7 atoms, 6 bonds, 1 residue, 1 model selected
> color sel #ff8ad8ff
[Repeated 1 time(s)]
> select clear
> color #!8 byhetero
> select #8/A:347
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #8/A:347
11 atoms, 11 bonds, 1 residue, 1 model selected
> color sel blue
> color sel hot pink
> select
> #8/B:10-45,53-58,65-87,90-106,127-135,145-157,165-171,179-181,189-194,206-213,218-239
1117 atoms, 1134 bonds, 150 residues, 1 model selected
> select #8/B:26
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/B:26
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel #ff8ad8ff
[Repeated 1 time(s)]
> select #8/B:96
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #8/B:96
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 12 atom styles
> color sel #ff8ad8ff
[Repeated 1 time(s)]
> color sel byhetero
> select #8/B:125
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #8/B:125
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #8/B:188
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #8/B:188
4 atoms, 3 bonds, 1 residue, 1 model selected
> color sel yellow
> color sel #ff8ad8ff
[Repeated 1 time(s)]
> select #8/B:146
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/B:146
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> select #8/B:201
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/B:201
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel #ff8ad8ff
[Repeated 1 time(s)]
> select clear
> select #8/B:49
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 7 atom styles
> select #8/B:44
7 atoms, 6 bonds, 1 residue, 1 model selected
> color sel #0433ffff
> color sel byhetero
> select clear
> select #8/B:44
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #8/B:146
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/B:146
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel #ff8ad8ff
> select #8/B:19
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #8/B:19
5 atoms, 4 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 5 atom styles
> color sel #ff8ad8ff
[Repeated 1 time(s)]
> hide sel atoms
> select clear
> select
> #8/B:10-45,53-58,65-87,90-106,127-135,145-157,165-171,179-181,189-194,206-213,218-239
1117 atoms, 1134 bonds, 150 residues, 1 model selected
> select
> #8/A:188-190,213-243,250-275,296-298,300-329,341-365,384-390,392-437,445-461,482-499,504-521,523-542,544-566,568-572,578-602
2369 atoms, 2414 bonds, 297 residues, 1 model selected
> select #8/A:226-227
19 atoms, 20 bonds, 2 residues, 1 model selected
> select #8/A:226-227
19 atoms, 20 bonds, 2 residues, 1 model selected
> select #8/A:226
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #8/A:226
14 atoms, 15 bonds, 1 residue, 1 model selected
> color sel #ff8ad8ff
[Repeated 1 time(s)]
> select #8/B:205
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #8/B:205
4 atoms, 3 bonds, 1 residue, 1 model selected
> color sel #ff8ad8ff
[Repeated 1 time(s)]
> select #8/B:181
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #8/B:181
6 atoms, 5 bonds, 1 residue, 1 model selected
> color sel #ff8ad8ff
[Repeated 2 time(s)]
> select #8/B:189
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #8/B:189
6 atoms, 5 bonds, 1 residue, 1 model selected
> color sel #ff8ad8ff
[Repeated 1 time(s)]
> select
> #8/A:188-190,213-243,250-275,296-298,300-329,341-365,384-390,392-437,445-461,482-499,504-521,523-542,544-566,568-572,578-602
2369 atoms, 2414 bonds, 297 residues, 1 model selected
> select
> #8/A:188-190,213-243,250-275,296-298,300-329,341-365,384-390,392-437,445-461,482-499,504-521,523-542,544-566,568-572,578-602
2369 atoms, 2414 bonds, 297 residues, 1 model selected
> select
> #8/A:188-190,213-243,250-275,296-298,300-329,341-365,384-390,392-437,445-461,482-499,504-521,523-542,544-566,568-572,578-602
2369 atoms, 2414 bonds, 297 residues, 1 model selected
> select #8/A:342
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/A:342
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel #ff8ad8ff
[Repeated 1 time(s)]
> select #8/A:256
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/A:256-257
19 atoms, 19 bonds, 2 residues, 1 model selected
> select #8/A:256
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/A:256
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel #ff8ad8ff
[Repeated 1 time(s)]
> undo
[Repeated 6 time(s)]
> select #8/A:256
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/A:256
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel #ff8ad8ff
[Repeated 1 time(s)]
> show sel atoms
> select zone #8/A:256 5 #8
Selected 56 atoms
> select #8/A:326
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #8/A:326
7 atoms, 6 bonds, 1 residue, 1 model selected
> color sel #ff8ad8ff
[Repeated 1 time(s)]
> select #8/A:273
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/A:273
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel #ff8ad8ff
[Repeated 3 time(s)]
> color sel #76d6ffff
> show sel atoms
> style sel stick
Changed 8 atom styles
> color sel #ff8ad8ff
> select #8/A:211
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #8/A:211
12 atoms, 12 bonds, 1 residue, 1 model selected
> color sel #ff8ad8ff
[Repeated 3 time(s)]
> color sel #ff40ffff
> color sel #ff2600ff
> color sel #009051ff
> color sel #000000ff
> color sel #ff8ad8ff
> show sel atoms
> style sel stick
Changed 12 atom styles
> select #8/A:293
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel #ff8ad8ff
> select #8/A:298
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel #ff8ad8ff
> color sel byhetero
> select #8/A:223
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/A:223
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/A:223
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel #000000ff
> style sel stick
Changed 8 atom styles
> show sel atoms
> color sel #ff8ad8ff
[Repeated 1 time(s)]
> color sel byhetero
> select #8/A:226
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #8/A:226-227
19 atoms, 20 bonds, 2 residues, 1 model selected
> select #8/A:226-227
19 atoms, 20 bonds, 2 residues, 1 model selected
> select #8/A:226
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #8/A:226
14 atoms, 15 bonds, 1 residue, 1 model selected
> color sel #000000ff
> style sel stick
Changed 14 atom styles
> show sel atoms
> color sel #fd5af1ff
> color sel byhetero
> select #8/A:228
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #8/A:228
6 atoms, 5 bonds, 1 residue, 1 model selected
> color sel #fd5af1ff
[Repeated 1 time(s)]
> color sel #f3d5f3ff
> color sel #ebade7ff
> select #8/A:226
14 atoms, 15 bonds, 1 residue, 1 model selected
> select up
251 atoms, 258 bonds, 31 residues, 1 model selected
> select down
14 atoms, 15 bonds, 1 residue, 1 model selected
> color sel #f3d5f3ff
> color sel #ebade7ff
> show sel atoms
[Repeated 3 time(s)]
> style sel stick
Changed 14 atom styles
> select #8/A:228
6 atoms, 5 bonds, 1 residue, 1 model selected
> style sel stick
Changed 6 atom styles
> show sel cartoons
> style sel stick
Changed 6 atom styles
> hide sel atoms
> style sel stick
Changed 6 atom styles
> style sel stick
Changed 6 atom styles
> select #8/A:228
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel cartoons
[Repeated 4 time(s)]
> style sel stick
Changed 6 atom styles
> style sel stick
Changed 6 atom styles
> select up
251 atoms, 258 bonds, 31 residues, 1 model selected
> select down
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #8/A:228
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #8/A:228
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> select #8/A:229
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/A:229
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel #ebade7ff
[Repeated 1 time(s)]
> show sel atoms
> style sel stick
Changed 8 atom styles
> select #8/A:232-233
14 atoms, 13 bonds, 2 residues, 1 model selected
> select #8/A:232-233
14 atoms, 13 bonds, 2 residues, 1 model selected
> select #8/A:232
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/A:232
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel #ebade7ff
[Repeated 2 time(s)]
> color sel #fd5af1ff
> color sel #ebade7ff
> select #8/A:234
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #8/A:234
7 atoms, 6 bonds, 1 residue, 1 model selected
> color sel #ebade7ff
[Repeated 1 time(s)]
> style sel stick
Changed 7 atom styles
> show sel atoms
> color sel byhetero
> select #8/A:237
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #8/A:237
7 atoms, 6 bonds, 1 residue, 1 model selected
> color sel #ebade7ff
[Repeated 1 time(s)]
> show sel atoms
> style sel stick
Changed 7 atom styles
> color sel byhetero
> select #8/A:239
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel #ebade7ff
> color sel byhetero
> select #8/A:245
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #8/A:245-246
12 atoms, 11 bonds, 2 residues, 1 model selected
> color sel #ebade7ff
[Repeated 1 time(s)]
> show sel atoms
> style sel stick
Changed 12 atom styles
> undo
[Repeated 4 time(s)]
> redo
> select #8/A:245
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #8/A:245
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #8/A:245
6 atoms, 5 bonds, 1 residue, 1 model selected
> color sel #ebade7ff
[Repeated 1 time(s)]
> show sel cartoons
> show sel atoms
> style sel stick
Changed 6 atom styles
> color sel byhetero
> select zone #8/A:245 5 #8
Selected 40 atoms
> select zone #8/A:245 5 #8/B
Nothing selected
> select #8/A:293
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/A:293
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/A:253
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #8/A:253
11 atoms, 10 bonds, 1 residue, 1 model selected
> color sel #000000ff
> color sel #ff8ad8ff
> color sel #fd5af1ff
> color sel #ebade7ff
> color sel byhetero
> select #8/A:293
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/A:293
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/A:298
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #8/A:298
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #8/A:302
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #8/A:302
6 atoms, 5 bonds, 1 residue, 1 model selected
> color sel #ebade7ff
[Repeated 1 time(s)]
> select #8/A:322
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/A:322
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel #ebade7ff
[Repeated 1 time(s)]
> show sel atoms
> select #8/A:347
11 atoms, 11 bonds, 1 residue, 1 model selected
> color sel #ebade7ff
[Repeated 1 time(s)]
> show sel atoms
> select #8/A:342
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel #ebade7ff
[Repeated 1 time(s)]
> show sel atoms
> color sel byhetero
> select #8/A:326
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 7 atom styles
> color sel #ebade7ff
[Repeated 1 time(s)]
> select #8/A:256
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel #ebade7ff
[Repeated 1 time(s)]
> select #8/B:96
12 atoms, 12 bonds, 1 residue, 1 model selected
> color sel #ebade7ff
[Repeated 1 time(s)]
> select #8/B:101
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel #ebade7ff
[Repeated 1 time(s)]
> show sel atoms
> style sel stick
Changed 8 atom styles
> select clear
> select #8/B:85
7 atoms, 6 bonds, 1 residue, 1 model selected
> color sel #ebade7ff
[Repeated 1 time(s)]
> color sel byhetero
> select #8/B:81
4 atoms, 3 bonds, 1 residue, 1 model selected
> color sel #ebade7ff
[Repeated 1 time(s)]
> style sel stick
Changed 4 atom styles
> style sel stick
Changed 4 atom styles
> show sel atoms
[Repeated 3 time(s)]
> select #8/B:78
4 atoms, 3 bonds, 1 residue, 1 model selected
> color sel #ebade7ff
[Repeated 1 time(s)]
> select #8/B:79
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel #ebade7ff
[Repeated 1 time(s)]
> color sel byhetero
> select #8/B:65
7 atoms, 7 bonds, 1 residue, 1 model selected
> color sel #ebade7ff
> color sel byhetero
> select #8/B:26
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel #ebade7ff
> color sel byhetero
> select #8/B:27
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #8/A:325
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/A:325
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel #929000ff
> color sel #ebade7ff
> show sel atoms
> select #8/A:328
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #8/A:328
11 atoms, 11 bonds, 1 residue, 1 model selected
> color sel #ebade7ff
[Repeated 1 time(s)]
> show sel atoms
> style sel stick
Changed 11 atom styles
> select #8/A:339
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #8/A:339
5 atoms, 4 bonds, 1 residue, 1 model selected
> color sel #ebade7ff
[Repeated 1 time(s)]
> show sel atoms
> style sel stick
Changed 5 atom styles
> select #8/A:342
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/A:342
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel #ebade7ff
[Repeated 1 time(s)]
> show sel atoms
> color sel byhetero
> select #8/A:344
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #8/A:344
6 atoms, 5 bonds, 1 residue, 1 model selected
> color sel #ebade7ff
[Repeated 1 time(s)]
> show sel atoms
> style sel stick
Changed 6 atom styles
> select #8/A:347
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #8/A:347
11 atoms, 11 bonds, 1 residue, 1 model selected
> color sel #ebade7ff
[Repeated 2 time(s)]
> show sel atoms
[Repeated 1 time(s)]
> color sel byhetero
> select #8/A:348
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #8/A:348
10 atoms, 10 bonds, 1 residue, 1 model selected
> color sel #ebade7ff
[Repeated 1 time(s)]
> show sel atoms
> show sel cartoons
> style sel stick
Changed 10 atom styles
> color sel byhetero
> select zone #8/A:348 5 #8/B
Nothing selected
> select #8/A:358
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #8/A:358
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel #ebade7ff
> show sel atoms
> style sel stick
Changed 9 atom styles
> color sel byhetero
> select #8/A:377
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #8/A:377
6 atoms, 5 bonds, 1 residue, 1 model selected
> color sel #ebade7ff
[Repeated 1 time(s)]
> show sel atoms
> style sel stick
Changed 6 atom styles
> color sel byhetero
> select #8/A:302
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> select #8/A:394
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/A:394
7 atoms, 7 bonds, 1 residue, 1 model selected
> color sel #ebade7ff
[Repeated 1 time(s)]
> show sel atoms
> style sel stick
Changed 7 atom styles
> color sel byhetero
[Repeated 2 time(s)]
> select #8/A:417
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #8/A:417
11 atoms, 10 bonds, 1 residue, 1 model selected
> color sel #000000ff
> color sel #ebade7ff
> style sel stick
Changed 11 atom styles
> show sel atoms
> color sel byhetero
> select #8/A:420
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/A:420
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel #ebade7ff
[Repeated 1 time(s)]
> show sel atoms
> style sel stick
Changed 8 atom styles
> select #8/A:540
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/A:540
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel #000000ff
> color sel #ebade7ff
> style sel stick
Changed 8 atom styles
> show sel atoms
> color sel byhetero
> select #8/A:543
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/A:543
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel #ebade7ff
[Repeated 1 time(s)]
> style sel stick
Changed 8 atom styles
> show sel atoms
> color sel byhetero
> select #8/A:548
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #8/A:548-549
15 atoms, 14 bonds, 2 residues, 1 model selected
> color sel #ebade7ff
[Repeated 1 time(s)]
> show sel atoms
> style sel stick
Changed 15 atom styles
> color sel byhetero
> select #8/A:551
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #8/A:551
7 atoms, 6 bonds, 1 residue, 1 model selected
> color sel #ebade7ff
[Repeated 1 time(s)]
> style sel stick
Changed 7 atom styles
> hide sel atoms
> color sel byhetero
> show sel atoms
> select #8/A:576
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/A:576
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel #ebade7ff
[Repeated 1 time(s)]
> show sel atoms
> style sel stick
Changed 8 atom styles
> color sel byhetero
> select #8/A:595
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/A:594-595
12 atoms, 11 bonds, 2 residues, 1 model selected
> select #8/A:594
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #8/A:594
4 atoms, 3 bonds, 1 residue, 1 model selected
> color sel #ebade7ff
[Repeated 1 time(s)]
> select #8/A:598
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #8/A:598
4 atoms, 3 bonds, 1 residue, 1 model selected
> color sel #ebade7ff
[Repeated 1 time(s)]
> select #8/A:603
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #8/A:603
6 atoms, 5 bonds, 1 residue, 1 model selected
> color sel #ebade7ff
[Repeated 2 time(s)]
> style sel stick
Changed 6 atom styles
> show sel atoms
> color sel byhetero
> save
> /Users/payalpratap/Desktop/Structural_Biology/UCSF_Local_Directory/Fusion4_Tspan12_Bril/Chimera/Tspan12_Fzd4_FEVR_mutants.cxs
> includeMaps true
> hide sel atoms
[Repeated 1 time(s)]
> select up
984 atoms, 1004 bonds, 123 residues, 1 model selected
> select up
993 atoms, 1012 bonds, 124 residues, 1 model selected
> select up
3109 atoms, 3179 bonds, 392 residues, 1 model selected
> select up
8974 atoms, 9197 bonds, 1163 residues, 1 model selected
> select up
46199 atoms, 47185 bonds, 4803 residues, 11 models selected
> select up
46199 atoms, 47185 bonds, 4803 residues, 11 models selected
> select up
46199 atoms, 47185 bonds, 4803 residues, 11 models selected
> select up
46199 atoms, 47185 bonds, 4803 residues, 11 models selected
> hide sel & #!8 atoms
> undo
> select clear
> select #8/B:146
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/B:146
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/B:81
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #8/B:81
4 atoms, 3 bonds, 1 residue, 1 model selected
> color sel #ebade7ff
[Repeated 2 time(s)]
> select
> #8/B:10-45,53-58,65-87,90-106,127-135,145-157,165-171,179-181,189-194,206-213,218-239
1117 atoms, 1134 bonds, 150 residues, 1 model selected
> select #8/B:39
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/B:39
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/B:42
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #8/B:42
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #8/B:84
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #8/B:84
4 atoms, 3 bonds, 1 residue, 1 model selected
> color sel #ebade7ff
[Repeated 1 time(s)]
> style sel stick
Changed 4 atom styles
> show sel atoms
[Repeated 2 time(s)]
> style sel stick
Changed 4 atom styles
> style sel stick
Changed 4 atom styles
> show sel atoms
> hide sel atoms
[Repeated 2 time(s)]
> select #8/B:19
5 atoms, 4 bonds, 1 residue, 1 model selected
> color sel #ebade7ff
[Repeated 1 time(s)]
> select #8/A:273
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel #ebade7ff
> select #8/A:223
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel #ebade7ff
> color sel byhetero
> select #8/A:273
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel byhetero
> select #8/B:146
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel #ebade7ff
> color sel byhetero
> select #8/B:210
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel #ebade7ff
> select #8/B:189
6 atoms, 5 bonds, 1 residue, 1 model selected
> color sel #ebade7ff
> select add #8/B:188
10 atoms, 8 bonds, 2 residues, 1 model selected
> select add #8/B:181
16 atoms, 13 bonds, 3 residues, 1 model selected
> select add #8/B:201
24 atoms, 20 bonds, 4 residues, 1 model selected
> color sel #ebade7ff
> select add #8/B:205
28 atoms, 23 bonds, 5 residues, 1 model selected
> color sel #ebade7ff
> select clear
> select #8/B:190
6 atoms, 5 bonds, 1 residue, 1 model selected
> color sel #256af7ff
> color sel blue
> select clear
> select #8/B:134
11 atoms, 10 bonds, 1 residue, 1 model selected
> color sel #ebade7ff
> select add #8/B:49
18 atoms, 16 bonds, 2 residues, 1 model selected
> color sel #ebade7ff
> select add #8/B:210
26 atoms, 23 bonds, 3 residues, 1 model selected
> color sel #ebade7ff
> color sel byhetero
> select clear
> select #8/A:298
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel #ebade7ff
> color sel byhetero
> select add #8/A:293
17 atoms, 15 bonds, 2 residues, 1 model selected
> select add #8/A:214
23 atoms, 20 bonds, 3 residues, 1 model selected
> select subtract #8/A:293
15 atoms, 13 bonds, 2 residues, 1 model selected
> select down
15 atoms, 13 bonds, 2 residues, 1 model selected
> select up
272 atoms, 278 bonds, 34 residues, 1 model selected
> select up
2125 atoms, 2175 bonds, 269 residues, 1 model selected
> select up
2136 atoms, 2186 bonds, 270 residues, 1 model selected
> select clear
> select #8/A:226
14 atoms, 15 bonds, 1 residue, 1 model selected
> color sel byhetero
> select clear
> save
> /Users/payalpratap/Desktop/Structural_Biology/UCSF_Local_Directory/Fusion4_Tspan12_Bril/Chimera/Tspan12_Fzd4_FEVR_mutants.cxs
> includeMaps true
> hide #!8 atoms
> show #!8 atoms
> undo
[Repeated 1 time(s)]
> save
> /Users/payalpratap/Desktop/Structural_Biology/UCSF_Local_Directory/Fusion4_Tspan12_Bril/Chimera/Tspan12_Fzd4_FEVR_mutants.cxs
> includeMaps true
——— End of log from Tue Aug 4 09:23:10 2026 ———
> view name session-start
opened ChimeraX session
> select #8/B:184
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #8/B:184
11 atoms, 10 bonds, 1 residue, 1 model selected
> color sel #ebade7ff
> undo
> select #8/B:26
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/B:26
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/A:279
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #8/A:273-274
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #8/A:273-274
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #8/A:273
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/A:273
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/A:253
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #8/A:253
11 atoms, 10 bonds, 1 residue, 1 model selected
> color sel cyan
> undo
> select #8/B:71
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #8/B:71
6 atoms, 5 bonds, 1 residue, 1 model selected
> color sel orange
> show sel atoms
> style sel stick
Changed 6 atom styles
> select #8/B:72
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #8/B:72
6 atoms, 5 bonds, 1 residue, 1 model selected
> style sel stick
Changed 6 atom styles
> show sel atoms
> color sel byhetero
> select up
165 atoms, 167 bonds, 23 residues, 1 model selected
> color sel byhetero
> select #8/B:144
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #8/B:145
14 atoms, 15 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 14 atom styles
> select up
128 atoms, 135 bonds, 13 residues, 1 model selected
> select add #8/B:143
140 atoms, 147 bonds, 14 residues, 1 model selected
> select add #8/B:144
151 atoms, 157 bonds, 15 residues, 1 model selected
> select add #8/B:141
158 atoms, 164 bonds, 16 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 158 atom styles
> select #8/A:289
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel #ebade7ff
[Repeated 1 time(s)]
> color sel byhetero
> show #!7 models
> hide #!7 models
> hide sel atoms
[Repeated 3 time(s)]
> select add #8
8974 atoms, 9197 bonds, 5 pseudobonds, 1163 residues, 2 models selected
> hide sel atoms
> select #8/B:71
6 atoms, 5 bonds, 1 residue, 1 model selected
> color sel blue
> select #8/B:27
6 atoms, 5 bonds, 1 residue, 1 model selected
> color sel blue
> select #8/B:161
4 atoms, 3 bonds, 1 residue, 1 model selected
> color sel blue
> select clear
> select #8/A:293
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel #ebade7ff
[Repeated 1 time(s)]
> select #8/A:211
12 atoms, 12 bonds, 1 residue, 1 model selected
> color sel #ebade7ff
[Repeated 1 time(s)]
> select #8/B:147
7 atoms, 6 bonds, 1 residue, 1 model selected
> color sel #0433ffff
> select clear
> select #8/B:147
7 atoms, 6 bonds, 1 residue, 1 model selected
> color sel blue
> select clear
> undo
[Repeated 7 time(s)]
> redo
> undo
[Repeated 3 time(s)]No undo action is available
> redo
[Repeated 10 time(s)]No redo action is available
> save
> /Users/payalpratap/Desktop/Structural_Biology/UCSF_Local_Directory/Fusion4_Tspan12_Bril/Chimera/Tspan12_Fzd4_FEVR_mutants.cxs
> includeMaps true
——— End of log from Tue Aug 4 16:40:37 2026 ———
> view name session-start
opened ChimeraX session
> lighting flat
Drag select of 447 residues
> select up
3967 atoms, 4054 bonds, 521 residues, 1 model selected
> select up
4295 atoms, 4404 bonds, 563 residues, 1 model selected
> select up
8974 atoms, 9197 bonds, 1163 residues, 1 model selected
> select down
4295 atoms, 4404 bonds, 563 residues, 1 model selected
> hide sel cartoons
> save /Users/payalpratap/Desktop/mutants.png supersample 3
> transparentBackground true
> select #8/A:417
11 atoms, 10 bonds, 1 residue, 1 model selected
> select add #8/A:420
19 atoms, 17 bonds, 2 residues, 1 model selected
> select add #8/A:328
30 atoms, 28 bonds, 3 residues, 1 model selected
> select add #8/A:326
37 atoms, 34 bonds, 4 residues, 1 model selected
> select add #8/A:325
45 atoms, 41 bonds, 5 residues, 1 model selected
> select add #8/A:339
50 atoms, 45 bonds, 6 residues, 1 model selected
> select add #8/A:540
58 atoms, 52 bonds, 7 residues, 1 model selected
> select add #8/A:543
66 atoms, 59 bonds, 8 residues, 1 model selected
> select add #8/A:549
74 atoms, 66 bonds, 9 residues, 1 model selected
> select add #8/A:548
81 atoms, 72 bonds, 10 residues, 1 model selected
> select add #8/A:551
88 atoms, 78 bonds, 11 residues, 1 model selected
> select add #8/A:394
95 atoms, 85 bonds, 12 residues, 1 model selected
> select add #8/A:358
104 atoms, 93 bonds, 13 residues, 1 model selected
> select add #8/A:226
118 atoms, 108 bonds, 14 residues, 1 model selected
> select add #8/A:223
126 atoms, 115 bonds, 15 residues, 1 model selected
> select subtract #8/A:325
118 atoms, 108 bonds, 14 residues, 1 model selected
> select add #8/A:325
126 atoms, 115 bonds, 15 residues, 1 model selected
> select add #8/A:322
134 atoms, 122 bonds, 16 residues, 1 model selected
> select add #8/A:342
142 atoms, 129 bonds, 17 residues, 1 model selected
> select add #8/A:344
148 atoms, 134 bonds, 18 residues, 1 model selected
> select add #8/A:347
159 atoms, 145 bonds, 19 residues, 1 model selected
> select add #8/A:348
169 atoms, 155 bonds, 20 residues, 1 model selected
> select add #8/A:234
176 atoms, 161 bonds, 21 residues, 1 model selected
> select add #8/A:232
184 atoms, 168 bonds, 22 residues, 1 model selected
> select add #8/A:229
192 atoms, 175 bonds, 23 residues, 1 model selected
> select add #8/A:228
198 atoms, 180 bonds, 24 residues, 1 model selected
> select add #8/A:598
202 atoms, 183 bonds, 25 residues, 1 model selected
> select add #8/A:256
210 atoms, 190 bonds, 26 residues, 1 model selected
> select add #8/A:253
221 atoms, 200 bonds, 27 residues, 1 model selected
> select add #8/A:603
227 atoms, 205 bonds, 28 residues, 1 model selected
> select add #8/A:245
233 atoms, 210 bonds, 29 residues, 1 model selected
> select add #8/A:298
242 atoms, 218 bonds, 30 residues, 1 model selected
> select add #8/A:302
248 atoms, 223 bonds, 31 residues, 1 model selected
> select add #8/A:289
257 atoms, 231 bonds, 32 residues, 1 model selected
> select add #8/A:293
265 atoms, 238 bonds, 33 residues, 1 model selected
> select add #8/A:211
277 atoms, 250 bonds, 34 residues, 1 model selected
> select add #8/A:576
285 atoms, 257 bonds, 35 residues, 1 model selected
> color sel hot pink
> select add #8/A:273
293 atoms, 264 bonds, 36 residues, 1 model selected
> select add #8/A:594
297 atoms, 267 bonds, 37 residues, 1 model selected
> select add #8/A:239
305 atoms, 274 bonds, 38 residues, 1 model selected
> select add #8/A:237
312 atoms, 280 bonds, 39 residues, 1 model selected
> select subtract #8/A:594
308 atoms, 277 bonds, 38 residues, 1 model selected
> color sel hot pink
> select clear
> select #8/A:594
4 atoms, 3 bonds, 1 residue, 1 model selected
> color sel magenta
> color sel hot pink
> select clear
> select #8/A:377
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add #8/B:79
14 atoms, 12 bonds, 2 residues, 1 model selected
> select add #8/B:78
18 atoms, 15 bonds, 3 residues, 1 model selected
> select add #8/B:81
22 atoms, 18 bonds, 4 residues, 1 model selected
> select add #8/B:85
29 atoms, 24 bonds, 5 residues, 1 model selected
> select add #8/B:84
33 atoms, 27 bonds, 6 residues, 1 model selected
> select add #8/B:19
38 atoms, 31 bonds, 7 residues, 1 model selected
> select add #8/B:26
46 atoms, 38 bonds, 8 residues, 1 model selected
> select add #8/B:101
54 atoms, 45 bonds, 9 residues, 1 model selected
> select add #8/B:65
61 atoms, 52 bonds, 10 residues, 1 model selected
> select add #8/B:188
65 atoms, 55 bonds, 11 residues, 1 model selected
> select add #8/B:189
71 atoms, 60 bonds, 12 residues, 1 model selected
> select add #8/B:138
83 atoms, 72 bonds, 13 residues, 1 model selected
> select add #8/B:146
91 atoms, 79 bonds, 14 residues, 1 model selected
> select add #8/B:134
102 atoms, 89 bonds, 15 residues, 1 model selected
> select add #8/B:49
109 atoms, 95 bonds, 16 residues, 1 model selected
> select add #8/B:201
117 atoms, 102 bonds, 17 residues, 1 model selected
> select add #8/B:205
121 atoms, 105 bonds, 18 residues, 1 model selected
> select add #8/B:210
129 atoms, 112 bonds, 19 residues, 1 model selected
> color sel hot pink
> select add #8/B:181
135 atoms, 117 bonds, 20 residues, 1 model selected
> select add #8/B:96
147 atoms, 129 bonds, 21 residues, 1 model selected
> color sel hot pink
> select clear
> save /Users/payalpratap/Desktop/mutants.png supersample 3
> transparentBackground true
> save
> /Users/payalpratap/Desktop/Structural_Biology/UCSF_Local_Directory/Fusion4_Tspan12_Bril/Chimera/Tspan12_Fzd4_FEVR_mutants.cxs
——— End of log from Wed Aug 12 15:30:28 2026 ———
> view name session-start
opened ChimeraX session
> lighting simple
> lighting soft
> save /Users/payalpratap/Desktop/mutants_left-view_soft.png supersample 3
> transparentBackground true
> lighting flat
> lighting full
> save /Users/payalpratap/Desktop/mutants_left-view_full.png supersample 3
> transparentBackground true
> lighting simple
> save /Users/payalpratap/Desktop/mutants_left-view_simple.png supersample 3
> transparentBackground true
> lighting shadows true
> lighting full
> lighting flat
> lighting full
> lighting shadows false
> graphics silhouettes false
> lighting simple
> lighting soft
> lighting full
> lighting flat
> graphics silhouettes false
> graphics silhouettes true
> lighting flat
> save /Users/payalpratap/Desktop/mutants_left-view_flat.png supersample 3
> transparentBackground true
> lighting soft
> ui tool show H-Bonds
> hide #8 target a
> ~hbonds
> show #!8 cartoons
> hide #!8 cartoons
> undo
> ui tool show Meeting
> hide #8.1 models
> show #8.1 models
> hide #8.1 models
> show #8.1 models
> hide #8.1 models
> show #8.1 models
> hide #8.1 models
> show #8.1 models
> lighting flat
> lighting full
> lighting soft
> lighting simple
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> save /Users/payalpratap/Desktop/mutants_right-view_soft.png supersample 3
> transparentBackground true
> select #8/B:65
7 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> lighting soft
> select #8/A:301
4 atoms, 3 bonds, 1 residue, 1 model selected
> select clear
> ui tool show "Side View"
> select clear
> select #8/B:36
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #8/B:36
11 atoms, 10 bonds, 1 residue, 1 model selected
> select clear
> select #8/A:300
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> select #8/A:300
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #8/A:300
7 atoms, 6 bonds, 1 residue, 1 model selected
> select zone 5 #7/B:65
Missing or invalid "near" argument: invalid objects specifier
> select zone 5 #7/B:65 #7/A
Missing or invalid "near" argument: invalid objects specifier
> select zone 5 #8/B:65 #8/A
Missing or invalid "near" argument: invalid objects specifier
> select clear
> select zone 5 #8/B:65 #8/A
Missing or invalid "near" argument: invalid objects specifier
> select zone #8/B:65 5 #8/A
Selected 14 atoms
> show sel atoms
> style sel stick
Changed 14 atom styles
> select up
44 atoms, 39 bonds, 6 residues, 1 model selected
> style sel stick
Changed 44 atom styles
> show sel atoms
> style sel stick
Changed 44 atom styles
> select clear
> hide #8.1 models
> select clear
> select zone #8/B:65 4#8/A
Missing or invalid "range" argument: Expected a number
> select zone #8/B:65 4 #8/A
Selected 3 atoms
> undo
No undo action is available
> hide sel atoms
> select up
44 atoms, 39 bonds, 6 residues, 1 model selected
> hide sel atoms
> hide #8.1 models
> select zone #8/B:65 4 #8/A
Selected 3 atoms
> show sel atoms
> select up
15 atoms, 13 bonds, 2 residues, 1 model selected
> show sel atoms
> select clear
> select zone #8/B:65 5 #8/A
Selected 14 atoms
> show sel atoms
> style sel stick
Changed 14 atom styles
> show sel atoms
> select up
44 atoms, 39 bonds, 6 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 44 atom styles
> select #8/A:279@CZ
1 atom, 1 residue, 1 model selected
> select #8/B:64
10 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 10 atom styles
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> hide sel atoms
> select #8/B:65
7 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> lighting flat
> lighting shadows true intensity 0.5
> lighting flat
> lighting soft
> lighting simple
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows true
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting full
> lighting shadows false
> lighting shadows true
> lighting flat
> lighting shadows true intensity 0.5
> lighting shadows false
> save /Users/payalpratap/Desktop/mutants_P65A_flat.png supersample 3
> transparentBackground true
> lighting soft
> save /Users/payalpratap/Desktop/mutants_P65A_soft.png supersample 3
> transparentBackground true
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> hide #!8 atoms
> select #8/A:289
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel bychain
> undo
> color sel byhetero
> select clear
> select zone #8/A:289 5 #8/A,B
Selected 52 atoms
> select zone #8/A:289 5 #8/B
Selected 19 atoms
> show sel atoms
> select up
37 atoms, 38 bonds, 3 residues, 1 model selected
> show sel atoms
> select clear
> lighting soft
> save /Users/payalpratap/Desktop/mutants_E289R_soft.png supersample 3
> transparentBackground true
> lighting flat
> save /Users/payalpratap/Desktop/mutants_E289R_flat.png supersample 3
> transparentBackground true
> hide #!8 atoms
> select clear
> select #8/B:79
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> select clear
> select #8/A:239
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select zone #8/A:239 5 #8/B
Selected 4 atoms
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select zone #8/B:M79 5 #8/A
No atoms or surfaces specified
> select zone #8/B:79 5 #8/A
Selected 15 atoms
> show sel atoms
> style sel stick
Changed 15 atom styles
> select up
28 atoms, 25 bonds, 4 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 28 atom styles
> color sel byhetero
> select clear
> undo
> select clear
> select zone #8/B:79 5 #8/B
Selected 38 atoms
> show sel atoms
> style sel stick
Changed 38 atom styles
> select up
83 atoms, 83 bonds, 11 residues, 1 model selected
> show sel cartoons
> show sel atoms
> show sel cartoons
> style sel stick
Changed 83 atom styles
> hide sel atoms
> select zone #8/B:79 4 #8/B
Selected 20 atoms
> show sel atoms
> select up
71 atoms, 71 bonds, 9 residues, 1 model selected
> show sel atoms
> select #8/B:82
12 atoms, 12 bonds, 1 residue, 1 model selected
> select add #8/B:83
18 atoms, 17 bonds, 2 residues, 1 model selected
> hide sel atoms
> select #8/B:79
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/B:80
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #8/B:77
15 atoms, 13 bonds, 2 residues, 1 model selected
> hide sel atoms
> select #8/B:96
12 atoms, 12 bonds, 1 residue, 1 model selected
> select clear
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting flat
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting flat
> save /Users/payalpratap/Desktop/mutants_L239P_M79R_flat.png supersample 3
> transparentBackground true
> lighting soft
> lighting shadows true intensity 0.5
> save /Users/payalpratap/Desktop/mutants_L239P_M79R_soft.png supersample 3
> transparentBackground true
> lighting flat
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> save /Users/payalpratap/Desktop/mutants_L239P_M79R_soft2.png supersample 3
> transparentBackground true
> lighting shadows true
> save /Users/payalpratap/Desktop/mutants_L239P_M79R_soft.png supersample 3
> transparentBackground true
> lighting flat
> save /Users/payalpratap/Desktop/mutants_L239P_M79R_soft.png supersample 3
> transparentBackground true
> save /Users/payalpratap/Desktop/mutants_L239P_M79R_flat.png supersample 3
> transparentBackground true
> lighting soft
> save /Users/payalpratap/Desktop/mutants_L239P_M79R_soft.png supersample 3
> transparentBackground true
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> save /Users/payalpratap/Desktop/mutants_L239P_M79R_soft.png supersample 3
> transparentBackground true
> lighting shadows true
> save /Users/payalpratap/Desktop/mutants_L239P_M79R_soft.png supersample 3
> transparentBackground true
> select #8/B:134
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select zone #8/B:134 4 #8/A
Nothing selected
> select zone #8/B:134 5 #8/A
Selected 1 atoms
> show sel atoms
> select zone #8/B:134 5 #8/B
Selected 58 atoms
> show sel atoms
> style sel stick
Changed 58 atom styles
> show sel atoms
> select up
119 atoms, 118 bonds, 15 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 119 atom styles
> undo
No undo action is available
> hide sel atoms
> select clear
> select #8/B:134
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select add #8/B:22
14 atoms, 15 bonds, 1 residue, 1 model selected
> select add #8/B:75
22 atoms, 22 bonds, 2 residues, 1 model selected
> select add #8/B:76
30 atoms, 29 bonds, 3 residues, 1 model selected
> hide sel atoms
> select clear
> lighting flat
> save /Users/payalpratap/Desktop/mutants_L239P_M79R_G78R_flat.png supersample
> 3 transparentBackground true
> lighting soft
> save /Users/payalpratap/Desktop/mutants_L239P_M79R_G78R_soft.png supersample
> 3 transparentBackground true
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> save /Users/payalpratap/Desktop/mutants_L239P_M79R_G78R_soft2.png
> supersample 3 transparentBackground true
> lighting shadows true
> lighting shadows false
> lighting shadows true
> save /Users/payalpratap/Desktop/mutants_L239P_M79R_G78R_soft.png supersample
> 3 transparentBackground true
> lighting flat
> save /Users/payalpratap/Desktop/mutants_L239P_M79R_G78R_flat.png supersample
> 3 transparentBackground true
> lighting soft
> save /Users/payalpratap/Desktop/mutants_L239P_M79R_G78R_soft.png supersample
> 3 transparentBackground true
> lighting shadows true intensity 0.5
> save /Users/payalpratap/Desktop/mutants_L239P_M79R_G78R_flat.png supersample
> 3 transparentBackground true
> lighting flat
> save /Users/payalpratap/Desktop/mutants_L239P_M79R_G78R_flat.png supersample
> 3 transparentBackground true
> lighting soft
> save /Users/payalpratap/Desktop/mutants_L239P_M79R_G78R_soft.png supersample
> 3 transparentBackground true
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> save /Users/payalpratap/Desktop/mutants_L239P_M79R_G78R_soft2.png
> supersample 3 transparentBackground true
> select #8/B:73
11 atoms, 11 bonds, 1 residue, 1 model selected
> style sel stick
Changed 11 atom styles
> show sel atoms
> select add #8/B:76
19 atoms, 18 bonds, 2 residues, 1 model selected
> show sel atoms
Drag select of 1 residues
> select #8/B:79
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #8/A:239
16 atoms, 14 bonds, 2 residues, 1 model selected
> hide sel atoms
> select #8/B:98
4 atoms, 3 bonds, 1 residue, 1 model selected
> select clear
> select #8/A:287
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
159 atoms, 160 bonds, 20 residues, 1 model selected
> select up
2125 atoms, 2175 bonds, 269 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 2125 atom styles
> select #8/B:145
14 atoms, 15 bonds, 1 residue, 1 model selected
> select down
14 atoms, 15 bonds, 1 residue, 1 model selected
> select up
128 atoms, 135 bonds, 13 residues, 1 model selected
> style sel stick
Changed 128 atom styles
> show sel atoms
> combine #8
> hide #!8 models
> hide #!10 models
> show #!10 models
> select add #8
8974 atoms, 9197 bonds, 5 pseudobonds, 1163 residues, 2 models selected
> select subtract #8
Nothing selected
> select clear
> hide #!10 atoms
> select #10/B:102
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
139 atoms, 143 bonds, 17 residues, 1 model selected
> select up
749 atoms, 767 bonds, 99 residues, 1 model selected
> show #!3 models
> hide #!10 models
> show #!2 models
> hide #!3 models
> show #!4 models
> hide #!4 models
> show #!3 models
> hide #!2 models
> hide #!3 models
> show #!4 models
> show #!5 models
> hide #!5 models
> hide #!4 models
> show #!5 models
> hide #!5 models
> show #!6 models
> hide #!6 models
> show #!7 models
> hide #!7 models
> show #!8 models
> hide #!8 models
> show #8.1 models
> hide #8.1 models
> hide #!8 models
> show #9 models
> hide #9 models
> show #!10 models
> select up
769 atoms, 788 bonds, 101 residues, 1 model selected
> select up
1450 atoms, 1495 bonds, 184 residues, 1 model selected
> select up
1455 atoms, 1499 bonds, 185 residues, 1 model selected
> select up
1570 atoms, 1614 bonds, 208 residues, 1 model selected
> select up
8974 atoms, 9197 bonds, 1163 residues, 1 model selected
> select down
1570 atoms, 1614 bonds, 208 residues, 1 model selected
> color sel blue
> select #10/A:364
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
199 atoms, 205 bonds, 25 residues, 1 model selected
> select up
2125 atoms, 2175 bonds, 269 residues, 1 model selected
> color sel lime
> select up
2136 atoms, 2186 bonds, 270 residues, 1 model selected
> select up
3109 atoms, 3179 bonds, 392 residues, 1 model selected
> select up
8974 atoms, 9197 bonds, 1163 residues, 1 model selected
> select down
3109 atoms, 3179 bonds, 392 residues, 1 model selected
> color sel lime
> select clear
> select #10/B:75
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #10/B:76
16 atoms, 14 bonds, 2 residues, 1 model selected
> select add #10/B:22
30 atoms, 29 bonds, 3 residues, 1 model selected
> show sel atoms
> color sel byhetero
> select #10/B:233
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #10/B:79
8 atoms, 7 bonds, 1 residue, 1 model selected
> style sel stick
Changed 8 atom styles
> show sel atoms
> color sel byhetero
> select #10/B:19
5 atoms, 4 bonds, 1 residue, 1 model selected
> select clear
> select #10/A:239
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> lighting flat
> save /Users/payalpratap/Desktop/mutants_W22A_I75A_I76A_flat.png supersample
> 3 transparentBackground true
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting full
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting soft
> save /Users/payalpratap/Desktop/mutants_W22A_I75A_I76A_soft.png supersample
> 3 transparentBackground true
> lighting shadows true intensity 0.5
> save /Users/payalpratap/Desktop/mutants_W22A_I75A_I76A_soft2.png supersample
> 3 transparentBackground true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> save /Users/payalpratap/Desktop/mutants_W22A_I75A_I76A_soft3.png supersample
> 3 transparentBackground true
> select #8/B:95
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #8/B:95
14 atoms, 15 bonds, 1 residue, 1 model selected
> show #!10 atoms
> hide #!10 atoms
> hide #!10 models
> show #!7 models
> show #!8 models
> hide #!7 models
> show sel atoms
> hide sel atoms
> select up
139 atoms, 143 bonds, 17 residues, 1 model selected
> select up
749 atoms, 767 bonds, 99 residues, 1 model selected
> select up
769 atoms, 788 bonds, 101 residues, 1 model selected
> select up
1450 atoms, 1495 bonds, 184 residues, 1 model selected
> select up
1455 atoms, 1499 bonds, 185 residues, 1 model selected
> select up
1570 atoms, 1614 bonds, 208 residues, 1 model selected
> select up
8974 atoms, 9197 bonds, 1163 residues, 1 model selected
> select up
55173 atoms, 56382 bonds, 5966 residues, 12 models selected
> select up
55173 atoms, 56382 bonds, 5966 residues, 12 models selected
> select up
55173 atoms, 56382 bonds, 5966 residues, 12 models selected
> hide sel & #!8 atoms
> select #8/B:95
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #8/B:95
14 atoms, 15 bonds, 1 residue, 1 model selected
> show sel atoms
> ui tool show "Side View"
> select up
139 atoms, 143 bonds, 17 residues, 1 model selected
> select up
749 atoms, 767 bonds, 99 residues, 1 model selected
> select up
769 atoms, 788 bonds, 101 residues, 1 model selected
> select up
1450 atoms, 1495 bonds, 184 residues, 1 model selected
> select up
1455 atoms, 1499 bonds, 185 residues, 1 model selected
> select clear
> select zone #8/B:134 5 #8/B
Selected 58 atoms
> select zone #8/B:134 4 #8/B
Selected 28 atoms
> show sel atoms
> style sel stick
Changed 28 atom styles
> select up
104 atoms, 102 bonds, 13 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 104 atom styles
> select #8/B:134
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> select clear
> show #!10 models
> hide #!8 models
> select #10/B:146
8 atoms, 7 bonds, 1 residue, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain #10/B
Alignment identifier is 10/B
> select #10/B:95
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #10/B:95
14 atoms, 15 bonds, 1 residue, 1 model selected
> style sel stick
Changed 14 atom styles
> show sel atoms
> hide sel atoms
> select #10/B:145-146
22 atoms, 23 bonds, 2 residues, 1 model selected
> select #10/B:145-146
22 atoms, 23 bonds, 2 residues, 1 model selected
> select #10/B:145
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #10/B:145
14 atoms, 15 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> select zone #8/B:145 4 #8/B
Selected 24 atoms
> select #10/B:145
14 atoms, 15 bonds, 1 residue, 1 model selected
> select zone #10/B:145 4 #10/A
Selected 6 atoms
> show sel atoms
> select up
21 atoms, 20 bonds, 3 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 21 atom styles
> color sel byhetero
> select clear
> select #10/A:208
5 atoms, 4 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> lighting flat
> save /Users/payalpratap/Desktop/mutants_W145KE_flat.png supersample 3
> transparentBackground true
> lighting soft
> save /Users/payalpratap/Desktop/mutants_W145KE_soft.png supersample 3
> transparentBackground true
> lighting shadows true intensity 0.5
> save /Users/payalpratap/Desktop/mutants_W145KE_soft2.png supersample 3
> transparentBackground true
> lighting shadows false
> save /Users/payalpratap/Desktop/mutants_W145KE_soft3.png supersample 3
> transparentBackground true
> select #10/B:95
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #10/B:95
14 atoms, 15 bonds, 1 residue, 1 model selected
> show sel atoms
Drag select of 22 atoms, 22 bonds, 17 residues
> hide sel atoms
> select clear
> select #10/B:95
14 atoms, 15 bonds, 1 residue, 1 model selected
> select up
139 atoms, 143 bonds, 17 residues, 1 model selected
> select up
749 atoms, 767 bonds, 99 residues, 1 model selected
> select zone #10/B:95 4 #10/A
Selected 2 atoms
> show sel atoms
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> color sel byhetero
> select clear
> select zone #10/B:95 4 #10/B
Selected 21 atoms
> show sel atoms
> style sel stick
Changed 21 atom styles
> select up
66 atoms, 64 bonds, 8 residues, 1 model selected
> style sel stick
Changed 66 atom styles
> show sel atoms
> hide sel atoms
> select clear
> lighting flat
> save /Users/payalpratap/Desktop/mutants_W95K_flat.png supersample 3
> transparentBackground true
> lighting soft
> save /Users/payalpratap/Desktop/mutants_W95K_soft.png supersample 3
> transparentBackground true
> lighting shadows true intensity 0.5
> save /Users/payalpratap/Desktop/mutants_W95K_soft2.png supersample 3
> transparentBackground true
> lighting shadows false
> save /Users/payalpratap/Desktop/mutants_W95K_soft3.png supersample 3
> transparentBackground true
> select #10/B:91
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #10/B:91-95
43 atoms, 44 bonds, 5 residues, 1 model selected
> lighting flat
> hide sel atoms
> select up
139 atoms, 143 bonds, 17 residues, 1 model selected
> select up
749 atoms, 767 bonds, 99 residues, 1 model selected
> select up
769 atoms, 788 bonds, 101 residues, 1 model selected
> select up
1450 atoms, 1495 bonds, 184 residues, 1 model selected
> select up
1455 atoms, 1499 bonds, 185 residues, 1 model selected
> select up
1570 atoms, 1614 bonds, 208 residues, 1 model selected
> select up
8974 atoms, 9197 bonds, 1163 residues, 1 model selected
> select up
55173 atoms, 56382 bonds, 5966 residues, 12 models selected
> select up
55173 atoms, 56382 bonds, 5966 residues, 12 models selected
> hide sel & #!10 atoms
> select clear
> select #10/B:79
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #10/B:78
12 atoms, 10 bonds, 2 residues, 1 model selected
> show #!8 models
> hide #!8 models
> color sel hot pink
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!8 models
> select #10/A:239
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel hot pink
> select clear
> select #10/B:65
7 atoms, 7 bonds, 1 residue, 1 model selected
> color sel hot pink
> select clear
> select #10/A:289
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> color sel hot pink
> select clear
> hide #10.1 models
> show #10.1 models
> save /Users/payalpratap/Desktop/mutants_FEVR_interface_left_flat.png
> supersample 3 transparentBackground true
> lighting soft
> save /Users/payalpratap/Desktop/mutants_FEVR_interface_left_soft.png
> supersample 3 transparentBackground true
> lighting shadows true intensity 0.5
> save /Users/payalpratap/Desktop/mutants_FEVR_interface_left_soft2.png
> supersample 3 transparentBackground true
> lighting shadows false
> save /Users/payalpratap/Desktop/mutants_FEVR_interface_left_soft3.png
> supersample 3 transparentBackground true
> lighting shadows true
> lighting shadows false
> turn -y 180
> lighting flat
> save /Users/payalpratap/Desktop/mutants_FEVR_interface_right_flat.png
> supersample 3 transparentBackground true
> lighting soft
> save /Users/payalpratap/Desktop/mutants_FEVR_interface_right_soft.png
> supersample 3 transparentBackground true
> lighting shadows true intensity 0.5
> save /Users/payalpratap/Desktop/mutants_FEVR_interface_right_soft2.png
> supersample 3 transparentBackground true
> lighting shadows false
> save /Users/payalpratap/Desktop/mutants_FEVR_interface_right_soft3.png
> supersample 3 transparentBackground true
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.10 (2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M4
OpenGL vendor: Apple
Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac16,1
Model Number: MW2U3LL/A
Chip: Apple M4
Total Number of Cores: 10 (4 performance and 6 efficiency)
Memory: 16 GB
System Firmware Version: 11881.140.96
OS Loader Version: 11881.140.96
Software:
System Software Overview:
System Version: macOS 15.6.1 (24G90)
Kernel Version: Darwin 24.6.0
Time since boot: 49 days, 20 hours, 55 minutes
Graphics/Displays:
Apple M4:
Chipset Model: Apple M4
Type: GPU
Bus: Built-In
Total Number of Cores: 10
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: Yes
Connection Type: Internal
Acer ET322QU:
Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
UI Looks like: 2560 x 1440 @ 75.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 1.0.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.4.0
babel: 2.17.0
beautifulsoup4: 4.13.3
blockdiag: 3.0.0
blosc2: 3.5.0
build: 1.2.2.post1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.2
ChimeraX-AddCharge: 1.5.19
ChimeraX-AddH: 2.2.7
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.20.2
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Aniso: 1.1.4
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.60.7
ChimeraX-AtomicLibrary: 14.1.18
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-Boltz: 1.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.5.1
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.10
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.4
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: 1.4.1
ChimeraX-Hbonds: 2.5.1
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.6.2
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
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: 2.2.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.10.1
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.19
ChimeraX-ModelPanel: 1.5.1
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-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14.1
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.10
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.3
ChimeraX-ProfileGrids: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.3
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
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: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.7
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.1
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.45.2
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
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: 1.1.5
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.2
coverage: 7.9.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.12
debugpy: 1.8.14
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.0
filelock: 3.18.0
fonttools: 4.58.4
funcparserlib: 2.0.0a0
glfw: 2.9.0
grako: 3.16.5
h5py: 3.14.0
html2text: 2024.2.26
idna: 3.10
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.1.0
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.7
jedi: 0.19.1
Jinja2: 3.1.6
jupyter_client: 8.6.3
jupyter_core: 5.8.1
jupyterlab_widgets: 3.0.15
kiwisolver: 1.4.8
line_profiler: 4.2.0
lxml: 5.3.1
lz4: 4.4.4
MarkupSafe: 3.0.2
matplotlib: 3.10.1
matplotlib-inline: 0.1.7
msgpack: 1.1.0
ndindex: 1.10.0
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.11.0
numpy: 1.26.4
OpenMM: 8.2.0
openvr: 1.26.701
packaging: 24.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 10.4.0
pip: 25.0.1
pkginfo: 1.11.1
platformdirs: 4.3.8
pluggy: 1.6.0
prompt_toolkit: 3.0.51
psutil: 7.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.32
Pygments: 2.18.0
pynmrstar: 3.3.5
pynrrd: 1.0.0
PyOpenGL: 3.1.9
PyOpenGL-accelerate: 3.1.9
pyopenxr: 1.1.4501
pyparsing: 3.2.3
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.8.1
PyQt6-Qt6: 6.8.2
PyQt6-WebEngine-commercial: 6.8.0
PyQt6-WebEngine-Qt6: 6.8.2
PyQt6_sip: 13.10.0
pytest: 8.4.1
pytest-cov: 6.2.1
python-dateutil: 2.9.0.post0
pytz: 2025.2
pyzmq: 27.0.0
qtconsole: 5.5.2
QtPy: 2.4.3
qtshim: 1.1
RandomWords: 0.4.0
requests: 2.32.3
roman-numerals-py: 3.1.0
scipy: 1.14.0
setuptools: 78.1.0
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.7
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.1.0
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.7.1
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.4
tornado: 6.5.1
traitlets: 5.14.3
typing_extensions: 4.14.0
tzdata: 2025.2
urllib3: 2.5.0
wcwidth: 0.2.13
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.14
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