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Opened 2 months ago
Last modified 2 months ago
#19012 closed defect
ChimeraX bug report submission — at Initial Version
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-26.0-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 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 0x000000030805b000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 579 in _handle_results
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000030704f000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 531 in _handle_tasks
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000306043000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py", line 415 in select
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py", line 930 in wait
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 502 in _wait_for_updates
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 522 in _handle_workers
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000305037000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000030402b000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000030301f000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000302013000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000301007000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000017fcd3000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000017ecc7000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000017dcbb000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000017ccaf000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000017bca3000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Current thread 0x00000001ee3f0800 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 330 in event_loop
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1054 in init
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1217 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, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, lxml._elementpath, lxml.etree, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, chimerax.surface._surface, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, PIL._imagingmath, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, psutil._psutil_osx, psutil._psutil_posix, chimerax.mlp._mlp, chimerax.chem_group._chem_group, chimerax.atom_search.ast, cython.cimports.libc.math, scipy._lib._ccallback_c, scipy.linalg._fblas, scipy.linalg._flapack, scipy.linalg.cython_lapack, scipy.linalg._cythonized_array_utils, scipy.linalg._solve_toeplitz, scipy.linalg._decomp_lu_cython, scipy.linalg._matfuncs_sqrtm_triu, scipy.linalg.cython_blas, scipy.linalg._matfuncs_expm, scipy.linalg._decomp_update, scipy.sparse._sparsetools, _csparsetools, scipy.sparse._csparsetools, scipy.sparse.linalg._dsolve._superlu, scipy.sparse.linalg._eigen.arpack._arpack, scipy.sparse.linalg._propack._spropack, scipy.sparse.linalg._propack._dpropack, scipy.sparse.linalg._propack._cpropack, scipy.sparse.linalg._propack._zpropack, scipy.sparse.csgraph._tools, scipy.sparse.csgraph._shortest_path, scipy.sparse.csgraph._traversal, scipy.sparse.csgraph._min_spanning_tree, scipy.sparse.csgraph._flow, scipy.sparse.csgraph._matching, scipy.sparse.csgraph._reordering, scipy.optimize._group_columns, scipy._lib.messagestream, scipy.optimize._trlib._trlib, scipy.optimize._lbfgsb, _moduleTNC, scipy.optimize._moduleTNC, scipy.optimize._cobyla, scipy.optimize._slsqp, scipy.optimize._minpack, scipy.optimize._lsq.givens_elimination, scipy.optimize._zeros, scipy.optimize._highs.cython.src._highs_wrapper, scipy.optimize._highs._highs_wrapper, scipy.optimize._highs.cython.src._highs_constants, scipy.optimize._highs._highs_constants, scipy.linalg._interpolative, scipy.optimize._bglu_dense, scipy.optimize._lsap, scipy.spatial._ckdtree, scipy.spatial._qhull, scipy.spatial._voronoi, scipy.spatial._distance_wrap, scipy.spatial._hausdorff, scipy.special._ufuncs_cxx, scipy.special._ufuncs, scipy.special._specfun, scipy.special._comb, scipy.special._ellip_harm_2, scipy.spatial.transform._rotation, scipy.optimize._direct, chimerax.segment._segment (total: 125)
{"app_name":"ChimeraX","timestamp":"2025-10-02 12:29:20.00 +0100","app_version":"1.9.0","slice_uuid":"17982d98-65bc-3327-8526-577ec996453c","build_version":"1.9.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 26.0 (25A354)","roots_installed":0,"name":"ChimeraX","incident_id":"75F58010-6216-4B10-9768-D1406F346AB4"}
{
"uptime" : 380000,
"procRole" : "Background",
"version" : 2,
"userID" : 502,
"deployVersion" : 210,
"modelCode" : "Mac14,9",
"coalitionID" : 10122,
"osVersion" : {
"train" : "macOS 26.0",
"build" : "25A354",
"releaseType" : "User"
},
"captureTime" : "2025-10-02 12:29:09.2203 +0100",
"codeSigningMonitor" : 2,
"incident" : "75F58010-6216-4B10-9768-D1406F346AB4",
"pid" : 88955,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-09-29 17:47:35.2413 +0100",
"procStartAbsTime" : 4586723398561,
"procExitAbsTime" : 9227394234085,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.9.0","CFBundleVersion":"1.9.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"EDF733A5-C41D-5B3D-9B5C-1980F15A2C03","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "8082133D-FF55-A5C9-9B39-07ADD6399E0D",
"developerMode" : 1,
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"codeSigningAuxiliaryInfo" : 0,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRFOD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkQng\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"bootSessionUUID" : "A37B014E-8424-4EE1-907D-91EA963A5558",
"wakeTime" : 170794,
"sleepWakeUUID" : "068446EA-5249-4011-934A-D1327892DF24",
"sip" : "enabled",
"vmRegionInfo" : "0x168 is not in any region. Bytes before following region: 4300177048\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 1004f8000-1004fc000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000168","rawCodes":[1,360],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000168"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":88955},
"vmregioninfo" : "0x168 is not in any region. Bytes before following region: 4300177048\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 1004f8000-1004fc000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
"extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
"faultingThread" : 0,
"threads" : 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===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open 6XIT
6xit title:
Cryo-EM structure of the G protein-gated inward rectifier K+ channel GIRK2
(Kir3.2) in complex with PIP2 [more info...]
Chain information for 6xit #1
---
Chain | Description | UniProt
A B C D | G protein-activated inward rectifier potassium channel 2 | A0A338P6L0_MOUSE 52-380
Non-standard residues in 6xit #1
---
K — potassium ion
PIO —
[(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-
cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate (dioctanoyl l-alpha-
phosphatidyl-d-myo-inositol 4,5-diphosphate)
> rename #1 Kir3.2_docked
> ui tool show Toolbar
> set bgColor white
> open 6XIS
6xis title:
Cryo-EM structure of the G protein-gated inward rectifier K+ channel GIRK2
(Kir3.2) in apo form [more info...]
Chain information for 6xis #2
---
Chain | Description | UniProt
A B C D | G protein-activated inward rectifier potassium channel 2 | A0A338P6L0_MOUSE 52-380
> rename #2 Kir3.1_extended
> 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
> tile
2 models tiled
> hide #!2.1 models
> open 3JYC
3jyc title:
Crystal structure of the eukaryotic strong inward-rectifier K+ channel Kir2.2
at 3.1 Angstrom resolution [more info...]
Chain information for 3jyc #3
---
Chain | Description
A | Inward-rectifier K+ channel Kir2.2
Non-standard residues in 3jyc #3
---
K — potassium ion
3jyc mmCIF Assemblies
---
1| author_and_software_defined_assembly
> open 3sPI
3spi title:
Inward rectifier potassium channel Kir2.2 in complex with PIP2 [more info...]
Chain information for 3spi #4
---
Chain | Description | UniProt
A | Inward-rectifier K+ channel Kir2.2 | D2YW45_CHICK 36-378
Non-standard residues in 3spi #4
---
K — potassium ion
PIO —
[(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-
cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate (dioctanoyl l-alpha-
phosphatidyl-d-myo-inositol 4,5-diphosphate)
3spi mmCIF Assemblies
---
1| author_and_software_defined_assembly
> 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
> tile
4 models tiled
> close #3
> close #4
> open /Users/omallen/Downloads/3SPI.pdb1
3SPI.pdb1 title:
Inward rectifier potassium channel KIR2.2 In complex with PIP2 [more info...]
Chain information for 3SPI.pdb1
---
Chain | Description
3.1/A | No description available
3.2/A 3.3/A 3.4/A | No description available
> open /Users/omallen/Downloads/3JYC.pdb1
3JYC.pdb1 title:
Crystal structure of the eukaryotic strong inward-rectifier K+ channel KIR2.2
At 3.1 angstrom resolution [more info...]
Chain information for 3JYC.pdb1
---
Chain | Description
4.1/A | No description available
4.2/A 4.3/A 4.4/A | No description available
> combine #3.1 #3.2 #3.3 #3.4
Remapping chain ID 'A' in 3SPI.pdb1 #3.2 to 'B'
Remapping chain ID 'A' in 3SPI.pdb1 #3.3 to 'C'
Remapping chain ID 'A' in 3SPI.pdb1 #3.4 to 'D'
> rename #5 Kir2.2
> rename #5 Kir2.2_docked_3SPI
> combine #4.1 #4.2 #4.3 #4.4
Remapping chain ID 'A' in 3JYC.pdb1 #4.2 to 'B'
Remapping chain ID 'A' in 3JYC.pdb1 #4.3 to 'C'
Remapping chain ID 'A' in 3JYC.pdb1 #4.4 to 'D'
> close #4
> close #3
> rename #6 "Kir2.2_Extended "
> tile
4 models tiled
> preset cartoons/nucleotides licorice/ovals
Using preset: Cartoons/Nucleotides / Licorice/Ovals
Changed 36 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
> tile columns 4
4 models tiled
> hide #!1 models
> hide #!2 models
> view orient
> ui tool show Matchmaker
> matchmaker #!6 to #5
Computing secondary structure
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 Kir2.2_docked_3SPI, chain A (#5) with Kir2.2_Extended , chain A
(#6), sequence alignment score = 1610.2
RMSD between 172 pruned atom pairs is 0.454 angstroms; (across all 321 pairs:
10.379)
> hide #1.1 models
> hide #!6.2 models
Drag select of 76 atoms, 71 bonds, 875 residues
> matchmaker #!6 & sel to #5 & sel
Computing secondary structure
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 Kir2.2_docked_3SPI, chain B (#5) with Kir2.2_Extended , chain A
(#6), sequence alignment score = 522.2
RMSD between 101 pruned atom pairs is 0.411 angstroms; (across all 104 pairs:
0.658)
> matchmaker #!6 & sel to #5 & sel
Computing secondary structure
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 Kir2.2_docked_3SPI, chain B (#5) with Kir2.2_Extended , chain A
(#6), sequence alignment score = 522.2
RMSD between 101 pruned atom pairs is 0.411 angstroms; (across all 104 pairs:
0.658)
> select clear
Drag select of 1590 residues
> show sel surfaces
> hide sel cartoons
> hide sel surfaces
> undo
> show sel surfaces
Drag select of 28 atoms, 23 bonds, 757 residues
> matchmaker #!6 & sel to #5 & sel
Computing secondary structure
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 Kir2.2_docked_3SPI, chain A (#5) with Kir2.2_Extended , chain D
(#6), sequence alignment score = 484.6
RMSD between 95 pruned atom pairs is 0.336 angstroms; (across all 95 pairs:
0.336)
> select clear
> ~tile
Drag select of 6 atoms, 4 bonds, 739 residues
> matchmaker #!6 & sel to #5 & sel
Computing secondary structure
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 Kir2.2_docked_3SPI, chain A (#5) with Kir2.2_Extended , chain A
(#6), sequence alignment score = 464.1
RMSD between 91 pruned atom pairs is 0.325 angstroms; (across all 91 pairs:
0.325)
> matchmaker #!2 to #1
Computing secondary structure
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 Kir3.2_docked, chain A (#1) with Kir3.1_extended, chain C (#2),
sequence alignment score = 1628
RMSD between 170 pruned atom pairs is 0.796 angstroms; (across all 310 pairs:
6.565)
> select clear
> show #!1 models
> show #!2 models
> hide #!5 models
> hide #!6 models
> view orient
> matchmaker #!2 to #1
Computing secondary structure
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 Kir3.2_docked, chain A (#1) with Kir3.1_extended, chain C (#2),
sequence alignment score = 1628
RMSD between 170 pruned atom pairs is 0.796 angstroms; (across all 310 pairs:
6.565)
Drag select of 3 atoms, 793 residues
> matchmaker #!2 to #1
Computing secondary structure
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 Kir3.2_docked, chain A (#1) with Kir3.1_extended, chain C (#2),
sequence alignment score = 1628
RMSD between 170 pruned atom pairs is 0.796 angstroms; (across all 310 pairs:
6.565)
> matchmaker #!2 & sel to #1 & sel
Computing secondary structure
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 Kir3.2_docked, chain A (#1) with Kir3.1_extended, chain B (#2),
sequence alignment score = 487.4
RMSD between 64 pruned atom pairs is 0.779 angstroms; (across all 97 pairs:
2.819)
Drag select of 1 atoms, 1546 residues, 1 bonds
> matchmaker #!2 & sel to #1 & sel
Computing secondary structure
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 Kir3.2_docked, chain B (#1) with Kir3.1_extended, chain C (#2),
sequence alignment score = 923.3
RMSD between 173 pruned atom pairs is 0.825 angstroms; (across all 188 pairs:
1.087)
> open /Users/omallen/Downloads/3SYA.pdb1
3SYA.pdb1 title:
Crystal structure of the G protein-gated inward rectifier K+ channel GIRK2
(KIR3.2) In complex with sodium and PIP2 [more info...]
Chain information for 3SYA.pdb1
---
Chain | Description
3.1/A | No description available
3.2/A 3.3/A 3.4/A | No description available
> combine #3.1 #3.2 #3.3 #3.4
Remapping chain ID 'A' in 3SYA.pdb1 #3.2 to 'B'
Remapping chain ID 'A' in 3SYA.pdb1 #3.3 to 'C'
Remapping chain ID 'A' in 3SYA.pdb1 #3.4 to 'D'
> close #3
> rename #4 3SYA
> view orient
> matchmaker #!4 to #1 & sel
Computing secondary structure
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 Kir3.2_docked, chain B (#1) with 3SYA, chain A (#4), sequence
alignment score = 982
RMSD between 200 pruned atom pairs is 0.486 angstroms; (across all 202 pairs:
0.604)
> view orient
> rename #4 Kir3.2_docked_Xtal_3SYA
> preset cartoons/nucleotides licorice/ovals
Using preset: Cartoons/Nucleotides / Licorice/Ovals
Changed 20 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
> hide #!2 models
> open /Users/omallen/Downloads/3SYO.pdb1
3SYO.pdb1 title:
Crystal structure of the G protein-gated inward rectifier K+ channel GIRK2
(KIR3.2) In complex with sodium [more info...]
Chain information for 3SYO.pdb1
---
Chain | Description
3.1/A | No description available
3.2/A 3.3/A 3.4/A | No description available
> combine #3.1 #3.2 #3.3 #3.4
Remapping chain ID 'A' in 3SYO.pdb1 #3.2 to 'B'
Remapping chain ID 'A' in 3SYO.pdb1 #3.3 to 'C'
Remapping chain ID 'A' in 3SYO.pdb1 #3.4 to 'D'
> combine #3.1 #3.2 #3.3 #3.4
Remapping chain ID 'A' in 3SYO.pdb1 #3.2 to 'B'
Remapping chain ID 'A' in 3SYO.pdb1 #3.3 to 'C'
Remapping chain ID 'A' in 3SYO.pdb1 #3.4 to 'D'
> close #8
> rename #7 Kir3.2_extended_Xtal_3SYO
> close #3
> matchmaker #!7 to #1 & sel
Computing secondary structure
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 Kir3.2_docked, chain B (#1) with Kir3.2_extended_Xtal_3SYO, chain A
(#7), sequence alignment score = 977.8
RMSD between 195 pruned atom pairs is 0.514 angstroms; (across all 197 pairs:
0.709)
> preset cartoons/nucleotides licorice/ovals
Using preset: Cartoons/Nucleotides / Licorice/Ovals
Changed 24 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
> show #!2 models
> hide #!1 models
> hide #!4 models
> matchmaker #!7 to #2 & sel
Computing secondary structure
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 Kir3.1_extended, chain C (#2) with Kir3.2_extended_Xtal_3SYO, chain
A (#7), sequence alignment score = 926.6
RMSD between 176 pruned atom pairs is 0.903 angstroms; (across all 190 pairs:
1.335)
> matchmaker #!7 to #2 & sel
Computing secondary structure
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 Kir3.1_extended, chain C (#2) with Kir3.2_extended_Xtal_3SYO, chain
A (#7), sequence alignment score = 926.6
RMSD between 176 pruned atom pairs is 0.903 angstroms; (across all 190 pairs:
1.335)
> matchmaker #!7 to #2
Computing secondary structure
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 Kir3.1_extended, chain C (#2) with Kir3.2_extended_Xtal_3SYO, chain
A (#7), sequence alignment score = 1616.6
RMSD between 176 pruned atom pairs is 0.903 angstroms; (across all 298 pairs:
5.735)
> matchmaker #!7 to #2
Computing secondary structure
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 Kir3.1_extended, chain C (#2) with Kir3.2_extended_Xtal_3SYO, chain
A (#7), sequence alignment score = 1616.6
RMSD between 176 pruned atom pairs is 0.903 angstroms; (across all 298 pairs:
5.735)
> ui mousemode right "move picked models"
> view matrix models
> #2,-0.12905,0.99095,-0.03695,66.448,-0.23958,-0.067314,-0.96854,408.86,-0.96226,-0.11614,0.2461,327.52
> matchmaker #!7 to #2
Computing secondary structure
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 Kir3.1_extended, chain C (#2) with Kir3.2_extended_Xtal_3SYO, chain
A (#7), sequence alignment score = 1616.6
RMSD between 176 pruned atom pairs is 0.903 angstroms; (across all 298 pairs:
5.735)
> save "/Users/omallen/OneDrive - The Francis Crick Institute/PhD/Paper
> work/Comms Biol/Revisions/chimerasessions/Kir structures.cxs"
> tile
2 models tiled
> select add #7
21716 atoms, 9782 bonds, 9 pseudobonds, 2811 residues, 6 models selected
> show sel & #!2,7 cartoons
> select clear
> show #!4 models
> show #!1 models
> tile
4 models tiled
> ui tool show "Color Actions"
> color bypolymer
> color bychain
> undo
> lighting full
> graphics silhouettes true
> graphics silhouettes false
> lighting flat
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting full
> lighting soft
> lighting shadows true intensity 0.5
> lighting simple
> graphics silhouettes false
> lighting flat
> color #7 #9437ffff
> color #7 #ff8ad8ff
> color #7 #ff2f92ff
> color #7 #941751ff
> color #7 #531b93ff
> color #7 #931e6eff
> color #7 #a4217bff
> color #7 #6f4fa4ff
> color #7 #ab7affff
> color #7 #825dc1ff
> hide #!7.2 models
> hide #7.1 models
> save "/Users/omallen/OneDrive - The Francis Crick Institute/PhD/Paper
> work/Comms Biol/Revisions/Figures/Kirstructures.png" width 2000 height 1256
> supersample 3
> save "/Users/omallen/OneDrive - The Francis Crick Institute/PhD/Paper
> work/Comms Biol/Revisions/chimerasessions/Kir structures.cxs"
> color #1 #537adbff
> color #1 #5579dbff
> select ligand
432 atoms, 432 bonds, 12 residues, 3 models selected
> color (#!1,4 & sel) yellow
> color (#!1,4 & sel) light gray
> color (#!1,4 & sel) byhetero
> select clear
> save "/Users/omallen/OneDrive - The Francis Crick Institute/PhD/Paper
> work/Comms Biol/Revisions/chimerasessions/Kir structures.cxs"
> save "/Users/omallen/OneDrive - The Francis Crick Institute/PhD/Paper
> work/Comms Biol/Revisions/Figures/Kirstructures2.png" width 2000 height 1256
> supersample 3
> hide #!4 models
> hide #!2 models
> hide #!1 models
> hide #!7 models
> show #!6 models
> show #!5 models
> tile
2 models tiled
> color #5 #76e536ff
> color #5 #42801eff
> select ligand
432 atoms, 432 bonds, 12 residues, 3 models selected
> color (#!5 & sel) light gray
> color (#!5 & sel) byhetero
> select clear
> save "/Users/omallen/OneDrive - The Francis Crick Institute/PhD/Paper
> work/Comms Biol/Revisions/Figures/kir2_2strucs.png" width 2000 height 1256
> supersample 3
> matchmaker #!6 to #5
Computing secondary structure
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 Kir2.2_docked_3SPI, chain A (#5) with Kir2.2_Extended , chain A
(#6), sequence alignment score = 1610.2
RMSD between 172 pruned atom pairs is 0.454 angstroms; (across all 321 pairs:
10.379)
> ~tile
> select add #5
10812 atoms, 11037 bonds, 8 pseudobonds, 1348 residues, 2 models selected
> hide sel cartoons
> select #5/A:130-170
312 atoms, 318 bonds, 41 residues, 1 model selected
> show sel cartoons
> hide sel cartoons
> select #5/A:140-190
387 atoms, 392 bonds, 51 residues, 1 model selected
> show sel cartoons
> hide sel cartoons
> select #5/A:150-190
307 atoms, 310 bonds, 41 residues, 1 model selected
> show sel cartoons
> hide sel cartoons
> select #5/A:155-190
269 atoms, 272 bonds, 36 residues, 1 model selected
> show sel cartoons
> select add #6
10465 atoms, 10673 bonds, 10 pseudobonds, 1340 residues, 6 models selected
> hide sel cartoons
> hide sel atoms
> undo
> select add #5
21008 atoms, 21438 bonds, 18 pseudobonds, 2652 residues, 11 models selected
> hide sel atoms
> select subtract #6
10812 atoms, 11037 bonds, 8 pseudobonds, 1348 residues, 10 models selected
> select subtract #5
4 models selected
> select #/A:155-190
Expected an objects specifier or a keyword
> select #5/A:155-190
269 atoms, 272 bonds, 36 residues, 1 model selected
> show sel cartoons
> select #6/A:155-190
269 atoms, 272 bonds, 36 residues, 1 model selected
> show sel cartoons
> select add #6
10196 atoms, 10401 bonds, 10 pseudobonds, 1304 residues, 5 models selected
> select subtract #6
4 models selected
> matchmaker #!6 to #5
Computing secondary structure
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 Kir2.2_docked_3SPI, chain A (#5) with Kir2.2_Extended , chain A
(#6), sequence alignment score = 1610.2
RMSD between 172 pruned atom pairs is 0.454 angstroms; (across all 321 pairs:
10.379)
> open /Volumes/lab-
> enchevr/home/users/enchevr/cluster_processing/gJC0030/cryosparc_P3_J5133_002_volume_map.mrc
Opened cryosparc_P3_J5133_002_volume_map.mrc as #3, grid size 128,128,128,
pixel 3.18, shown at level 0.0254, step 1, values float32
> hide #!5 models
> hide #!6 models
> view orient
> volume #3 level 1.302
> open /Volumes/lab-
> enchevr/home/users/enchevr/cluster_processing/gJC0035to37/cryosparc_P3_J5300_005_volume_map_sharp.mrc
Opened cryosparc_P3_J5300_005_volume_map_sharp.mrc as #8, grid size
256,256,256, pixel 1.58, shown at level 0.317, step 1, values float32
> volume #8 level 1.919
> open /Volumes/lab-
> enchevr/home/users/enchevr/cluster_processing/gJC0035to37/Refine3D/job051/run_class001.mrc
Opened run_class001.mrc as #9, grid size 256,256,256, pixel 1.58, shown at
level 0.0134, step 1, values float32
> volume #9 level 0.06143
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 88, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 154, in status
r.draw_background()
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 88, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 154, in status
r.draw_background()
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 88, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 154, in status
r.draw_background()
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 88, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 154, in status
r.draw_background()
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 88, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 154, in status
r.draw_background()
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 88, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 154, in status
r.draw_background()
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 88, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 154, in status
r.draw_background()
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 88, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 154, in status
r.draw_background()
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
> open /Users/omallen/Library/CloudStorage/OneDrive-
> TheFrancisCrickInstitute/PP/Cul2_VHL/crown_dimer_inEMmap-coot-0.pdb
Summary of feedback from opening /Users/omallen/Library/CloudStorage/OneDrive-
TheFrancisCrickInstitute/PP/Cul2_VHL/crown_dimer_inEMmap-coot-0.pdb
---
warnings | Start residue of secondary structure not found: HELIX 54 54 LEU 1 158 LEU 1 169 1 12
Start residue of secondary structure not found: HELIX 55 55 PRO 1 172 ARG 1
177 1 6
Start residue of secondary structure not found: HELIX 56 56 ARG 1 182 LEU 1
184 1 3
Start residue of secondary structure not found: HELIX 57 57 TYR 1 185 GLU 1
189 1 5
Start residue of secondary structure not found: HELIX 58 58 VAL 1 194 MET 1
211 1 18
69 messages similar to the above omitted
crown_dimer_inEMmap-coot-0.pdb title:
(NEDD8)-CRL2VHL-MZ1-BRD4BD2-ub(G76S, K48C)-UBE2R1(C93K, S138C, C191S,
C223S)-ub [more info...]
Chain information for crown_dimer_inEMmap-coot-0.pdb #10
---
Chain | Description | UniProt
1 | No description available |
B | von hippel-lindau disease tumor suppressor | VHL_HUMAN 54-213
C | elongin-B | ELOB_HUMAN 1-104
C1 | No description available |
D | elongin-C | L7N190_MYOLU 16-112
D1 | No description available |
E | CUL-2 | CUL2_HUMAN 1-745
E1 | No description available |
R | RBX1 |
R1 | No description available |
Non-standard residues in crown_dimer_inEMmap-coot-0.pdb #10
---
ALAB — (alab)
ARGB — (ARGB)
ASNB — (ASNB)
ASPB — (ASPB)
CYSB — (cysb)
GLNB — (GLNB)
GLUB — (glub)
GLYB — (glyb)
HISB — (hisb)
ILEB — (ileb)
LEUB — (leub)
LYSB — (lysb)
METB — (metb)
PHEB — (pheb)
PROB — (prob)
SERB — (serb)
THRB — (THRB)
TRPB — (TRPB)
TYRB — (tyrb)
VALB — (valb)
ZN — zinc ion
ZNR — (ZNR)
> hide #!10 surfaces
> hide #!10 atoms
> show #!10 cartoons
> select #10/E1:376
16 atoms, 15 bonds, 1 residue, 1 model selected
> select add #10/E1:465
27 atoms, 25 bonds, 2 residues, 1 model selected
> select add #10/E1:466
34 atoms, 31 bonds, 3 residues, 1 model selected
> select #10/1
2616 atoms, 2648 bonds, 1 pseudobond, 161 residues, 2 models selected
> mlp sel
Map values for surface "crown_dimer_inEMmap-coot-0.pdb_1 SES surface": minimum
54.76, mean 170, maximum 266.4
To also show corresponding color key, enter the above mlp command and add key
true
> mlp sel
Map values for surface "crown_dimer_inEMmap-coot-0.pdb_1 SES surface": minimum
1.016e+16, mean 7.225e+27, maximum 1.738e+29
To also show corresponding color key, enter the above mlp command and add key
true
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Could not come up with unique atom name in mega-residue
LEUB+SERB+VALB+ARGB+LYSB+VALB+PROB+VALB+GLUB+GLNB+ASNB+LEUB+TYRB+CYSB+ARGB+ARGB+ARGB+GLUB+LEUB+LYSB+ASPB+LEUB+ILEB+THRB+VALB+TYRB+ARGB+VALB+SERB+PROB+LEUB+LEUB+TYRB+THRB+GLUB+ILEB+ASPB+ASNB+LEUB+ALAB+GLUB+PHEB+ASPB+ILEB+HISB+PROB+PROB+GLNB+ASNB+GLYB+VALB+ASPB+GLNB+VALB+LYSB+ASNB+ASPB+LEUB+LEUB+SERB+GLUB+PROB+ARGB+VALB+LEUB+PHEB+THRB+LEUB+GLNB+GLUB+GLUB+THRB+ARGB+GLNB+ILEB+ASNB+ALAB+VALB+HISB+LEUB+GLNB+LEUB+ARGB+GLYB+METB+ASPB+GLYB+HISB+ASPB+THRB+GLYB+ALAB+ASPB+ARGB+PHEB+LEUB+TRPB+LEUB+HISB+GLYB+ARGB+TYRB+SERB+HISB+ILEB+ARGB+ARGB+GLYB+THRB+GLYB+PROB+PROB+LEUB+THRB+PROB+TYRB+PROB+GLNB+PROB+GLUB+GLYB+ASPB+PHEB+ASNB+LEUB+TRPB+VALB+PROB+LEUB+VALB+VALB+ARGB+PROB+SERB+ARGB+ASNB+CYSB+PHEB+ILEB+VALB+GLNB+SERB+PROB+GLUB+ARGB+SERB+ASNB+VALB+SERB+ARGB+LEUB+VALB+PROB+ARGB+PROB+ARGB+GLYB+ALAB+GLUB+METB
> hide sel surfaces
> select #10/C1
1647 atoms, 1663 bonds, 104 residues, 1 model selected
> select #10/E
10756 atoms, 10867 bonds, 658 residues, 1 model selected
> mlp sel
Map values for surface "crown_dimer_inEMmap-coot-0.pdb_E SES surface": minimum
-28.08, mean -2.865, maximum 27.9
To also show corresponding color key, enter the above mlp command and add key
true
> show sel atoms
> ui tool show Contacts
> contacts sel intraMol false ignoreHiddenModels true select true reveal true
1347 contacts
> mlp sel
Map values for surface "crown_dimer_inEMmap-coot-0.pdb_B SES surface": minimum
-25.31, mean -3.016, maximum 24.27
Map values for surface "crown_dimer_inEMmap-coot-0.pdb_D SES surface": minimum
-26.49, mean -2.329, maximum 26.98
Map values for surface "crown_dimer_inEMmap-coot-0.pdb_E SES surface": minimum
-28.08, mean -2.865, maximum 27.9
Map values for surface "crown_dimer_inEMmap-coot-0.pdb_E1 SES surface":
minimum -27.95, mean -2.92, maximum 26.62
Map values for surface "crown_dimer_inEMmap-coot-0.pdb_R SES surface": minimum
-25.86, mean -1.656, maximum 32.5
Map values for surface "crown_dimer_inEMmap-coot-0.pdb_R1 SES surface":
minimum -25.04, mean -2.076, maximum 24.45
To also show corresponding color key, enter the above mlp command and add key
true
> mlp sel
Map values for surface "crown_dimer_inEMmap-coot-0.pdb_B SES surface": minimum
-25.31, mean -3.016, maximum 24.27
Map values for surface "crown_dimer_inEMmap-coot-0.pdb_D SES surface": minimum
-26.49, mean -2.329, maximum 26.98
Map values for surface "crown_dimer_inEMmap-coot-0.pdb_E SES surface": minimum
-28.08, mean -2.865, maximum 27.9
Map values for surface "crown_dimer_inEMmap-coot-0.pdb_E1 SES surface":
minimum -27.95, mean -2.92, maximum 26.62
Map values for surface "crown_dimer_inEMmap-coot-0.pdb_R SES surface": minimum
-25.86, mean -1.656, maximum 32.5
Map values for surface "crown_dimer_inEMmap-coot-0.pdb_R1 SES surface":
minimum -25.04, mean -2.076, maximum 24.45
To also show corresponding color key, enter the above mlp command and add key
true
> close #10
> close #11
> show #!9 models
> open 5n4w
5n4w title:
Crystal structure of the Cul2-Rbx1-EloBC-VHL ubiquitin ligase complex [more
info...]
Chain information for 5n4w #10
---
Chain | Description | UniProt
A | Cullin-2 | CUL2_HUMAN 1-745
B | Elongin-B | ELOB_HUMAN 1-104
C | Elongin-C | ELOC_HUMAN 17-112
R | E3 ubiquitin-protein ligase RBX1 | RBX1_HUMAN 1-102
V | Von Hippel-Lindau disease tumor suppressor | VHL_HUMAN 54-213
Non-standard residues in 5n4w #10
---
ZN — zinc ion
3 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> hide #!10 atoms
> show #!10 cartoons
> view matrix models
> #10,0.8737,-0.19688,0.44484,212.08,-0.41454,0.17717,0.89262,176.07,-0.25455,-0.96429,0.073175,279.19
> view matrix models
> #10,0.56666,-0.48876,0.66333,222.85,-0.78337,-0.56913,0.24985,224.58,0.25541,-0.66121,-0.70539,181.2
> ui tool show "Fit in Map"
> fitmap #10 inMap #9
Fit molecule 5n4w (#10) to map run_class001.mrc (#9) using 7719 atoms
average map value = 0.04377, steps = 200
shifted from previous position = 23.4
rotated from previous position = 34.8 degrees
atoms outside contour = 5857, contour level = 0.061429
Position of 5n4w (#10) relative to run_class001.mrc (#9) coordinates:
Matrix rotation and translation
0.48211678 -0.02360497 0.87578891 222.37359187
-0.82792709 -0.33920712 0.44662654 233.07799226
0.28653123 -0.94041551 -0.18308064 222.99548022
Axis -0.81197692 0.34495251 -0.47085162
Axis point 0.00000000 207.50734557 -58.10861118
Rotation angle (degrees) 121.33798628
Shift along axis -205.15916825
> view matrix models
> #10,0.48506,-0.021109,0.87423,221.64,-0.82538,-0.34133,0.44972,232.18,0.2889,-0.93971,-0.18299,222.33
> view matrix models
> #10,0.70101,-0.21152,0.68106,214.93,-0.70743,-0.085524,0.70159,217.91,-0.090156,-0.97362,-0.20959,244.96
> fitmap #10 inMap #9
Fit molecule 5n4w (#10) to map run_class001.mrc (#9) using 7719 atoms
average map value = 0.05398, steps = 116
shifted from previous position = 10.4
rotated from previous position = 17.3 degrees
atoms outside contour = 4718, contour level = 0.061429
Position of 5n4w (#10) relative to run_class001.mrc (#9) coordinates:
Matrix rotation and translation
0.68498024 0.04726472 0.72702690 208.49566223
-0.72845643 0.06138985 0.68233607 211.33126595
-0.01238165 -0.99699415 0.07648112 242.38189117
Axis -0.84297838 0.37116311 -0.38939105
Axis point 0.00000000 242.60128271 -80.27616259
Rotation angle (degrees) 95.08159838
Shift along axis -191.70030544
> open /Volumes/lab-
> enchevr/home/users/enchevr/cluster_processing/gJC0022/CRL2_VHL_dimer_9A.mrc
Opened CRL2_VHL_dimer_9A.mrc as #11, grid size 256,256,256, pixel 1.61, shown
at level 0.0168, step 1, values float32
> hide #!10 models
> volume #11 level 0.06174
> open /Volumes/lab-
> enchevr/home/users/enchevr/cluster_processing/gJC0022/CRL2_VHL_monomer_relion_refine39.mrc
Opened CRL2_VHL_monomer_relion_refine39.mrc as #12, grid size 256,256,256,
pixel 1.61, shown at level 0.00361, step 1, values float32
> open /Volumes/lab-
> enchevr/home/users/enchevr/cluster_processing/gJC0022/Class3D/3d_re_ext_noOG_mono/run_it025_class001.mrc
Opened run_it025_class001.mrc as #13, grid size 256,256,256, pixel 1.61, shown
at level 0.0109, step 1, values float32
> volume #13 level 0.02639
> close #13
> open /Volumes/lab-
> enchevr/home/users/enchevr/cluster_processing/gJC0022/Class3D/job092/run_it021_class001.mrc
Opened run_it021_class001.mrc as #13, grid size 128,128,128, pixel 1.61, shown
at level 0.0361, step 1, values float32
> view orient
> close #12
> close #13
> open /Volumes/lab-
> enchevr/home/users/enchevr/cluster_processing/gJC0022/Class3D/job092/run_it021_class002.mrc
Opened run_it021_class002.mrc as #12, grid size 128,128,128, pixel 1.61, shown
at level 0.0349, step 1, values float32
> close #11
> close #12
> open /Volumes/lab-
> enchevr/home/users/enchevr/cluster_processing/gJC0022/Class3D/job092/run_it021_class003.mrc
Opened run_it021_class003.mrc as #11, grid size 128,128,128, pixel 1.61, shown
at level 0.0474, step 1, values float32
> close #11
> open /Volumes/lab-
> enchevr/home/users/enchevr/cluster_processing/gJC0022/Class3D/job092/run_it021_class004.mrc
Opened run_it021_class004.mrc as #11, grid size 128,128,128, pixel 1.61, shown
at level 0.0482, step 1, values float32
> close #11
> open /Volumes/lab-
> enchevr/home/users/enchevr/cluster_processing/gJC0030/cryosparc_P3_J5133_002_volume_map.mrc
Opened cryosparc_P3_J5133_002_volume_map.mrc as #11, grid size 128,128,128,
pixel 3.18, shown at level 0.0254, step 1, values float32
> view orient
> volume #11 level 1.316
> close #11
> close #8
> close #9
> close #3
> open /Users/omallen/Library/CloudStorage/OneDrive-
> TheFrancisCrickInstitute/PhD/FinalDepositedMapsAndModels/Apo/cryosparc_P256_J1166_008_volume_map_sharp.mrc
Opened cryosparc_P256_J1166_008_volume_map_sharp.mrc as #3, grid size
440,440,440, pixel 0.65, shown at level 0.0436, step 2, values float32
> open /Users/omallen/Library/CloudStorage/OneDrive-
> TheFrancisCrickInstitute/PhD/FinalDepositedMapsAndModels/Apo/apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb
Chain information for
apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb #8
---
Chain | Description
A B C D | No description available
> view orient
> volume #3 step 1
> volume #3 level 0.1282
> color #8 #ff80ccff
> ui tool show "Color Actions"
> color plum
> undo
> color #8 #ff00ccff
> color #8 #990066ff
> color #8 #ff99ccff
> color #8 #cc6699ff
> select add #8
17098 atoms, 17328 bonds, 8 pseudobonds, 1158 residues, 2 models selected
> ui tool show "Color Actions"
> color sel plum
> color sel orchid
> color sel plum
> select clear
> select #8/A:95
14 atoms, 13 bonds, 1 residue, 1 model selected
> show sel cartoons
> show sel atoms
> view sel
> color sel byhetero
> volume #3 level -0.02149
> volume #3 level 0.01106
> volume #3 level 0.05012
> volume #3 color #b2b2b274
> delH
Unknown command: delH
> delete H
> volume #3 level 0.0371
> surface dust #3 size 6.5
> select #8/A
2181 atoms, 2239 bonds, 2 pseudobonds, 289 residues, 2 models selected
> select #8/A B C
Expected a keyword
> select #8/B
2181 atoms, 2239 bonds, 2 pseudobonds, 289 residues, 2 models selected
> hide sel cartoons
> select #8/C
2181 atoms, 2239 bonds, 2 pseudobonds, 289 residues, 2 models selected
> hide sel cartoons
> select #8/D
2181 atoms, 2239 bonds, 2 pseudobonds, 289 residues, 2 models selected
> hide sel cartoons
> select #8/A
2181 atoms, 2239 bonds, 2 pseudobonds, 289 residues, 2 models selected
> ui tool show "Surface Zone"
> surface zone #3 nearAtoms sel distance 3.9
> surface zone #3 nearAtoms sel distance 3.88
> surface zone #3 nearAtoms sel distance 31.83
> surface unzone #3
> select clear
> ui tool show "Side View"
> surface dust #3 size 6.5
> volume #3 color #b2b2b234
> select clear
> graphics silhouettes false
> graphics silhouettes true
> volume #3 level 0.0375
> volume #3 level 0.036
> volume #3 level 0.035
> volume #3 level 0.034
> volume #3 style mesh
> volume #3 style surface
> volume #3 color #999999
> volume #3 color #99999931
> save "/Users/omallen/OneDrive - The Francis Crick Institute/PhD/Paper
> work/Comms Biol/Revisions/Figures/Glyc_Zoomed In.png" width 2000 height 1174
> supersample 3
> save "/Users/omallen/OneDrive - The Francis Crick Institute/PhD/Paper
> work/Comms Biol/Revisions/Figures/Glyc_Zoomed In.cxs"
> view orient
> select add #8
8726 atoms, 8956 bonds, 8 pseudobonds, 1158 residues, 2 models selected
> hide sel atoms
> select #8/A:95
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> save "/Users/omallen/OneDrive - The Francis Crick Institute/PhD/Paper
> work/Comms Biol/Revisions/Figures/Glyc_Zoomed_out_onesub.cxs"
> save "/Users/omallen/OneDrive - The Francis Crick Institute/PhD/Paper
> work/Comms Biol/Revisions/Figures/Glyc_Zoomed_out_onesub.png" width 2000
> height 1283 supersample 3
> select add #8
8726 atoms, 8956 bonds, 8 pseudobonds, 1158 residues, 2 models selected
> show sel cartoons
> select #8/:95
Expected an objects specifier or a keyword
> select #8:95
32 atoms, 28 bonds, 4 residues, 1 model selected
> show sel atoms
> color sel byhetero
> select clear
> select add #8
8726 atoms, 8956 bonds, 8 pseudobonds, 1158 residues, 2 models selected
> show sel surfaces
> preset cartoons/nucleotides licorice/ovals
Using preset: Cartoons/Nucleotides / Licorice/Ovals
Changed 7716 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
> style sel sphere
Changed 8726 atom styles
> show sel cartoons
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 8724 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 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 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
> preset "initial styles" "original look"
Using preset: Initial Styles / Original Look
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> undo
> ui tool show "Color Actions"
> color sel plum
> select ions
16 atoms, 16 residues, 5 models selected
> color (#!8 & sel) purple
> select clear
> select #8:95
32 atoms, 28 bonds, 4 residues, 1 model selected
> show sel atoms
> color (#!8 & sel) byhetero
> select clear
> volume #3 level 0.032
> volume #3 level 0.03
> volume #3 level 0.027
> save "/Users/omallen/OneDrive - The Francis Crick Institute/PhD/Paper
> work/Comms Biol/Revisions/Figures/Glyc_Zoomed_out_foursub.png" width 2000
> height 1283 supersample 3
> save "/Users/omallen/OneDrive - The Francis Crick Institute/PhD/Paper
> work/Comms Biol/Revisions/Figures/Glyc_Zoomed_out_foursub.cxs"
> select add #8
8726 atoms, 8956 bonds, 8 pseudobonds, 1158 residues, 2 models selected
> hide sel cartoons
> hide sel atoms
> select #8/A
2181 atoms, 2239 bonds, 2 pseudobonds, 289 residues, 2 models selected
> show sel cartoons
> select #8/A:95
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> undo
> select clear
> save "/Users/omallen/OneDrive - The Francis Crick Institute/PhD/Paper
> work/Comms Biol/Revisions/Figures/Glyc_Zoomed_out_onesub_slab.cxs"
> save "/Users/omallen/OneDrive - The Francis Crick Institute/PhD/Paper
> work/Comms Biol/Revisions/Figures/Glyc_Zoomed_out_onesub_slab.png" width
> 2000 height 1283 supersample 3
> select #8/A:95
8 atoms, 7 bonds, 1 residue, 1 model selected
> view sel
> view matrix models #3,1,0,0,0.015224,0,1,0,0.059115,0,0,1,0.35771
> undo
> ui mousemode right zoom
> select clear
> save "/Users/omallen/OneDrive - The Francis Crick Institute/PhD/Paper
> work/Comms Biol/Revisions/Figures/Glyc_Zoomed In2.png" width 2000 height
> 1283 supersample 3
> save "/Users/omallen/OneDrive - The Francis Crick Institute/PhD/Paper
> work/Comms Biol/Revisions/Figures/Glyc_Zoomed In3.png" width 2000 height
> 1283 supersample 3
> volume #3 level 0.1783
> volume #3 level 0.1027
> volume #3 level 0.05942
> volume #3 level -0.01623
> volume #3 level 0.0324
> hide #!8 models
> show #!8 models
> hide #!8 models
> open /Users/omallen/Downloads/cryosparc_P313_J756_003_volume_map.mrc
Opened cryosparc_P313_J756_003_volume_map.mrc as #9, grid size 256,256,256,
pixel 1.58, shown at level 0.144, step 1, values float32
> view orient
> open 6SJ7
6sj7 title:
Structure of the human DDB1-DDA1-DCAF15 E3 ubiquitin ligase bound to RBM39 and
Indisulam [more info...]
Chain information for 6sj7 #11
---
Chain | Description | UniProt
A | DDB1- and CUL4-associated factor 15 | DCA15_HUMAN 1-600
B | DNA damage-binding protein 1 | DDB1_HUMAN 1-1140
C | RNA binding protein 39 | Q7Z3L0_HUMAN 248-328
D | DET1- and DDB1-associated protein 1 | DDA1_HUMAN 2-102
Non-standard residues in 6sj7 #11
---
EF6 — N~1~-(3-chloro-1H-indol-7-yl)benzene-1,4-disulfonamide (Indisulam)
> ui mousemode right "move picked models"
> hide #!11.1 models
> view matrix models
> #11,0.71475,0.38388,-0.58461,174.52,-0.6763,0.59236,-0.43787,294.97,0.17821,0.70834,0.683,-5.6429
> view matrix models
> #11,-0.88799,-0.11778,0.44453,291.14,0.18333,0.79585,0.57708,44.891,-0.42175,0.59393,-0.68511,266.26
> ui tool show "Fit in Map"
> fitmap #11 inMap #9
Fit molecule 6sj7 (#11) to map cryosparc_P313_J756_003_volume_map.mrc (#9)
using 10007 atoms
average map value = 0.7233, steps = 296
shifted from previous position = 30.5
rotated from previous position = 24.8 degrees
atoms outside contour = 854, contour level = 0.1437
Position of 6sj7 (#11) relative to cryosparc_P313_J756_003_volume_map.mrc (#9)
coordinates:
Matrix rotation and translation
-0.96673591 0.19683731 0.16333023 269.52054256
0.25460354 0.80164449 0.54087259 39.00515569
-0.02446887 0.56446540 -0.82509399 250.87525081
Axis 0.11921943 0.94898804 0.29190484
Axis point 137.77969920 0.00000000 112.83953566
Rotation angle (degrees) 174.32146085
Shift along axis 142.37921000
> molmap #11 onGrid #9
Missing or invalid "resolution" argument: Expected a number
> molmap #11 16 onGrid #9
Opened 6sj7 map 16 as #12, grid size 256,256,256, pixel 1.58, shown at level
0.0525, step 1, values float32
> fitmap #12 inMap #9
Fit map 6sj7 map 16 in map cryosparc_P313_J756_003_volume_map.mrc using 76622
points
correlation = 0.8649, correlation about mean = 0.4178, overlap = 1.131e+04
steps = 84, shift = 0.687, angle = 1.38 degrees
Position of 6sj7 map 16 (#12) relative to
cryosparc_P313_J756_003_volume_map.mrc (#9) coordinates:
Matrix rotation and translation
0.99988241 -0.00855465 0.01272709 -0.89910725
0.00831586 0.99979059 0.01869838 -6.06949391
-0.01288438 -0.01859035 0.99974416 7.37574193
Axis -0.77233455 0.53047192 0.34942652
Axis point -0.00000000 391.22616132 330.45659224
Rotation angle (degrees) 1.38327003
Shift along axis 0.05199530
> volume #9 level 0.3458
> volume #12 level 0.001839
> volume #12 level 0.01833
> view matrix models
> #12,0.45373,-0.8057,-0.38076,376.39,0.80977,0.55114,-0.20129,-17.403,0.37203,-0.21699,0.9025,-4.0655
> view matrix models
> #12,0.9108,-0.34067,-0.23321,145.67,0.31558,0.9387,-0.13873,-20.497,0.26617,0.05276,0.96248,-57.694
> ui tool show "Segment Map"
Segmenting cryosparc_P313_J756_003_volume_map.mrc, density threshold 0.345814
Showing 14 region surfaces
78 watershed regions, grouped to 14 regions
Showing cryosparc_P313_J756_003_volume_map.seg - 14 regions, 14 surfaces
> select #13.1
1 model selected
> select add #13.9
2 models selected
> select add #13.14
3 models selected
> select add #13.13
4 models selected
> select add #13.6
5 models selected
> select add #13.4
6 models selected
> select subtract #13.4
5 models selected
> select add #13.4
6 models selected
> select add #13.12
7 models selected
Deleted 7 regions
> select clear
> select #13.7
1 model selected
Saving 7 regions to mrc file...
Opened map_7_regions.mrc as #14, grid size 58,73,68, pixel 1.58, shown at step
1, values float32
Wrote map_7_regions.mrc
> volume resample #14 onGrid #9
Opened map_7_regions.mrc resampled as #15, grid size 256,256,256, pixel 1.58,
shown at step 1, values float32
> save /Volumes/lab-
> enchevr/home/users/omallen/EM_datasets/gNOM081/map_7_regions_resampled.mrc
> models #15
> volume #15 level 1.292
> hide #!13 models
> volume #15 level 0.4511
> hide #!9 models
> volume #15 level 0.3517
> volume #15 level 0.3041
> show #!9 models
> open /Users/omallen/Downloads/cryosparc_P313_J759_mask.mrc
Opened cryosparc_P313_J759_mask.mrc as #16, grid size 256,256,256, pixel 1.58,
shown at level 1, step 1, values float32
> volume #16 level 1
> volume #16 level 0.9588
> volume #16 level 1
> open /Volumes/lab-
> enchevr/home/users/omallen/EM_datasets/gNOM081/Refine3D/job062/run_class001.mrc
Opened run_class001.mrc as #17, grid size 256,256,256, pixel 1.58, shown at
level 0.0116, step 1, values float32
> hide #!9 models
> hide #!11 models
> volume #17 level 0.03334
> show #!11 models
> ui tool show "Fit in Map"
> fitmap #11 inMap #17
Fit molecule 6sj7 (#11) to map run_class001.mrc (#17) using 10007 atoms
average map value = 0.0313, steps = 240
shifted from previous position = 13.8
rotated from previous position = 60.5 degrees
atoms outside contour = 5698, contour level = 0.033338
Position of 6sj7 (#11) relative to run_class001.mrc (#17) coordinates:
Matrix rotation and translation
-0.64234097 -0.74479546 0.18077003 343.22633017
-0.34156107 0.48933352 0.80242679 103.36828308
-0.68610066 0.45368759 -0.56871210 300.11049324
Axis -0.34267907 0.85180689 0.39622730
Axis point 234.89367307 0.00000000 66.00875952
Rotation angle (degrees) 149.41325564
Shift along axis 89.34530485
> volume #17 color #b2ffb266
> select #11/C
619 atoms, 630 bonds, 79 residues, 1 model selected
> color sel red
> select clear
> volume #17 level 0.002008
> volume #17 level 0.02459
> view matrix models
> #11,-0.64234,-0.7448,0.18077,342.43,-0.34156,0.48933,0.80243,100.04,-0.6861,0.45369,-0.56871,294.55
> undo
> view matrix models
> #11,0.67268,0.71217,0.2008,9.4553,0.52746,-0.65184,0.54488,180.42,0.51893,-0.26061,-0.81412,278.95
> fitmap #11 inMap #17
Fit molecule 6sj7 (#11) to map run_class001.mrc (#17) using 10007 atoms
average map value = 0.03151, steps = 384
shifted from previous position = 9.27
rotated from previous position = 39 degrees
atoms outside contour = 3240, contour level = 0.024589
Position of 6sj7 (#11) relative to run_class001.mrc (#17) coordinates:
Matrix rotation and translation
0.08979009 0.91122303 0.40200788 30.74415073
0.78350020 -0.31381773 0.53632627 101.75575288
0.61487005 0.26681647 -0.74212115 194.42736612
Axis -0.73553430 -0.58093407 -0.34857552
Axis point 0.00000000 47.67444457 88.99258705
Rotation angle (degrees) 169.44339584
Shift along axis -149.49938255
> volume #17 level 0.04068
> open /Volumes/lab-
> enchevr/home/users/omallen/EM_datasets/gNOM081/MaskCreate/job063/mask.mrc
Opened mask.mrc as #18, grid size 256,256,256, pixel 1.58, shown at level
0.928, step 1, values float32
> volume #18 level 1
> volume #17 level 0.01443
> volume #17 level 0.02459
> hide #!11 models
> define axis
Axis 'root #/axis' centered at [321.32502677 156.20559228 181.8597633 ] with
direction [0.99374045 0.11090819 0.01339028], radius 72.5463, and length
437.392
> hide #19 models
> close #19
> open /Users/omallen/Library/CloudStorage/OneDrive-
> TheFrancisCrickInstitute/PhD/FinalDepositedMapsAndModels/Apo/apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb
Chain information for
apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb #19
---
Chain | Description
A B C D | No description available
> color #19 plum
> open /Users/omallen/Library/CloudStorage/OneDrive-
> TheFrancisCrickInstitute/PhD/FinalDepositedMapsAndModels/PIP/PIP.pdb
Chain information for PIP.pdb #20
---
Chain | Description
A B C D | No description available
> color #20 tan
> define axis #19/A:130-145 helix 1
Expected a keyword
> define axis #19/A:130-145 name helix 1
Expected a keyword
> define axis #19/A:130-145 name helix1
Axis 'apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb
#19/helix1' centered at [126.91378569 147.26547845 163.11951946] with
direction [ 0.33965673 0.2027149 -0.91844432], radius 3.42558, and length
27.9339
> define axis #19/A:146-165 name helix2
Axis 'apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb
#19/helix2' centered at [140.42476112 150.98442922 138.96805527] with
direction [ 0.48456634 0.1824387 -0.85551831], radius 3.69231, and length
35.5654
> define axis #20/B:146-165 name helix2
Axis 'PIP.pdb #20/helix2' centered at [135.32000615 138.29886849 126.33923009]
with direction [ 0.20806586 -0.46569925 0.86013534], radius 3.85312, and
length 35.4863
> define axis #20/B:130-145 name helix1
Axis 'PIP.pdb #20/helix1' centered at [128.30159345 150.84037494 102.23041697]
with direction [-0.0989714 0.3819789 -0.91885624], radius 3.40584, and length
28.3154
> view orient
> dssp
Computing secondary structure
> view matrix models
> #20,0.49764,0.82476,0.26857,-81.95,0.86684,-0.48384,-0.12034,103.34,0.030698,0.29269,-0.95571,205.51
> ui tool show Matchmaker
> matchmaker #!20 to #19
Computing secondary structure
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
apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb,
chain B (#19) with PIP.pdb, chain B (#20), sequence alignment score = 1373.9
RMSD between 266 pruned atom pairs is 0.668 angstroms; (across all 289 pairs:
1.165)
> view matrix models
> #20.2,1,-1.0949e-15,6.9389e-18,1.2194,2.9406e-16,1,-5.5511e-17,0.0046535,-1.5613e-17,-1.7347e-18,1,0.51765
> undo
> view matrix models
> #20,0.91434,-0.40301,0.039457,66.558,-0.40269,-0.91519,-0.016148,334.98,0.042618,-0.001124,-0.99909,258.88
> matchmaker #!20 to #19
Computing secondary structure
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
apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb,
chain B (#19) with PIP.pdb, chain B (#20), sequence alignment score = 1373.9
RMSD between 266 pruned atom pairs is 0.668 angstroms; (across all 289 pairs:
1.165)
> preset cartoons/nucleotides licorice/ovals
Using preset: Cartoons/Nucleotides / Licorice/Ovals
Changed 7796 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
> select #19.2
1 model selected
> select #19.3
1 model selected
> select #19.2
1 model selected
> close #19.2
> select #19.3
1 model selected
> ~select #19.3
Nothing selected
> select #19.3
1 model selected
> close #19.3
> define axis #19/B:130-145 name helix1
Axis 'apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb
#19/helix1' centered at [138.72323696 126.92555733 163.04858197] with
direction [-0.2043703 0.34036144 -0.91781636], radius 3.42999, and length
27.7661
> define axis #19/B:146-165 name helix2
Axis 'apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb
#19/helix2' centered at [134.99428095 140.43821806 138.84666192] with
direction [-0.18361269 0.48631942 -0.8542715 ], radius 3.69519, and length
35.3353
> select add #19
17098 atoms, 17328 bonds, 8 pseudobonds, 1158 residues, 4 models selected
> select add #20
35123 atoms, 35599 bonds, 12 pseudobonds, 2358 residues, 8 models selected
> hide sel cartoons
> hide sel atoms
> select clear
> angle helix1 helix2
Missing or invalid "objects" argument: invalid objects specifier
Choose exactly one axis or plane in table
Either three or four atoms must be selected!
> select #19.2
1 model selected
> select #19.3
1 model selected
> select #20.2
1 model selected
> select #20.3
1 model selected
> close #19.2-3#20.2-3
> select add #19
17098 atoms, 17328 bonds, 8 pseudobonds, 1158 residues, 2 models selected
> select add #20
35123 atoms, 35599 bonds, 12 pseudobonds, 2358 residues, 4 models selected
> show sel cartoons
> hide sel cartoons
> select #19/A:130-165
538 atoms, 541 bonds, 36 residues, 1 model selected
> show sel cartoons
> hide sel cartoons
> select #19/A:130-162
503 atoms, 505 bonds, 33 residues, 1 model selected
> show sel cartoons
> hide sel cartoons
> select #19/A:135-162
446 atoms, 447 bonds, 28 residues, 1 model selected
> show sel cartoons
> select #20/A:135-162
446 atoms, 447 bonds, 28 residues, 1 model selected
> show sel cartoons
> hide sel cartoons
> select #20/B:135-162
446 atoms, 447 bonds, 28 residues, 1 model selected
> show sel cartoons
> hide sel cartoons
> select #20/C:135-162
446 atoms, 447 bonds, 28 residues, 1 model selected
> show sel cartoons
> hide sel cartoons
> select #20/D:135-162
446 atoms, 447 bonds, 28 residues, 1 model selected
> show sel cartoons
> select clear
> lighting flat
> lighting full
> lighting soft
> select #19/A:160
19 atoms, 18 bonds, 1 residue, 1 model selected
> select add #20/D:160
38 atoms, 36 bonds, 2 residues, 2 models selected
> show sel cartoons
> show sel atoms
> hide sel atoms
> show sel atoms
> color sel byhetero
> hide sel atoms
> select #20/D:161
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #20/D:160
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #20/D:160 @CA
1 atom, 1 residue, 1 model selected
> style sel sphere
Changed 1 atom style
> style sel ball
Changed 1 atom style
> show sel surfaces
> show sel atoms
> hide sel surfaces
> select #20/D:160 @CA and sel #19/A:160 @CA
Expected a keyword
> select #20/D:160 @CA, sel #19/A:160 @CA
2 atoms, 2 residues, 2 models selected
> ui tool show Distances
> distance #20/D:160@CA #19/A:160@CA
Distance between PIP.pdb #20/D ILE 160 CA and
apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb #19/A
ILE 160 CA: 3.274Å
> select #20/D:161 @CA, sel #19/A:161 @CA
2 atoms, 2 residues, 2 models selected
> distance #19/A:161@CA #20/D:161@CA
Distance between
apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb #19/A
ALA 161 CA and PIP.pdb #20/D ALA 161 CA: 3.956Å
> select #20/D:162 @CA, sel #19/A:162 @CA
2 atoms, 2 residues, 2 models selected
> distance #19/A:162@CA #20/D:162@CA
Distance between
apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb #19/A
ARG 162 CA and PIP.pdb #20/D ARG 162 CA: 2.964Å
> select #20/D:159 @CA, sel #19/A:159 @CA
2 atoms, 2 residues, 2 models selected
> distance #19/A:159@CA #20/D:159@CA
Distance between
apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb #19/A
LYS 159 CA and PIP.pdb #20/D LYS 159 CA: 1.843Å
> ~distance #19/A:162@CA #20/D:162@CA
> ~distance #19/A:159@CA #20/D:159@CA
> distance style color black
> select clear
> select #20/D:153 @CA, sel #19/A:153 @CA
2 atoms, 2 residues, 2 models selected
> distance #19/A:153@CA #20/D:153@CA
Distance between
apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb #19/A
THR 153 CA and PIP.pdb #20/D THR 153 CA: 0.730Å
> show sel atoms
> select up
28 atoms, 26 bonds, 2 residues, 3 models selected
> show sel atoms
> hide sel atoms
> select #20/D:157 @CA, sel #19/A:157 @CA
2 atoms, 2 residues, 2 models selected
> distance #19/A:157@CA #20/D:157@CA
Distance between
apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb #19/A
VAL 157 CA and PIP.pdb #20/D VAL 157 CA: 1.298Å
> ~distance #19/A:157@CA #20/D:157@CA
> ~distance #19/A:153@CA #20/D:153@CA
> select clear
> lighting simple
> lighting soft
> lighting full
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting full
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> SilhouetteWidth 1
Unknown command: SilhouetteWidth 1
> silhouetteWidth 1
Unknown command: silhouetteWidth 1
> set silhouetteWidth 1
> color #19 orchid
> color #19 plum
> distance style decimalPlaces 2
> distance style decimalPlaces 1
> distance style dashes 10
> distance style dashes 11
> distance style dashes 10
> distance style dashes 9
> distance style dashes 8
> distance style dashes 7
> distance style dashes 8
> lighting flat
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting soft
> lighting simple
> lighting soft
> ui tool show "Color Actions"
> color plum
> undo
> color orchid
> undo
> hide #21.1 models
> ui tool show "Side View"
> save "/Users/omallen/Library/CloudStorage/OneDrive-
> TheFrancisCrickInstitute/PhD/Paper work/Comms
> Biol/Revisions/Tm2_distance.png" width 2000 height 1372 supersample 3
> distance style radius 0.05
> color #19 #d2a4d3ff
> color #19 #c197c2ff
> select add #19
17098 atoms, 17328 bonds, 8 pseudobonds, 1158 residues, 2 models selected
> ui tool show "Color Actions"
> color sel plum
> color sel violet
> color sel thistle
> color sel pale violet red
> color sel medium purple
> color sel purple
> color sel dark magenta
> color sel dark orchid
> color sel medium violet red
> color sel medium orchid
> color sel orchid
> color sel blue violet
> color sel hot pink
> color sel dark violet
> color sel deep pink
> color sel magenta
> color sel plum
> color sel hot pink
> color sel plum
> select clear
> distance style color #919191
> distance style color #797979
> distance style color #5e5e5e
> select clear
> lighting simple
> undo
> lighting soft
> lighting full
> lighting soft
> save "/Users/omallen/Library/CloudStorage/OneDrive-
> TheFrancisCrickInstitute/PhD/Paper work/Comms
> Biol/Revisions/Tm2_distance2.png" width 2000 height 1372 supersample 3
> define axis #19/A:15-162 name helix1
Axis 'apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb
#19/helix1' centered at [134.57020804 153.82308149 159.60914644] with
direction [ 0.2838401 0.08694491 -0.95492166], radius 7.16566, and length
66.8098
> tube helix_axis radius 0.2
Unknown command: tube helix_axis radius 0.2
> open /Volumes/lab-
> enchevr/home/users/omallen/EM_datasets/gNOM081/Class3D/job064/run_it025_class001.mrc
Opened run_it025_class001.mrc as #22, grid size 256,256,256, pixel 1.58, shown
at level 1.45e-05, step 1, values float32
> open /Volumes/lab-
> enchevr/home/users/omallen/EM_datasets/gNOM081/Class3D/job064/run_it025_class002.mrc
Opened run_it025_class002.mrc as #23, grid size 256,256,256, pixel 1.58, shown
at level 3.7e-06, step 1, values float32
> open /Volumes/lab-
> enchevr/home/users/omallen/EM_datasets/gNOM081/Class3D/job064/run_it025_class003.mrc
Opened run_it025_class003.mrc as #24, grid size 256,256,256, pixel 1.58, shown
at level 1.84e-05, step 1, values float32
> open /Volumes/lab-
> enchevr/home/users/omallen/EM_datasets/gNOM081/Class3D/job064/run_it025_class004.mrc
Opened run_it025_class004.mrc as #25, grid size 256,256,256, pixel 1.58, shown
at level 5.19e-06, step 1, values float32
> hide #!19 models
> hide #!20 models
> hide #!21 models
> tile
4 models tiled
> volume #25 level 0.03333
> volume #24 level 0.03377
> volume #23 level 0.03536
> volume #22 level 0.04029
> view matrix models
> #24,-0.13795,0.6547,0.74319,-39.079,-0.96379,-0.26161,0.051559,405.56,0.22819,-0.70917,0.66709,65.401
> view matrix models
> #24,-0.09808,0.9905,0.096334,11.045,-0.85286,-0.13354,0.50478,259.19,0.51285,-0.03265,0.85786,-189.06
> view matrix models
> #23,-0.41384,0.32522,-0.85028,317.07,0.51048,-0.69044,-0.51254,265.69,-0.75375,-0.64616,0.11972,543.58
> view matrix models
> #23,0.28316,-0.63997,-0.71433,372.69,0.62838,-0.43888,0.64228,-61.471,-0.72455,-0.63073,0.27786,483.08
> volume #25 level 0.005773
> volume #25 level 0.04583
> volume #24 level 0.03988
> hide #!22 models
> hide #!23 models
> hide #!24 models
> hide #!25 models
> show #!22 models
> hide #!22 models
> show #!19 models
> show #!20 models
> hide #!19 models
> show #!19 models
> select #19.2
1 model selected
> select #19.2
1 model selected
> hide #19.2 models
> ui tool show Matchmaker
> matchmaker #!20 to #19
Computing secondary structure
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
apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb,
chain B (#19) with PIP.pdb, chain B (#20), sequence alignment score = 1373.9
RMSD between 266 pruned atom pairs is 0.668 angstroms; (across all 289 pairs:
1.165)
> view orient
> matchmaker #!20 to #19
Computing secondary structure
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
apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb,
chain B (#19) with PIP.pdb, chain B (#20), sequence alignment score = 1373.9
RMSD between 266 pruned atom pairs is 0.668 angstroms; (across all 289 pairs:
1.165)
> ~tile
> matchmaker #!20 to #19
Computing secondary structure
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
apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb,
chain B (#19) with PIP.pdb, chain B (#20), sequence alignment score = 1373.9
RMSD between 266 pruned atom pairs is 0.668 angstroms; (across all 289 pairs:
1.165)
> hide #19.1 models
> color #19 #cf88baff
> show #!21 models
> view orient
> lighting soft
> save "/Users/omallen/Library/CloudStorage/OneDrive-
> TheFrancisCrickInstitute/PhD/Paper work/Comms
> Biol/Revisions/Tm2_distance3_colourfixed.png" width 2000 height 1372
> supersample 3
> show #21.1 models
> color #21 #393939ff models
> save "/Users/omallen/Library/CloudStorage/OneDrive-
> TheFrancisCrickInstitute/PhD/Paper work/Comms
> Biol/Revisions/Tm2_distance3_colourfixed_withlabels.png" width 2000 height
> 1372 supersample 3
> show #19.2 models
> surface style #19 dot
> cofr sel
> close #19.2
> hide #!19 models
> hide #!20 models
> show #!4 models
> hide #!4 models
> show #!5 models
> show #!6 models
> view orient
> color #5 #008f00ff
> color #5 #009051ff
> color #5 #4f8f00ff
> color #5 #008f00ff
> color #6 #00fa92ff
> color #6 #99ff99ff
> color #5 #336633ff
> ui tool show Matchmaker
> matchmaker #!6 to #5
Computing secondary structure
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 Kir2.2_docked_3SPI, chain A (#5) with Kir2.2_Extended , chain A
(#6), sequence alignment score = 1610.2
RMSD between 172 pruned atom pairs is 0.454 angstroms; (across all 321 pairs:
10.379)
Drag select of 155 atoms, 157 bonds, 1014 residues
> matchmaker #!6 & sel to #5 & sel
Computing secondary structure
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 Kir2.2_docked_3SPI, chain C (#5) with Kir2.2_Extended , chain C
(#6), sequence alignment score = 588.3
RMSD between 110 pruned atom pairs is 0.613 angstroms; (across all 125 pairs:
5.614)
> select clear
> select add #5
10812 atoms, 11037 bonds, 8 pseudobonds, 1348 residues, 2 models selected
> select add #6
21008 atoms, 21438 bonds, 18 pseudobonds, 2652 residues, 10 models selected
> hide sel cartoons
> hide sel atoms
> select #5/A:130-160
243 atoms, 249 bonds, 31 residues, 1 model selected
> show sel cartoons
> hide sel cartoons
> select #5/A:150-180
225 atoms, 227 bonds, 31 residues, 1 model selected
> show sel cartoons
> hide sel cartoons
> select #5/A:156-186
227 atoms, 229 bonds, 31 residues, 1 model selected
> show sel cartoons
> select #6/A:156-186
227 atoms, 229 bonds, 31 residues, 1 model selected
> show sel cartoons
> select clear
> matchmaker #!6 & sel to #5 & sel
No 'to' model specified
Drag select of 62 residues
> matchmaker #!6 & sel to #5 & sel
Computing secondary structure
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 Kir2.2_docked_3SPI, chain A (#5) with Kir2.2_Extended , chain A
(#6), sequence alignment score = 148.7
RMSD between 31 pruned atom pairs is 0.597 angstroms; (across all 31 pairs:
0.597)
> undo
> redo
> matchmaker #!6 to #5
Computing secondary structure
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 Kir2.2_docked_3SPI, chain A (#5) with Kir2.2_Extended , chain A
(#6), sequence alignment score = 1610.2
RMSD between 172 pruned atom pairs is 0.454 angstroms; (across all 321 pairs:
10.379)
> select add #5
11039 atoms, 11266 bonds, 8 pseudobonds, 1379 residues, 4 models selected
> select add #6
21008 atoms, 21438 bonds, 18 pseudobonds, 2652 residues, 11 models selected
> show sel cartoons
Drag select of 963 residues
> matchmaker #!6 & sel to #5 & sel
Computing secondary structure
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 Kir2.2_docked_3SPI, chain A (#5) with Kir2.2_Extended , chain A
(#6), sequence alignment score = 568.5
RMSD between 110 pruned atom pairs is 0.613 angstroms; (across all 117 pairs:
0.945)
> matchmaker #!6 & sel to #5 & sel
Computing secondary structure
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 Kir2.2_docked_3SPI, chain A (#5) with Kir2.2_Extended , chain A
(#6), sequence alignment score = 568.5
RMSD between 110 pruned atom pairs is 0.613 angstroms; (across all 117 pairs:
0.945)
> select add #5
14503 atoms, 11037 bonds, 8 pseudobonds, 1831 residues, 11 models selected
> select add #6
21008 atoms, 21438 bonds, 18 pseudobonds, 2652 residues, 14 models selected
> hide sel cartoons
> select #5/A:156-186
227 atoms, 229 bonds, 31 residues, 1 model selected
> show sel cartoons
> select #6/A:156-186
227 atoms, 229 bonds, 31 residues, 1 model selected
> show sel cartoons
> select add #5
11039 atoms, 11266 bonds, 8 pseudobonds, 1379 residues, 4 models selected
> select subtract #5
227 atoms, 229 bonds, 31 residues, 6 models selected
> select add #5
11039 atoms, 11266 bonds, 8 pseudobonds, 1379 residues, 4 models selected
> select add #6
21008 atoms, 21438 bonds, 18 pseudobonds, 2652 residues, 11 models selected
> hide sel cartoons
> select #6/B:156-186
227 atoms, 229 bonds, 31 residues, 1 model selected
> show sel cartoons
> select #5/B:156-186
227 atoms, 229 bonds, 31 residues, 1 model selected
> show sel cartoons
> select add #6
10423 atoms, 10630 bonds, 10 pseudobonds, 1335 residues, 6 models selected
> select add #5
21008 atoms, 21438 bonds, 18 pseudobonds, 2652 residues, 11 models selected
> show sel cartoons
> select ions
22 atoms, 22 residues, 7 models selected
> show #!5-6 atoms
> hide #!5-6 atoms
> select ::name="K"
91 atoms, 91 residues, 8 models selected
> show sel & #!5-6 atoms
> hide sel & #!5-6 atoms
Drag select of 497 residues
> ui tool show Matchmaker
> matchmaker #!6 & sel to #5 & sel
Computing secondary structure
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 Kir2.2_docked_3SPI, chain C (#5) with Kir2.2_Extended , chain C
(#6), sequence alignment score = 353
RMSD between 69 pruned atom pairs is 0.301 angstroms; (across all 69 pairs:
0.301)
> select add #5
12756 atoms, 11037 bonds, 8 pseudobonds, 1598 residues, 11 models selected
> select add #6
21008 atoms, 21438 bonds, 18 pseudobonds, 2652 residues, 14 models selected
> hide sel cartoons
> select #5/A:156-186
227 atoms, 229 bonds, 31 residues, 1 model selected
> show sel cartoons
> select up
2659 atoms, 2720 bonds, 332 residues, 2 models selected
> select #6/A:156-186
227 atoms, 229 bonds, 31 residues, 1 model selected
> show sel cartoons
> view orient
> select clear
> select #5/A:185 @CA, sel #6/A:185 @CA
2 atoms, 2 residues, 2 models selected
> ui tool show Distances
> distance #5/A:185@CA #6/A:185@CA
Distance between Kir2.2_docked_3SPI #5/A ALA 185 CA and Kir2.2_Extended #6/A
ALA 185 CA: 2.8Å
> distance style color #666666
> distance style color #333333
> select #5/A:184 @CA, sel #6/A:184 @CA
2 atoms, 2 residues, 2 models selected
> distance #5/A:184@CA #6/A:184@CA
Distance between Kir2.2_docked_3SPI #5/A MET 184 CA and Kir2.2_Extended #6/A
MET 184 CA: 2.7Å
> distance style color #666666
> distance style color #333333
> distance style color black
> select clear
> distance style color white
> distance style color #cccccc
> distance style color #999999
> distance style color white
> distance style color black
> distance style color #666666
> hide #21.1 models
> save "/Users/omallen/Library/CloudStorage/OneDrive-
> TheFrancisCrickInstitute/PhD/Paper work/Comms
> Biol/Revisions/Figures/Kir2_TM2_distances.png" width 2000 height 1372
> supersample 3
> show #21.1 models
> hide #!21 models
> hide #21.1 models
> select add #5
10812 atoms, 11037 bonds, 8 pseudobonds, 1348 residues, 2 models selected
> select add #6
21008 atoms, 21438 bonds, 18 pseudobonds, 2652 residues, 10 models selected
> show sel cartoons
> view orient
> hide #!5 models
> select clear
> select #5/A:372 @CA, sel #5/A:118 @CA
2 atoms, 2 residues, 1 model selected
> select #6/A:372 @CA, sel #6/A:118 @CA
2 atoms, 2 residues, 1 model selected
> distance #6/A:118@CA #6/A:372@CA
Distance between Kir2.2_Extended #6/A ASP 118 CA and SER 372 CA: 127.0Å
> show #!21 models
> select #6/A:372 @CA, sel #6/B:118 @CA
2 atoms, 2 residues, 1 model selected
> distance #6/A:372@CA #6/B:118@CA
Distance between Kir2.2_Extended #6/A SER 372 CA and /B ASP 118 CA: 122.5Å
> hide #!21 models
> show #!5 models
> hide #!6 models
> select #5/A:372 @CA, sel #5/B:118 @CA
2 atoms, 2 residues, 1 model selected
> distance #5/A:372@CA #5/B:118@CA
Distance between Kir2.2_docked_3SPI #5/A SER 372 CA and /B ASP 118 CA: 116.6Å
> show #!21 models
> hide #!21 models
> show #!6 models
Drag select of 1599 residues
> matchmaker #!6 & sel to #5 & sel
Computing secondary structure
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 Kir2.2_docked_3SPI, chain B (#5) with Kir2.2_Extended , chain A
(#6), sequence alignment score = 943.3
RMSD between 177 pruned atom pairs is 0.492 angstroms; (across all 197 pairs:
12.111)
> hide #!6 models
> hide #!5 models
> show #!1 models
> show #1.1 models
> hide #1.1 models
> show #!2 models
> show #!4 models
> show #!7 models
> view orient
> hide #!7 models
> hide #!4 models
> matchmaker #!2 & sel to #1 & sel
No 'to' model specified
> matchmaker #!2 to #1
Computing secondary structure
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 Kir3.2_docked, chain A (#1) with Kir3.1_extended, chain C (#2),
sequence alignment score = 1628
RMSD between 170 pruned atom pairs is 0.796 angstroms; (across all 310 pairs:
6.565)
Drag select of 90 atoms, 946 residues, 85 bonds
> matchmaker #!2 & sel to #1 & sel
Computing secondary structure
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 Kir3.2_docked, chain C (#1) with Kir3.1_extended, chain C (#2),
sequence alignment score = 585.1
RMSD between 80 pruned atom pairs is 1.085 angstroms; (across all 119 pairs:
2.722)
Drag select of 3 atoms, 590 residues
> matchmaker #!2 & sel to #1 & sel
Computing secondary structure
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 Kir3.2_docked, chain A (#1) with Kir3.1_extended, chain B (#2),
sequence alignment score = 368.3
RMSD between 42 pruned atom pairs is 0.687 angstroms; (across all 74 pairs:
3.087)
> color #1 #000099ff
> color #1 #0000ccff
> color #1 #3333ccff
> color #1 #6666ccff
> color #1 #3333ccff
> color #1 #333399ff
> color #1 #6666ccff
> color #1 #3333ccff
> color #1 #6666ccff
> color #2 #3399ccff
> color #2 #3366ccff
> color #2 #6699ffff
> color #2 #3399ffff
> color #2 #3399ccff
> color #2 #6699ccff
> color #2 #99ccffff
> color #2 #009999ff
> color #2 #66ffffff
> color #2 #00ccccff
> color #2 #009999ff
> color #2 #66ccffff
> color #2 #33ccffff
> color #2 #00ccffff
> color #2 #00d4ffff
> color #2 #0099ccff
> color #1 #9999ffff
> color #1 #3333ccff
> color #1 #333399ff
> color #1 #3300ffff
> color #1 #3300ccff
> select clear
> select add #1
10403 atoms, 10644 bonds, 16 pseudobonds, 1315 residues, 2 models selected
> select add #2
19839 atoms, 20278 bonds, 24 pseudobonds, 2555 residues, 5 models selected
> hide sel cartoons
> hide sel atoms
> select #1/A:156-186
221 atoms, 223 bonds, 31 residues, 1 model selected
> show sel cartoons
> hide sel cartoons
> select #1/A:166-190
168 atoms, 168 bonds, 25 residues, 1 model selected
> show sel cartoons
> select #1/A:166-195
208 atoms, 209 bonds, 30 residues, 1 model selected
> show sel cartoons
> select #1/A:166-199
239 atoms, 241 bonds, 34 residues, 1 model selected
> show sel cartoons
> hide sel cartoons
> select #1/A:170-192
162 atoms, 162 bonds, 23 residues, 1 model selected
> show sel cartoons
> select #1/A:170-193
169 atoms, 169 bonds, 24 residues, 1 model selected
> show sel cartoons
> select #1/A:170-194
178 atoms, 178 bonds, 25 residues, 1 model selected
> show sel cartoons
> select #1/A:170-195
186 atoms, 186 bonds, 26 residues, 1 model selected
> show sel cartoons
> select #1/A:170-196
192 atoms, 192 bonds, 27 residues, 1 model selected
> show sel cartoons
> select #1/A:170-197
201 atoms, 201 bonds, 28 residues, 1 model selected
> show sel cartoons
> select #2/A:170-197
182 atoms, 182 bonds, 27 residues, 1 model selected
> show sel cartoons
> hide sel cartoons
> select #2/b:170-197
189 atoms, 189 bonds, 27 residues, 1 model selected
> show sel cartoons
> select clear
> view orient
> select #1/A:195 @CA, sel #2/B:195 @CA
2 atoms, 2 residues, 2 models selected
> distance #1/A:195@CA #2/B:195@CA
Distance between Kir3.2_docked #1/A ILE 195 CA and Kir3.1_extended #2/B ILE
195 CA: 3.4Å
> distance #1/A:195@CA #2/B:195@CA
Distance already exists; modify distance properties with 'distance style'
> show #!21 models
> close #22-25
> show #21.1 models
> distance style color black
> distance style color #333333
> distance style color #666666
> select #1/A:196 @CA, sel #2/B:196 @CA
2 atoms, 2 residues, 2 models selected
> distance #1/A:196@CA #2/B:196@CA
Distance between Kir3.2_docked #1/A SER 196 CA and Kir3.1_extended #2/B SER
196 CA: 3.5Å
> distance style color #333333
> distance style color #999999
> distance style color #666666
> hide #21.1 models
> select clear
> color #21 white models
> color #21 #ccccccff models
> save "/Users/omallen/Library/CloudStorage/OneDrive-
> TheFrancisCrickInstitute/PhD/Paper work/Comms
> Biol/Revisions/Figures/Kir3_TM2_distances.png" width 2000 height 1372
> supersample 3
> hide #!1 models
> hide #!2 models
> show #!4 models
> show #!7 models
> matchmaker #!7 & sel to #4 & sel
No 'to' model specified
> matchmaker #!7 to #4
Computing secondary structure
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 Kir3.2_docked_Xtal_3SYA, chain A (#4) with
Kir3.2_extended_Xtal_3SYO, chain A (#7), sequence alignment score = 1649.6
RMSD between 303 pruned atom pairs is 0.557 angstroms; (across all 309 pairs:
0.703)
> view orient
Drag select of 690 residues
> matchmaker #!7 & sel to #4 & sel
Computing secondary structure
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 Kir3.2_docked_Xtal_3SYA, chain B (#4) with
Kir3.2_extended_Xtal_3SYO, chain A (#7), sequence alignment score = 406.6
RMSD between 79 pruned atom pairs is 0.649 angstroms; (across all 79 pairs:
0.649)
> select clear
> hide #!4 models
> hide #!7 models
> show #21.1 models
> show #!1 models
> show #!2 models
> view orient
> select add #1
10403 atoms, 10644 bonds, 16 pseudobonds, 1315 residues, 2 models selected
> select add #2
19839 atoms, 20278 bonds, 24 pseudobonds, 2555 residues, 5 models selected
> show sel cartoons
> hide #!21 models
> hide #21.1 models
> tile
2 models tiled
> select #1 @L
Nothing selected
> select #1 @K
3 atoms, 3 residues, 1 model selected
> show sel atoms
> color sel purple
> select #2 @K
Nothing selected
> select ligand
599 atoms, 601 bonds, 17 residues, 5 models selected
> show sel & #!1 atoms
> color (#!1 & sel) gray
> color (#!1 & sel) byhetero
> select clear
> save "/Users/omallen/Library/CloudStorage/OneDrive-
> TheFrancisCrickInstitute/PhD/Paper work/Comms
> Biol/Revisions/Figures/Kir3Cryo_newcolours.png" width 2000 height 1372
> supersample 3
> select #1/A:381 @CA, sel #1/B:128 @CA
2 atoms, 2 residues, 1 model selected
> distance #1/A:381@CA #1/B:128@CA
Distance between Kir3.2_docked #1/A SER 381 CA and /B ASP 128 CA: 117.5Å
> show #!21 models
> show #21.1 models
> select #1/A:381 @CA, sel #1/C:128 @CA
2 atoms, 2 residues, 1 model selected
> distance #1/A:381@CA #1/C:128@CA
Distance between Kir3.2_docked #1/A SER 381 CA and /C ASP 128 CA: 110.6Å
> select #2/A:381 @CA, sel #2/C:128 @CA
2 atoms, 2 residues, 1 model selected
> distance #2/A:381@CA #2/C:128@CA
Distance between Kir3.1_extended #2/A SER 381 CA and /C ASP 128 CA: 120.5Å
> select #2/A:381 @CA, sel #2/B:128 @CA
2 atoms, 2 residues, 1 model selected
> distance #2/A:381@CA #2/B:128@CA
Distance between Kir3.1_extended #2/A SER 381 CA and /B ASP 128 CA: 117.8Å
> hide #!21 models
> hide #21.1 models
> matchmaker #!2 to #1
Computing secondary structure
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 Kir3.2_docked, chain A (#1) with Kir3.1_extended, chain C (#2),
sequence alignment score = 1628
RMSD between 170 pruned atom pairs is 0.796 angstroms; (across all 310 pairs:
6.565)
> view orient
Drag select of 3 atoms, 728 residues
> matchmaker #!2 to #1 & sel
Computing secondary structure
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 Kir3.2_docked, chain A (#1) with Kir3.1_extended, chain B (#2),
sequence alignment score = 435.8
RMSD between 55 pruned atom pairs is 0.771 angstroms; (across all 87 pairs:
2.917)
> select clear
> hide #!1 models
> hide #!2 models
> open /Volumes/lab-
> enchevr/home/users/omallen/EM_datasets/gNOM081/Refine3D/job068/run_class001.mrc
Opened run_class001.mrc as #22, grid size 256,256,256, pixel 1.58, shown at
level 0.0134, step 1, values float32
Cell requested for row 24 is out of bounds for table with 26 rows! Resizing
table model.
> volume #22 level 0.02948
> volume #22 level 0.02692
> volume #22 level 0.03127
> close #22
> close #18
> close #17
> close #16
> close #15
> close #14
> close #12
> close #9
> show #!8 models
> show #!20 models
> select add #20
18025 atoms, 18271 bonds, 4 pseudobonds, 1200 residues, 2 models selected
> select add #8
26751 atoms, 27227 bonds, 12 pseudobonds, 2358 residues, 5 models selected
> show sel cartoons
> tile
2 models tiled
> select clear
Drag select of 331 residues, 1 pseudobonds
> view matrix models
> #20,-0.16321,-0.21381,-0.96315,470.17,-0.75078,0.66027,-0.019353,155.36,0.64007,0.71995,-0.26828,-23.4
Drag select of 48 residues
> view matrix models
> #20,0.75528,-0.65366,0.047827,272.81,-0.14093,-0.23324,-0.96215,315.88,0.64007,0.71995,-0.26828,-23.4
> view matrix models
> #20,0.29123,-0.95519,0.052933,381.63,0.04883,-0.040417,-0.99799,265.81,0.95541,0.29323,0.034871,-46.716
> view matrix models
> #20,0.66256,-0.74856,0.02573,293.46,-0.0818,-0.10646,-0.99095,298.22,0.74452,0.65446,-0.13177,-46.643
> tile
2 models tiled
> view matrix models
> #20,0.24024,-0.97037,-0.025724,386.52,0.018723,0.031127,-0.99934,265.21,0.97053,0.2396,0.025646,-40.016
> view matrix models
> #8,0.38445,0.91981,0.078409,-52.614,0.033901,-0.098947,0.99452,15.975,0.92252,-0.37968,-0.069223,68.157
> view matrix models
> #8,-0.15124,0.98446,0.089229,12.157,-0.17678,-0.11575,0.97742,48.541,0.97256,0.13205,0.19154,-47.726
> view matrix models
> #20,-0.54084,-0.84105,0.011437,474.92,-0.034471,0.0085763,-0.99937,276.05,0.84042,-0.54089,-0.03363,97.873
> view matrix models
> #8,-0.46171,0.88703,-0.00085161,86.316,-0.05421,-0.027258,0.99816,16.795,0.88537,0.4609,0.060671,-64.432
> tile
2 models tiled
> select clear
> select ions
22 atoms, 22 residues, 7 models selected
> show sel & #!8,20 atoms
> color (#!8,20 & sel) purple
> select ligand
599 atoms, 601 bonds, 17 residues, 5 models selected
> show sel & #!20 atoms
> color (#!20 & sel) gray
> color (#!20 & sel) byhetero
> select clear
> save "/Users/omallen/Library/CloudStorage/OneDrive-
> TheFrancisCrickInstitute/PhD/Paper work/Comms
> Biol/Revisions/Figures/apo_Pip_tiled.png" width 2000 height 1429 supersample
> 3
> hide #20.1 models
> hide #8.1 models
> save "/Users/omallen/Library/CloudStorage/OneDrive-
> TheFrancisCrickInstitute/PhD/Paper work/Comms
> Biol/Revisions/Figures/apo_Pip_tiled.png" width 2000 height 1429 supersample
> 3
> open /Volumes/lab-
> enchevr/home/users/omallen/EM_datasets/gNOM081/Refine3D/job069/run_class001.mrc
Opened run_class001.mrc as #9, grid size 256,256,256, pixel 1.58, shown at
level 0.00186, step 1, values float32
> volume #9 level 0.03067
> hide #!20 models
> hide #!8 models
> hide #!9 models
> view orient
> show #!9 models
> show #!11 models
> ui tool show "Fit in Map"
> fitmap #11 inMap #9
Fit molecule 6sj7 (#11) to map run_class001.mrc (#9) using 10007 atoms
average map value = 0.03375, steps = 228
shifted from previous position = 32.3
rotated from previous position = 49.9 degrees
atoms outside contour = 4316, contour level = 0.030673
Position of 6sj7 (#11) relative to run_class001.mrc (#9) coordinates:
Matrix rotation and translation
0.99433780 -0.09061646 -0.05550682 101.79562929
-0.05910615 -0.90570343 0.41977110 293.48040104
-0.08831090 -0.41411347 -0.90593113 376.53075065
Axis -0.99851560 0.03928048 0.03773129
Axis point 0.00000000 190.30497819 157.71139516
Rotation angle (degrees) 155.31923086
Shift along axis -75.90948186
> volume #9 level 0.04591
> fitmap #11 inMap #9
Fit molecule 6sj7 (#11) to map run_class001.mrc (#9) using 10007 atoms
average map value = 0.03375, steps = 88
shifted from previous position = 3.96
rotated from previous position = 0.0427 degrees
atoms outside contour = 7849, contour level = 0.045909
Position of 6sj7 (#11) relative to run_class001.mrc (#9) coordinates:
Matrix rotation and translation
0.99428878 -0.09129715 -0.05526906 101.84986112
-0.05983739 -0.90571356 0.41964560 293.59742102
-0.08837040 -0.41394176 -0.90600380 376.55342324
Axis -0.99850279 0.03965004 0.03768370
Axis point 0.00000000 190.37015563 157.71751793
Rotation angle (degrees) 155.32827716
Shift along axis -75.86629249
> volume #9 level 0.01687
> open /Volumes/lab-
> enchevr/home/users/omallen/EM_datasets/gNOM081/Refine3D/job069/run_class001.mrc
Opened run_class001.mrc as #12, grid size 256,256,256, pixel 1.58, shown at
level 0.00186, step 1, values float32
> volume #12 level 0.03947
> volume #9 level 0.0521
> close #9
> fitmap #11 inMap #12
Fit molecule 6sj7 (#11) to map run_class001.mrc (#12) using 10007 atoms
average map value = 0.03418, steps = 224
shifted from previous position = 26.4
rotated from previous position = 54.5 degrees
atoms outside contour = 6577, contour level = 0.039471
Position of 6sj7 (#11) relative to run_class001.mrc (#12) coordinates:
Matrix rotation and translation
-0.46865470 0.85076609 -0.23782300 185.81509494
0.39283855 0.44184949 0.80650285 27.83733276
0.79122727 0.28454532 -0.54128856 143.19978766
Axis -0.42045772 -0.82894125 -0.36887899
Axis point 67.71969256 0.00000000 90.80998324
Rotation angle (degrees) 141.63261395
Shift along axis -154.02629851
> fitmap #11 inMap #12
Fit molecule 6sj7 (#11) to map run_class001.mrc (#12) using 10007 atoms
average map value = 0.03418, steps = 28
shifted from previous position = 0.0502
rotated from previous position = 0.0956 degrees
atoms outside contour = 6574, contour level = 0.039471
Position of 6sj7 (#11) relative to run_class001.mrc (#12) coordinates:
Matrix rotation and translation
-0.46791709 0.85105784 -0.23823117 185.75763912
0.39399654 0.44217314 0.80576026 27.78169444
0.79108803 0.28316674 -0.54221422 143.54115861
Axis -0.42091195 -0.82904350 -0.36813042
Axis point 67.60427484 0.00000000 90.97782049
Rotation angle (degrees) 141.62635577
Shift along axis -154.06171078
> volume #12 level 0.02424
> volume #12 color #ffb2ff5f
> fitmap #11 inMap #12
Fit molecule 6sj7 (#11) to map run_class001.mrc (#12) using 10007 atoms
average map value = 0.03418, steps = 56
shifted from previous position = 4.76
rotated from previous position = 0.0899 degrees
atoms outside contour = 2747, contour level = 0.024235
Position of 6sj7 (#11) relative to run_class001.mrc (#12) coordinates:
Matrix rotation and translation
-0.46862597 0.85077202 -0.23785840 185.81524204
0.39290483 0.44188825 0.80644932 27.83241111
0.79121137 0.28446738 -0.54135275 143.22098099
Axis -0.42047597 -0.82895418 -0.36882913
Axis point 67.71499591 0.00000000 90.82172599
Rotation angle (degrees) 141.63246184
Shift along axis -154.02670766
> volume #12 level 0.03328
> fitmap #11 inMap #12
Fit molecule 6sj7 (#11) to map run_class001.mrc (#12) using 10007 atoms
average map value = 0.03418, steps = 56
shifted from previous position = 3.87
rotated from previous position = 0.0178 degrees
atoms outside contour = 5053, contour level = 0.033282
Position of 6sj7 (#11) relative to run_class001.mrc (#12) coordinates:
Matrix rotation and translation
-0.46836291 0.85092116 -0.23784302 185.76367610
0.39304706 0.44175420 0.80645346 27.83085898
0.79129649 0.28422940 -0.54135335 143.24058560
Axis -0.42061606 -0.82890206 -0.36878653
Axis point 67.67736784 0.00000000 90.82243602
Rotation angle (degrees) 141.62653563
Shift along axis -154.02943948
> select ~sel & ##selected
Nothing selected
> ~tile
> fitmap #11 inMap #12
Fit molecule 6sj7 (#11) to map run_class001.mrc (#12) using 10007 atoms
average map value = 0.0003262, steps = 236
shifted from previous position = 47.3
rotated from previous position = 45.7 degrees
atoms outside contour = 10007, contour level = 0.033282
Position of 6sj7 (#11) relative to run_class001.mrc (#12) coordinates:
Matrix rotation and translation
0.70061388 -0.31864902 -0.63843793 186.55126673
0.36706448 0.92822770 -0.06047317 -54.96602944
0.61188550 -0.19197956 0.76729393 1.56492783
Axis -0.09183000 -0.87309222 0.47882901
Axis point 114.59604058 0.00000000 243.00785344
Rotation angle (degrees) 45.72781528
Shift along axis 31.60874306
> view matrix models
> #11,-0.8111,0.11823,0.57284,152.5,0.48208,-0.41949,0.76917,159.64,0.33125,0.90003,0.28325,112.95
> fitmap #11 inMap #12
Fit molecule 6sj7 (#11) to map run_class001.mrc (#12) using 10007 atoms
average map value = 0.03467, steps = 364
shifted from previous position = 49.5
rotated from previous position = 95.1 degrees
atoms outside contour = 5115, contour level = 0.033282
Position of 6sj7 (#11) relative to run_class001.mrc (#12) coordinates:
Matrix rotation and translation
0.50735679 0.69735299 -0.50624884 118.49709550
0.67430608 0.04452072 0.73710866 35.51158285
0.53656351 -0.71534379 -0.44764150 289.74214007
Axis -0.81224938 -0.58316793 -0.01288843
Axis point 0.00000000 84.76514035 157.18697421
Rotation angle (degrees) 116.60787607
Shift along axis -120.69273040
> view matrix models
> #11,-0.027121,-0.99858,-0.045791,220.74,0.87327,-0.0013743,-0.48724,230.03,0.48648,-0.053202,0.87207,142.37
> fitmap #11 inMap #12
Fit molecule 6sj7 (#11) to map run_class001.mrc (#12) using 10007 atoms
average map value = 0.03418, steps = 136
shifted from previous position = 4.26
rotated from previous position = 27.1 degrees
atoms outside contour = 5053, contour level = 0.033282
Position of 6sj7 (#11) relative to run_class001.mrc (#12) coordinates:
Matrix rotation and translation
-0.46847093 0.85085988 -0.23784964 185.78392314
0.39295787 0.44179848 0.80647268 27.83216714
0.79127688 0.28434413 -0.54132185 143.22248403
Axis -0.42055290 -0.82891874 -0.36882108
Axis point 67.69413823 0.00000000 90.81765829
Rotation angle (degrees) 141.62802180
Shift along axis -154.02604282
> 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
> view matrix models
> #11,-0.78356,0.60669,-0.13401,133.8,-0.25607,-0.51186,-0.82002,473.41,-0.5661,-0.60821,0.55643,375.67
> fitmap #11 inMap #12
Fit molecule 6sj7 (#11) to map run_class001.mrc (#12) using 10007 atoms
average map value = 0.03449, steps = 180
shifted from previous position = 8.6
rotated from previous position = 27.8 degrees
atoms outside contour = 4970, contour level = 0.033282
Position of 6sj7 (#11) relative to run_class001.mrc (#12) coordinates:
Matrix rotation and translation
0.69569132 -0.62402153 -0.35582401 241.26668748
-0.28241673 -0.69305292 0.66326346 266.39772163
-0.66049556 -0.36093600 -0.65838503 403.86318687
Axis -0.91297186 0.27158435 0.30450667
Axis point 0.00000000 238.23352020 196.25774460
Rotation angle (degrees) 145.88089166
Shift along axis -24.94120924
> volume #12 level 0.03185
> hide #!11 models
> open
> /Users/omallen/Downloads/cryosparc_P313_J764_component_000/J764_component_000_frame_000.mrc
Opened J764_component_000_frame_000.mrc as #9, grid size 256,256,256, pixel
1.58, shown at level 0.186, step 1, values float32
> open
> /Users/omallen/Downloads/cryosparc_P313_J764_component_000/J764_component_000_frame_001.mrc
Opened J764_component_000_frame_001.mrc as #14, grid size 256,256,256, pixel
1.58, shown at level 0.175, step 1, values float32
> open
> /Users/omallen/Downloads/cryosparc_P313_J764_component_000/J764_component_000_frame_002.mrc
Opened J764_component_000_frame_002.mrc as #15, grid size 256,256,256, pixel
1.58, shown at level 0.167, step 1, values float32
> open
> /Users/omallen/Downloads/cryosparc_P313_J764_component_000/J764_component_000_frame_003.mrc
Opened J764_component_000_frame_003.mrc as #16, grid size 256,256,256, pixel
1.58, shown at level 0.158, step 1, values float32
> open
> /Users/omallen/Downloads/cryosparc_P313_J764_component_000/J764_component_000_frame_004.mrc
Opened J764_component_000_frame_004.mrc as #17, grid size 256,256,256, pixel
1.58, shown at level 0.151, step 1, values float32
> open
> /Users/omallen/Downloads/cryosparc_P313_J764_component_000/J764_component_000_frame_005.mrc
Opened J764_component_000_frame_005.mrc as #18, grid size 256,256,256, pixel
1.58, shown at level 0.149, step 1, values float32
> open
> /Users/omallen/Downloads/cryosparc_P313_J764_component_000/J764_component_000_frame_006.mrc
Opened J764_component_000_frame_006.mrc as #22, grid size 256,256,256, pixel
1.58, shown at level 0.148, step 1, values float32
> open
> /Users/omallen/Downloads/cryosparc_P313_J764_component_000/J764_component_000_frame_007.mrc
Opened J764_component_000_frame_007.mrc as #23, grid size 256,256,256, pixel
1.58, shown at level 0.152, step 1, values float32
> open
> /Users/omallen/Downloads/cryosparc_P313_J764_component_000/J764_component_000_frame_008.mrc
Opened J764_component_000_frame_008.mrc as #24, grid size 256,256,256, pixel
1.58, shown at level 0.163, step 1, values float32
> open
> /Users/omallen/Downloads/cryosparc_P313_J764_component_000/J764_component_000_frame_009.mrc
Opened J764_component_000_frame_009.mrc as #25, grid size 256,256,256, pixel
1.58, shown at level 0.173, step 1, values float32
> view orient
> volume #12 level 0.03709
> volume #9 level 0.2566
> morph map #9 #14 #15 #16 #17 #18 #22 #23 #24 #25
Missing or invalid "structures" argument: invalid structures specifier
> volume morph #9 #14 #15 #16 #17 #18 #22 #23 #24 #25
Opened morph as #26, grid size 256,256,256, pixel 1.58, shown at step 1,
values float32
> volume #26 level 0.4972
> open /Volumes/lab-enchevr/home/users/omallen/EMReady/J743_Emready.mrc
Opened J743_Emready.mrc as #27, grid size 403,403,403, pixel 1, shown at level
0.000534, step 2, values float32
> volume #27 step 1
> volume #27 level 0.6289
> volume #27 level 2.896
> view orient
> show #!11 models
> ui tool show "Fit in Map"
> fitmap #11 inMap #27
Fit molecule 6sj7 (#11) to map J743_Emready.mrc (#27) using 10007 atoms
average map value = -0.01947, steps = 992
shifted from previous position = 5.5
rotated from previous position = 5.01 degrees
atoms outside contour = 10007, contour level = 2.8959
Position of 6sj7 (#11) relative to J743_Emready.mrc (#27) coordinates:
Matrix rotation and translation
-0.53074699 0.82519195 0.19330222 28.09888167
-0.59495104 -0.20031971 -0.77839907 460.23133519
-0.60360646 -0.52813836 0.59726791 368.46025924
Axis 0.15189650 0.48368613 -0.86196008
Axis point 200.25391132 320.72389772 0.00000000
Rotation angle (degrees) 124.53429428
Shift along axis -90.72239814
> view matrix models
> #11,-0.38608,0.90188,0.1938,-7.2077,-0.9199,-0.39206,-0.0081081,325.1,0.068669,-0.18141,0.98101,98.361
> view matrix models
> #11,-0.38608,0.90188,0.1938,114.6,-0.9199,-0.39206,-0.0081081,354.57,0.068669,-0.18141,0.98101,106.94
> fitmap #11 inMap #27
Fit molecule 6sj7 (#11) to map J743_Emready.mrc (#27) using 10007 atoms
average map value = 2.143, steps = 124
shifted from previous position = 4.77
rotated from previous position = 18 degrees
atoms outside contour = 6154, contour level = 2.8959
Position of 6sj7 (#11) relative to J743_Emready.mrc (#27) coordinates:
Matrix rotation and translation
-0.33703701 0.92749782 0.16172107 108.92911063
-0.87849186 -0.37158842 0.30028977 310.11554454
0.33861181 -0.04086187 0.94003838 67.67645465
Axis -0.18476366 -0.09580191 -0.97810244
Axis point 150.00885463 121.91561484 0.00000000
Rotation angle (degrees) 112.59988967
Shift along axis -116.03030750
> view matrix models
> #11,-0.34775,0.91745,0.19326,109.05,-0.90859,-0.38062,0.17203,324.1,0.23138,-0.11577,0.96595,87.111
> view matrix models
> #11,-0.78514,-0.60638,0.12596,352.48,0.61209,-0.79074,0.0086353,215.43,0.094364,0.083877,0.992,76.048
> view matrix models
> #11,-0.24201,-0.9701,0.018102,343.82,0.96841,-0.24035,0.066429,105.28,-0.060093,0.033607,0.99763,99.641
> fitmap #11 inMap #27
Fit molecule 6sj7 (#11) to map J743_Emready.mrc (#27) using 10007 atoms
average map value = 3.129, steps = 248
shifted from previous position = 5.98
rotated from previous position = 44.6 degrees
atoms outside contour = 4087, contour level = 2.8959
Position of 6sj7 (#11) relative to J743_Emready.mrc (#27) coordinates:
Matrix rotation and translation
-0.84058908 -0.52777873 -0.12189943 384.04332990
0.53377744 -0.84537263 -0.02065475 241.32088288
-0.09214932 -0.08242931 0.99232743 115.20977036
Axis -0.05807146 -0.02796672 0.99792062
Axis point 160.20443367 178.41234895 0.00000000
Rotation angle (degrees) 147.86715639
Shift along axis 85.91929558
> volume #27 level 4.522
> volume #27 level 2.255
> volume #27 color #b2ffb267
> molmap #11 16 onGrid #27
Opened 6sj7 map 16 as #28, grid size 403,403,403, pixel 1, shown at level
0.0526, step 1, values float32
> volume #28 level 3.315e-05
> volume #28 level 0.0142
No map chosen to save
> save "/Users/omallen/OneDrive - The Francis Crick
> Institute/PP/CRL4DCAF15/6sj7mask.mrc" models #28
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/omallen/Downloads/cryosparc_P313_J767_002_volume_map.mrc
Opened cryosparc_P313_J767_002_volume_map.mrc as #1, grid size 256,256,256,
pixel 1.58, shown at level 0.143, step 1, values float32
> open /Users/omallen/Downloads/cryosparc_P313_J767_002_volume_map.mrc
Opened cryosparc_P313_J767_002_volume_map.mrc as #2, grid size 256,256,256,
pixel 1.58, shown at level 0.143, step 1, values float32
OpenGL version: 4.1 Metal - 90.5
OpenGL renderer: Apple M2 Pro
OpenGL vendor: Apple
Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac14,9
Model Number: MPHE3B/A
Chip: Apple M2 Pro
Total Number of Cores: 10 (6 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 13822.1.2
OS Loader Version: 13822.1.2
Software:
System Software Overview:
System Version: macOS 26.0 (25A354)
Kernel Version: Darwin 25.0.0
Time since boot: 8 days, 4 hours, 14 minutes
Graphics/Displays:
Apple M2 Pro:
Chipset Model: Apple M2 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 16
Vendor: Apple (0x106b)
Metal Support: Metal 4
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
DELL U2419H:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
DELL U2419H:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 1.0.0
anyio: 4.7.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.1.0
babel: 2.16.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 3.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.0
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.16.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.8
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.9
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.6
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5
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: 1.2.1
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: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
ChimeraX-ModelPanel: 1.5
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
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.6
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: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.2
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: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.6
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.14
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
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: 1.18.1
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
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: 1.41
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: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.9
decorator: 5.1.1
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.55.3
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h11: 0.14.0
h5py: 3.12.1
html2text: 2024.2.26
httpcore: 1.0.7
httpx: 0.28.1
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jedi: 0.19.1
Jinja2: 3.1.4
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.7
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
msgpack: 1.0.8
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
prompt_toolkit: 3.0.48
psutil: 6.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.0
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine-commercial: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.0
RandomWords: 0.4.0
requests: 2.32.3
scipy: 1.14.0
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
sniffio: 1.3.1
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
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: 0.6.3
tables: 3.10.1
tcia_utils: 1.5.1
tifffile: 2024.7.24
tinyarray: 1.2.4
tornado: 6.4.2
traitlets: 5.14.3
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.2.3
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
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