![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 9 months ago
Closed 9 months ago
#16769 closed defect (can't reproduce)
Crash on Mac waking from sleep
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| 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-14.7.2-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Current thread 0x0000000203f58f80 (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.pdb_lib._load_libs, chimerax.map._map, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, chimerax.surface._surface, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, chimerax.atom_search.ast, chimerax.chem_group._chem_group, chimerax.coulombic._esp, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, PIL._imagingmath (total: 55)
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{
"uptime" : 220000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 502,
"deployVersion" : 210,
"modelCode" : "Mac15,3",
"coalitionID" : 28602,
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"build" : "23H311",
"releaseType" : "User"
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"captureTime" : "2025-02-03 12:30:01.6630 -0500",
"codeSigningMonitor" : 1,
"incident" : "A7A5F024-3F6B-49CE-A706-F1BAC11B2282",
"pid" : 739,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-02-02 17:27:06.9303 -0500",
"procStartAbsTime" : 4743944158082,
"procExitAbsTime" : 5288271159776,
"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":"3C0EF074-BC9F-58AE-8184-F4323E9FEBAF","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "CACB4695-AB31-C32A-6E85-B320AF1CE9EF",
"lowPowerMode" : 1,
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRd+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkWzg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"wakeTime" : 31,
"sleepWakeUUID" : "6869DAEE-7B8D-4B69-A314-11007C21B49C",
"sip" : "enabled",
"vmRegionInfo" : "0x18 is not in any region. Bytes before following region: 4300357608\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 100524000-100528000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000018","rawCodes":[1,24],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000018"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":739},
"vmregioninfo" : "0x18 is not in any region. Bytes before following region: 4300357608\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 100524000-100528000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
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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
> /Users/pryor/Documents/AlphaFold_Files/fold_1xkin_20c_1xlin_42b/fold_1xkin_20_1xlin_42b_model_0.cif
> format mmcif
Chain information for fold_1xkin_20_1xlin_42b_model_0.cif #1
---
Chain | Description
A | .
B | .
Computing secondary structure
> select alphafold contacts minResidueConfidence 0.8
Expected an objects specifier or a keyword
> alphafold contacts minResidueConfidence 0.8
Missing or invalid "atoms" argument: invalid atoms specifier
> alphafold contacts #1 minResidueConfidence 0.8
Expected a keyword
> alphafold contacts #1
Structure fold_1xkin_20_1xlin_42b_model_0.cif #1 does not have PAE data opened
> ui tool show "AlphaFold Error Plot"
> alphafold pae #1 file
> /Users/pryor/Documents/AlphaFold_Files/fold_1xkin_20c_1xlin_42b/fold_1xkin_20_1xlin_42b_full_data_0.json
> alphafold contacts #1
Found 3386 residue or atom pairs within distance 3
> color /A:178-482 lime
> color /B:404-472 magenta
> alphafold contacts #1
Found 3386 residue or atom pairs within distance 3
> alphafold pae #1 colorDomains true
> color bychain
> select add #1
8577 atoms, 8802 bonds, 3386 pseudobonds, 1091 residues, 2 models selected
> ui tool show "Color Actions"
> color sel bychain
> color sel red
> color sel bychain
> color sel byhetero
> color sel byelement
> color sel bynucleotide
> color sel bychain
> color sel bypolymer
> undo
> select subtract #1.1
8577 atoms, 8802 bonds, 1091 residues, 1 model selected
> hide #1.1 models
> show #1.1 models
> select /A
3983 atoms, 4091 bonds, 1504 pseudobonds, 494 residues, 2 models selected
> color (#!1 & sel) magenta
> select /B
4594 atoms, 4711 bonds, 1798 pseudobonds, 597 residues, 2 models selected
> color (#!1 & sel) lime
> ui mousemode right select
> select /A:195
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
> select /B:453
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:195
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:196
4 atoms, 3 bonds, 1 residue, 1 model selected
> select /A:197
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /A
3983 atoms, 4091 bonds, 1504 pseudobonds, 494 residues, 2 models selected
Alignment identifier is 1/A
> select /A:193
4 atoms, 3 bonds, 1 residue, 1 model selected
> select /A:193-204
87 atoms, 88 bonds, 26 pseudobonds, 12 residues, 2 models selected
> select /A:318
4 atoms, 3 bonds, 1 residue, 1 model selected
> select /B:419
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /A:194
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /A:193
4 atoms, 3 bonds, 1 residue, 1 model selected
> select /A:194
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> rainbow sel
> color sel bypolymer
> color sel bychain
> color sel bypolymer
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for fold_1xkin_20_1xlin_42b_model_0.cif_A SES surface #1.2:
minimum, -32.05, mean -0.21, maximum 14.67
To also show corresponding color key, enter the above coulombic command and
add key true
> hide sel surfaces
> hbonds sel reveal true
4 hydrogen bonds found
> interfaces select & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
> color sel byhetero
> select /A:195
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel bypolymer
> color sel byhetero
> hbonds sel reveal true
2 hydrogen bonds found
> select /A
3983 atoms, 4091 bonds, 1505 pseudobonds, 494 residues, 3 models selected
> color (#!1 & sel) light gray
> color (#!1 & sel) gray
> select /A:194
11 atoms, 10 bonds, 1 residue, 1 model selected
> color sel bypolymer
> select /A:195@CA
1 atom, 1 residue, 1 model selected
> color sel bypolymer
> select /A:195
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel bypolymer
> color sel bychain
> color sel bypolymer
> color sel byhetero
> select /A:194
11 atoms, 10 bonds, 1 residue, 1 model selected
> color sel byhetero
> select /A:193
4 atoms, 3 bonds, 1 residue, 1 model selected
> show sel atoms
> select /A:193
4 atoms, 3 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel bychain
> color sel bypolymer
> select /A:193
4 atoms, 3 bonds, 1 residue, 1 model selected
> select /B:411
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel bypolymer
> hbonds sel reveal true
3 hydrogen bonds found
> ui mousemode right clip
> ui mousemode right "clip rotate"
> ui mousemode right clip
> ui mousemode right select
> select /B:419
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /A:318
4 atoms, 3 bonds, 1 residue, 1 model selected
> select /A:319
9 atoms, 8 bonds, 1 residue, 1 model selected
Drag select of 3 residues
> select /A:193-204
87 atoms, 88 bonds, 26 pseudobonds, 12 residues, 2 models selected
> select /A:204
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel bypolymer
> color sel byhetero
> select /B:467
11 atoms, 10 bonds, 1 residue, 1 model selected
> color bfactor #1 palette alphafold
8577 atoms, 1091 residues, 1 surfaces, atom bfactor range 13.3 to 96.6
> hide #1.2 models
> show #1.2 models
> hide #1.2 models
> show #1.2 models
> hide #1.2 models
> hide #1.3 models
> show #1.3 models
> hide #1.3 models
> show #1.3 models
> hide #1.3 models
> show #1.2 models
> hide #1.2 models
> show #1.2 models
> hide #1.2 models
> show #1.2 models
> hide #1.2 models
> close #1.2
> close #1.3
> select add #1.1
3386 pseudobonds, 1 model selected
> alphafold contacts inter only
Missing or invalid "atoms" argument: invalid atoms specifier
> alphafold contacts inter only #1
Missing or invalid "atoms" argument: invalid atoms specifier
> alphafold contacts #1 inter only
Expected a keyword
> alphafold contacts #1 inter
Expected a keyword
> alphafold contacts #1 inter only
Expected a keyword
> alphafold contacts inter only
Missing or invalid "atoms" argument: invalid atoms specifier
> alphafold contacts inter
Missing or invalid "atoms" argument: invalid atoms specifier
> alphafold contacts inter
Missing or invalid "atoms" argument: invalid atoms specifier
> alphafold contacts
Missing or invalid "atoms" argument: empty atom specifier
> alphafold contacts #1
Found 3386 residue or atom pairs within distance 3
> alphafold contacts #1 inter
Expected a keyword
> alphafold contacts inter #1
Missing or invalid "atoms" argument: invalid atoms specifier
> alphafold contacts inter only #1
Missing or invalid "atoms" argument: invalid atoms specifier
> alphafold interfaces contacts #1
Missing or invalid "directory" argument: File 'contacts' does not exist
> alphafold contacts #1
Found 3386 residue or atom pairs within distance 3
> select alphafold contacts #1
Expected an objects specifier or a keyword
> select alphafold contacts intra
Expected an objects specifier or a keyword
> select alphafold contacts inter
Expected an objects specifier or a keyword
> select alphafold contacts inter #1
Expected an objects specifier or a keyword
> select alphafold contacts inter only
Expected an objects specifier or a keyword
> select alphafold contacts inter only #!
Expected an objects specifier or a keyword
> select alphafold contacts inter only #1
Expected an objects specifier or a keyword
> alphafold contacts inter only
Missing or invalid "atoms" argument: invalid atoms specifier
> alphafold contacts inter only #1:A #1:B
Missing or invalid "atoms" argument: invalid atoms specifier
> alphafold contacts #1:A #1:B
No alphafold specified for alphafold contacts
> alphafold contacts #1:A #1:B
No alphafold specified for alphafold contacts
> fold_1xkin_20_1xlin_42b_model_0.cif contacts #1:A #1:B
Unknown command: alphafold fold_1xkin_20_1xlin_42b_model_0.cif contacts #1:A
#1:B
> alphafold contacts #1:A #1:B
No alphafold specified for alphafold contacts
> alphafold contacts #1 ~inter
Expected a keyword
> alphafold contacts #1 inter
Expected a keyword
> alphafold contacts #1 inter only
Expected a keyword
> alphafold contacts #1:A
No alphafold specified for alphafold contacts
> alphafold contacts .:A
Missing or invalid "atoms" argument: invalid atoms specifier
> alphafold contacts #1.:A
Missing or invalid "atoms" argument: only initial part "#1" of atom specifier
valid
> alphafold contacts #1:a
No alphafold specified for alphafold contacts
> alphafold contacts #1:
Missing or invalid "atoms" argument: only initial part "#1" of atom specifier
valid
> alphafold contacts #1:.
Missing or invalid "atoms" argument: only initial part "#1" of atom specifier
valid
> alphafold contacts #1:A
No alphafold specified for alphafold contacts
> alphafold contacts #1:B
No alphafold specified for alphafold contacts
> alphafold contacts #1:chain A
Expected a keyword
> alphafold contacts #1:chainA
No alphafold specified for alphafold contacts
> alphafold contacts #1:ChainA
No alphafold specified for alphafold contacts
> alphafold contacts #1:Chain_A
No alphafold specified for alphafold contacts
> setattr #1 alphafold true
Missing or invalid "attrValue" argument: Expected a text string
> setattr 1 alphafold true
Unknown attribute target: '1'
> setattr #1 alphafold true
Missing or invalid "attrValue" argument: Expected a text string
> log metadata #1
No models had metadata
> log chains #1
Chain information for fold_1xkin_20_1xlin_42b_model_0.cif #1
---
Chain | Description
A | .
B | .
> setattr fold_1xkin_20_1xlin_42b_model_0.cif #1 alphafold true
Expected a keyword
> setattr fold_1xkin_20_1xlin_42b_model_0.cif alphafold true
Unknown attribute target: 'fold_1xkin_20_1xlin_42b_model_0.cif'
> conacts #1
Unknown command: alphafold conacts #1
> alphafold contacts #1
Found 3386 residue or atom pairs within distance 3
> alphafold pae show
Expected an atomic structure specifier or a keyword
> alphafold pae show #1
Expected an atomic structure specifier or a keyword
> alphafold pae #1 show
Expected a keyword
> alphafold pae #1
> hide interchain
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide ~interchain
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide ~interchain
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide ~interchain contacts
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide ~interchain bonds
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide ~interchain
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide ~interchain #1
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide ~interchain 1
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide ~interchain model 1
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide ~interchain_contacts
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide contacts ~interchain
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide contacts ~interchain
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide contacts
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide alphafold interchain
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide alphafold interchain #1
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide alphafold interchain contacts
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> selects alphafold contacts intra
Unknown command: selects alphafold contacts intra
> selects alphafold contacts inter
Unknown command: selects alphafold contacts inter
> select alphafold contacts
Expected an objects specifier or a keyword
> select alphafold contacts intra
Expected an objects specifier or a keyword
> select alphafold contacts
Expected an objects specifier or a keyword
> select alphafold contacts intra
Expected an objects specifier or a keyword
> select alphafold contacts inter
Expected an objects specifier or a keyword
> select alphafold contacts inter #1
Expected an objects specifier or a keyword
> select contacts inter
Expected an objects specifier or a keyword
> select contacts inter
Expected an objects specifier or a keyword
> select contacts ~inter
Expected an objects specifier or a keyword
> alphafold contacts #1 minResidueConfidence 0.8
Expected a keyword
> select clear
> alphafold contacts #1
Found 3386 residue or atom pairs within distance 3
> alphafold contacts #1 inter
Expected a keyword
> alphafold contacts #1:A #1:B
No alphafold specified for alphafold contacts
> alphafold contacts model #1:A #1:B
Missing or invalid "atoms" argument: invalid atoms specifier
> alphafold contacts model #1:A
Missing or invalid "atoms" argument: invalid atoms specifier
> alphafold contacts model #1
Missing or invalid "atoms" argument: invalid atoms specifier
> alphafold contacts model 1
Missing or invalid "atoms" argument: invalid atoms specifier
> alphafold contacts model 1:A
Missing or invalid "atoms" argument: invalid atoms specifier
> alphafold contacts 1
Missing or invalid "atoms" argument: invalid atoms specifier
> alphafold contacts #1
Found 3386 residue or atom pairs within distance 3
> alphafold contacts #2
No alphafold specified for alphafold contacts
> alphafold contacts #1
Found 3386 residue or atom pairs within distance 3
> alphafold contacts #3
No alphafold specified for alphafold contacts
> alphafold contacts #1:A
No alphafold specified for alphafold contacts
> alphafold contacts #1:ChainA
No alphafold specified for alphafold contacts
> alphafold contacts #1:Chain_A
No alphafold specified for alphafold contacts
> select /A
3983 atoms, 4091 bonds, 1504 pseudobonds, 494 residues, 2 models selected
> alphafold contacts #1:A
No alphafold specified for alphafold contacts
> alphafold contacts #1:/A
Missing or invalid "atoms" argument: only initial part "#1" of atom specifier
valid
> alphafold contacts #1/A
Found 42 residue or atom pairs within distance 3
> hide #!1 models
> show #!1 models
> select add #1
8577 atoms, 8802 bonds, 42 pseudobonds, 1091 residues, 2 models selected
> select subtract #1.1
8577 atoms, 8802 bonds, 1091 residues, 1 model selected
> color sel bychain
> ui mousemode right clip
> select /A
3983 atoms, 4091 bonds, 494 residues, 1 model selected
> color sel gray
> select /B
4594 atoms, 4711 bonds, 597 residues, 1 model selected
> color sel forest green
> ui mousemode right select
> select clear
> view
> select add #1
8577 atoms, 8802 bonds, 42 pseudobonds, 1091 residues, 2 models selected
Alignment identifier is 1/A
Alignment identifier is 1/B
> select /A:185-186
18 atoms, 17 bonds, 2 residues, 1 model selected
> select /A:185-213
228 atoms, 230 bonds, 29 residues, 1 model selected
> color /A:142-482 lime
> color /B:364-494 magenta
> color /A:177-482 lime
> color /B:403-469 magenta
> select
> /B:33-35,84-86,94-96,99-111,155-157,184-190,194-196,202-205,208-223,296-311,342-355,359-390,404-421,446-473,492-499
1347 atoms, 1356 bonds, 171 residues, 1 model selected
> select /B:296-297
14 atoms, 14 bonds, 2 residues, 1 model selected
> select /B:296-391
723 atoms, 735 bonds, 96 residues, 1 model selected
> select /B:445-446
18 atoms, 17 bonds, 2 residues, 1 model selected
> select /B:445-474
265 atoms, 269 bonds, 30 residues, 1 model selected
> select /B:491-492
12 atoms, 11 bonds, 2 residues, 1 model selected
> select /B:491-500
83 atoms, 84 bonds, 10 residues, 1 model selected
> select /B:403-404
18 atoms, 18 bonds, 2 residues, 1 model selected
> select /B:403-422
166 atoms, 167 bonds, 20 residues, 1 model selected
> select /B:401
7 atoms, 7 bonds, 1 residue, 1 model selected
> select /B:401-475
632 atoms, 647 bonds, 75 residues, 1 model selected
> alphafold pae #1 colorDomains true
> color bfactor #1 palette alphafold
8577 atoms, 1091 residues, atom bfactor range 13.3 to 96.6
> select clear
> select add #1
8577 atoms, 8802 bonds, 42 pseudobonds, 1091 residues, 2 models selected
> color sel bychain
> select clear
> hide #1.1 models
> save /Users/pryor/Desktop/KIN20_LIN42.jpg width 936 height 768 supersample 3
> ui mousemode right clip
> show #1.1 models
> ui mousemode right select
> select /A:194
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel atoms
> select /B:404
12 atoms, 12 bonds, 1 residue, 1 model selected
> hide sel atoms
> select /B:408
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select /A:195
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> save /Users/pryor/Desktop/KIN20_LIN42.jpg width 936 height 768 supersample 3
> select /B:411
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> save /Users/pryor/Desktop/KIN20_LIN42.jpg width 936 height 768 supersample 3
> color /A:177-482 lime
> color /B:403-458 magenta
> color /A:175-480 lime
> color /B:401-469 magenta
> save /Users/pryor/Desktop/KIN20_LIN42_int.jpg width 936 height 768
> supersample 3
Drag select of 1 residues
> ui mousemode right clip
> hide #!1 models
> hide #1.1 models
> open
> /Users/pryor/Documents/AlphaFold_Files/0_fold_kin_20c_lin42b_myrf_1_atp/0_fold_kin_20c_lin42b_myrf_1_atp_model_1.cif
Chain information for 0_fold_kin_20c_lin42b_myrf_1_atp_model_1.cif #2
---
Chain | Description
A | .
B | .
C | .
Computing secondary structure
> select add #2
15950 atoms, 16320 bonds, 2025 residues, 2 models selected
> select add #1
24519 atoms, 25122 bonds, 42 pseudobonds, 3115 residues, 3 models selected
> select subtract #1
15942 atoms, 16320 bonds, 2024 residues, 1 model selected
> ui mousemode right select
> color sel bychain
> select #2/C:36
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/C:35
6 atoms, 5 bonds, 1 residue, 1 model selected
Alignment identifier is 2/C
> select #2/C:35-36
14 atoms, 13 bonds, 2 residues, 1 model selected
> select #2/C:35-37
21 atoms, 20 bonds, 3 residues, 1 model selected
> ui mousemode right "clip rotate"
> ui mousemode right clip
> alphafold pae
No structure or PAE file specified.
> alphafold pae #2
No predicted aligned error (PAE) data opened for structure #2
Must choose path to predicted aligned file
> open
> /Users/pryor/Documents/AlphaFold_Files/0_fold_kin_20c_lin42b_myrf_1_atp/0_fold_kin_20c_lin42b_myrf_1_atp_full_data_1.json
Opened AlphaFold PAE with values for 2054 residues and atoms
> color #2/C:30-45 lime
> color
> #2/D:1@PB,O1B,O2B,O3B,PA,O1A,O2A,O3A,O5',C5',C4',O4',C3',O3',C2',O2',C1',N9,C8,N7,C5,C6,N6
> magenta
> hide #2 models
> show #!1 models
> select add #2
15942 atoms, 16320 bonds, 2024 residues, 1 model selected
> select subtract #2
Nothing selected
> select add #1
8577 atoms, 8802 bonds, 42 pseudobonds, 1091 residues, 2 models selected
Alignment identifier is 1/A
Alignment identifier is 1/B
> select #1/A:305
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/A:305-307
29 atoms, 29 bonds, 3 residues, 1 model selected
> select #1/A:193
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #1/A:193-208
116 atoms, 117 bonds, 16 residues, 1 model selected
> rainbow sel
> color sel bychain
> color sel bypolymer
> select
> #1/B:33-35,84-86,94-96,99-111,155-157,184-190,194-196,202-205,208-223,296-311,342-355,359-390,404-421,446-473,492-499
1347 atoms, 1356 bonds, 171 residues, 1 model selected
> select #1/B:403
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/B:403-473
602 atoms, 616 bonds, 71 residues, 1 model selected
> show #1.1 models
> select #1/A:193-208
116 atoms, 117 bonds, 16 residues, 1 model selected
> show sel atoms
> hide sel atoms
> select #1/A:194
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/A:194-195
20 atoms, 19 bonds, 2 residues, 1 model selected
> show sel atoms
> select #1/A:193
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #1/A:193
4 atoms, 3 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1/A:204
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #1/A:204
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1/A:200
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #1/A:200-201
15 atoms, 15 bonds, 2 residues, 1 model selected
> select #1/A:196-197
10 atoms, 9 bonds, 2 residues, 1 model selected
> select #1/A:196-202
43 atoms, 43 bonds, 7 residues, 1 model selected
> select #1/A:197
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/A:197-203
47 atoms, 47 bonds, 7 residues, 1 model selected
> color sel lime
> ui mousemode right select
> select clear
> select #1/A:205
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:205-210
46 atoms, 45 bonds, 6 residues, 1 model selected
> color sel lime
> select clear
> select #1/B:460
12 atoms, 12 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #1/B:453
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1/B:452
10 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1/B:404
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1/B:408
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1/B:411
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> ui mousemode right clip
> ui mousemode right "clip rotate"
> ui mousemode right clip
> ui mousemode right "clip rotate"
> ui mousemode right clip
> ui mousemode right select
> select clear
> ui mousemode right clip
> save /Users/pryor/Desktop/KIN20_LIN42_muts.jpg width 936 height 768
> supersample 3
> hide #!1 models
> hide #1.1 models
> show #2 models
> select add #2
15942 atoms, 16320 bonds, 2024 residues, 1 model selected
> color sel bychain
> ui mousemode right select
> select clear
> select #2/A
3991 atoms, 4099 bonds, 495 residues, 1 model selected
> close #1
> hide sel cartoons
> hide sel atoms
> show sel atoms
> undo
> hide sel atoms
> undo
> hide sel atoms
> show sel atoms
> undo
> hide sel cartoons
> hide sel atoms
> open
> /Users/pryor/Documents/AlphaFold_Files/fold_kin_20c_lin_42b_myrf_1_482_atp/fold_kin_20c_lin_42b_myrf_1_482_atp_model_0.cif
Chain information for fold_kin_20c_lin_42b_myrf_1_482_atp_model_0.cif #1
---
Chain | Description
A | .
B | .
C | .
Computing secondary structure
> hide #2 models
> select add #2
15942 atoms, 16320 bonds, 2024 residues, 1 model selected
> select subtract #2
Nothing selected
> select add #1
12414 atoms, 12724 bonds, 1575 residues, 1 model selected
> color sel bychain
Alignment identifier is 1/A
Alignment identifier is 1/B
Alignment identifier is 1/C
> select #1/C:35
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/C:35-38
27 atoms, 26 bonds, 4 residues, 1 model selected
> select #1/C:207
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/C:207-224
144 atoms, 147 bonds, 18 residues, 1 model selected
> select #1/C:203
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/C:203-229
208 atoms, 212 bonds, 27 residues, 1 model selected
> open
> /Users/pryor/Documents/AlphaFold_Files/fold_kin_20c_lin_42b_myrf_1_482_atp/fold_kin_20c_lin_42b_myrf_1_482_atp_model_1.cif
Chain information for fold_kin_20c_lin_42b_myrf_1_482_atp_model_1.cif #3
---
Chain | Description
A | .
B | .
C | .
Computing secondary structure
> hide #1 models
> select add #1
12414 atoms, 12724 bonds, 1575 residues, 1 model selected
> select subtract #1
Nothing selected
> select add #3
12414 atoms, 12724 bonds, 1575 residues, 1 model selected
> color sel bychain
Alignment identifier is 3/A
Alignment identifier is 3/B
Alignment identifier is 3/C
> select #3/C:35-36
14 atoms, 13 bonds, 2 residues, 1 model selected
> select #3/C:35-39
34 atoms, 34 bonds, 5 residues, 1 model selected
> select #3/C:69
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/C:69-84
129 atoms, 133 bonds, 16 residues, 1 model selected
> select #3/C:92
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #3/C:92-98
46 atoms, 46 bonds, 7 residues, 1 model selected
> close #1
> hide #3 models
> select add #3
12414 atoms, 12724 bonds, 1575 residues, 1 model selected
> select subtract #3
Nothing selected
> open
> /Users/pryor/Documents/AlphaFold_Files/fold_kin_20c_lin_42b_myrf_1_482_atp/fold_kin_20c_lin_42b_myrf_1_482_atp_model_2.cif
Chain information for fold_kin_20c_lin_42b_myrf_1_482_atp_model_2.cif #1
---
Chain | Description
A | .
B | .
C | .
Computing secondary structure
> select add #1
12414 atoms, 12724 bonds, 1575 residues, 1 model selected
> color sel bychain
> color #2/C:34 lime
> color #2/C:930-931 #2/D:1 magenta
> color #2/C:30-48 lime
> color #2/C:930-931 #2/D:1 magenta
Alignment identifier is 1/A
Alignment identifier is 1/B
Alignment identifier is 1/C
> select #1/C:35
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/C:35-38
27 atoms, 26 bonds, 4 residues, 1 model selected
> ui mousemode right distance
> select add #1
12414 atoms, 12724 bonds, 1575 residues, 1 model selected
> select subtract #1
Nothing selected
> distance #1/D:1@PG #1/D:1@O3G
Distance between fold_kin_20c_lin_42b_myrf_1_482_atp_model_2.cif #1/D ATP 1 PG
and O3G: 1.490Å
> ui mousemode right select
> select #1/C:35
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/C:36
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/C:36-37
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #1/C:35
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/C:35-38
27 atoms, 26 bonds, 4 residues, 1 model selected
> show sel atoms
> ui mousemode right distance
> distance #1/D:1@O3G #1/C:35@OG
Distance between fold_kin_20c_lin_42b_myrf_1_482_atp_model_2.cif #1/D ATP 1
O3G and /C SER 35 OG: 4.533Å
> ~distance #1/D:1@PG #1/D:1@O3G
> distance #1/D:1@PG #1/C:35@OG
Distance between fold_kin_20c_lin_42b_myrf_1_482_atp_model_2.cif #1/D ATP 1 PG
and /C SER 35 OG: 5.830Å
> ui mousemode right select
> delete
Missing or invalid "atoms" argument: empty atom specifier
> sec delete
Unknown command: sec delete
> sec hide
Unknown command: sec hide
> select delete
Expected an objects specifier or a keyword
> select del
Expected an objects specifier or a keyword
> select hide
Expected an objects specifier or a keyword
> hide sel
> select #1/C:35-36
14 atoms, 13 bonds, 2 residues, 1 model selected
> select #1/C:35-38
27 atoms, 26 bonds, 4 residues, 1 model selected
> select clear
> select #1/C:26
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/C:26-29
31 atoms, 30 bonds, 4 residues, 1 model selected
> select clear
> save /Users/pryor/Desktop/MYRF_phos_distance.jpg width 936 height 768
> supersample 3
> select clear
> hide sel
> select #1/C:26
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/C:26
7 atoms, 6 bonds, 1 residue, 1 model selected
> rainbow sel
> select #1/C:29
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/C:29
7 atoms, 6 bonds, 1 residue, 1 model selected
> rainbow sel
> select #1/C:35
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/C:35
6 atoms, 5 bonds, 1 residue, 1 model selected
> rainbow sel
> select #1/C:38
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/C:38
6 atoms, 5 bonds, 1 residue, 1 model selected
> rainbow sel
> select #1/C:41
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/C:41
6 atoms, 5 bonds, 1 residue, 1 model selected
> rainbow sel
> select #1/C:42
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/C:42
6 atoms, 5 bonds, 1 residue, 1 model selected
> rainbow sel
> select #1/C:45
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/C:45
6 atoms, 5 bonds, 1 residue, 1 model selected
> rainbow sel
> show sel atoms
> select #1/C:40-41
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #1/C:40-42
19 atoms, 18 bonds, 3 residues, 1 model selected
> select #1/C:41
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/C:41-42
12 atoms, 11 bonds, 2 residues, 1 model selected
> rainbow sel
> select #1/C:38
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/C:38
6 atoms, 5 bonds, 1 residue, 1 model selected
> rainbow sel
> select #1/C:41
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/C:41-42
12 atoms, 11 bonds, 2 residues, 1 model selected
> select #1/C:42
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/C:42
6 atoms, 5 bonds, 1 residue, 1 model selected
> rainbow sel
> select #1/C:41
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/C:41-42
12 atoms, 11 bonds, 2 residues, 1 model selected
> show sel atoms
> select #1/C:26
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/C:26
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1/C:29
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/C:29
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> ui mousemode right clip
> ui mousemode right "clip rotate"
> ui mousemode right clip
> ui mousemode right "clip rotate"
> ui mousemode right clip
> select #1/A:306
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/A:306-312
61 atoms, 62 bonds, 7 residues, 1 model selected
> show sel atoms
> color sel red
> color sel orange red
> color sel cyan
> color sel yellow
> color sel light sea green
> color sel red
> ui mousemode right select
> select clear
> select #1/A:309
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:309-310
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #1/A:308
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:308
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel orange
> select #1/A:312
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:312
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel orange
Drag select of 1 atoms
> select clear
> select #1/A:313
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:313-317
39 atoms, 39 bonds, 5 residues, 1 model selected
> select #1/A:306
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/A:306-307
21 atoms, 21 bonds, 2 residues, 1 model selected
> select #1/A:193
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #1/A:193-205
95 atoms, 96 bonds, 13 residues, 1 model selected
> select #1/A:200
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/A:200
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/A:193
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #1/A:193-197
36 atoms, 35 bonds, 5 residues, 1 model selected
> select clear
> select #1/A:193-197
36 atoms, 35 bonds, 5 residues, 1 model selected
> select
> #1/A:129-153,156-165,173-182,230-239,270-276,283-301,311-313,319-321,330-332,361-364,371-387,400-413,416-419,425-436,445-458,476-493
1435 atoms, 1451 bonds, 173 residues, 1 model selected
> select #1/A:312
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:312
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel bychain
> select #1/A:306
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/A:306-308
29 atoms, 29 bonds, 3 residues, 1 model selected
> select #1/A:309
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:309-312
32 atoms, 32 bonds, 4 residues, 1 model selected
> color sel bychain
> select clear
Drag select of 3 residues
> select clear
> select #1/A:308
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel cornflower blue
> color sel light sea green
> select #1/A:220
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:308
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel lime
> select #1/A:307
11 atoms, 10 bonds, 1 residue, 1 model selected
> color sel cyan
> select #1/A:306
10 atoms, 10 bonds, 1 residue, 1 model selected
> color sel cyan
> select clear
> select #1/A:309-312
32 atoms, 32 bonds, 4 residues, 1 model selected
> color sel cyan
> select #1/A:306
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/A:306-312
61 atoms, 62 bonds, 7 residues, 1 model selected
> color sel medium blue
> color sel blue
> color sel magenta
> select #1/A:308
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel hot pink
> color sel orange
> select clear
> select #1/A:305
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:305
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> ui mousemode right clip
> select #1/A:193
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #1/A:193-199
46 atoms, 45 bonds, 7 residues, 1 model selected
> color sel gray
> undo
> ui mousemode right "clip rotate"
> ui mousemode right clip
> color sel gray
> color sel white
> ui mousemode right select
> select clear
> select #1/A:193-199
46 atoms, 45 bonds, 7 residues, 1 model selected
> color sel bychain
> select #1/A:300
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/A:300
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/A:310
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A:310
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A:309
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:309
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:307
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/A:305
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:305
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:310
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A:310
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A:193-194
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #1/A:193-198
42 atoms, 41 bonds, 6 residues, 1 model selected
> select #1/A:182-183
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #1/A:182-196
128 atoms, 128 bonds, 15 residues, 1 model selected
> select #1/A:193-194
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #1/A:193-212
148 atoms, 149 bonds, 20 residues, 1 model selected
> select #1/A:201
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #1/A:201-206
51 atoms, 52 bonds, 6 residues, 1 model selected
> select #1/A:199
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #1/A:199-203
33 atoms, 33 bonds, 5 residues, 1 model selected
> color sel magenta
> select #1/A:329
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel magenta
> select clear
> ui mousemode right clip
> ui mousemode right "clip rotate"
> ui mousemode right clip
> ui mousemode right select
> select #1/C:26
7 atoms, 6 bonds, 1 residue, 1 model selected
> color sel red
> select #1/C:29
7 atoms, 6 bonds, 1 residue, 1 model selected
> color sel red
> select #1/C:35
6 atoms, 5 bonds, 1 residue, 1 model selected
> color sel red
> select clear
> select #1/C:38
6 atoms, 5 bonds, 1 residue, 1 model selected
> color sel red
> select #1/C:26@CA
1 atom, 1 residue, 1 model selected
> color sel yellow
> select #1/C:26
7 atoms, 6 bonds, 1 residue, 1 model selected
> color sel yellow
> select #1/C:29
7 atoms, 6 bonds, 1 residue, 1 model selected
> color sel yellow
> select #1/C:35
6 atoms, 5 bonds, 1 residue, 1 model selected
> color sel yellow
> select #1/C:38
6 atoms, 5 bonds, 1 residue, 1 model selected
> color sel yellow
> select clear
> select #1/C:41
6 atoms, 5 bonds, 1 residue, 1 model selected
> color sel yellow
> select #1/C:42
6 atoms, 5 bonds, 1 residue, 1 model selected
> color sel yellow
> select #1/C:45
6 atoms, 5 bonds, 1 residue, 1 model selected
> color sel yellow
> select #1/A:308
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel red
> select #1/A:308@CG
1 atom, 1 residue, 1 model selected
> select #1/A:308@OD2
1 atom, 1 residue, 1 model selected
> ui mousemode right distance
> distance #1/C:35@OG #1/A:308@OD2
Distance between fold_kin_20c_lin_42b_myrf_1_482_atp_model_2.cif #1/C SER 35
OG and /A ASP 308 OD2: 7.191Å
> ui mousemode right select
> select clear
> select #1/A:336
12 atoms, 12 bonds, 1 residue, 1 model selected
> select clear
> hide #!4 models
> show #!4 models
> ui mousemode right distance
> distance #1/C:35@OG #1/A:200@OG
Distance between fold_kin_20c_lin_42b_myrf_1_482_atp_model_2.cif #1/C SER 35
OG and /A SER 200 OG: 4.910Å
> distance #1/C:35@OG #1/D:1@PG
Distance already exists; modify distance properties with 'distance style'
> distance #1/D:1@PG #1/C:35@OG
Distance already exists; modify distance properties with 'distance style'
> hide #!4 models
> show #!4 models
> hide #4.1 models
> distance #1/C:35@OG #1/D:1@O3G
Distance already exists; modify distance properties with 'distance style'
> distance #1/D:1@O3G #1/C:35@OG
Distance already exists; modify distance properties with 'distance style'
> distance #1/D:1@O2G #1/C:35@OG
Distance between fold_kin_20c_lin_42b_myrf_1_482_atp_model_2.cif #1/D ATP 1
O2G and /C SER 35 OG: 6.397Å
> save /Users/pryor/Desktop/KIN20_MYRF_SMVS_sites_pocket.jpg width 936 height
> 768 supersample 3
> ui mousemode right select
> select clear
> select #1/C:35
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/C:35-45
72 atoms, 72 bonds, 11 residues, 1 model selected
> select #1/C:26-27
16 atoms, 15 bonds, 2 residues, 1 model selected
> select #1/C:26-29
31 atoms, 30 bonds, 4 residues, 1 model selected
> select #1/C:35-45
72 atoms, 72 bonds, 11 residues, 1 model selected
> select #1/C:26-29
31 atoms, 30 bonds, 4 residues, 1 model selected
> select #1/C:35-45
72 atoms, 72 bonds, 11 residues, 1 model selected
> hide #!4 models
> hide #1 models
> show #3 models
> select add #1
12414 atoms, 12724 bonds, 5 pseudobonds, 1575 residues, 2 models selected
> select subtract #1
Nothing selected
> ui mousemode right clip
> select #1/C:91
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/C:91-97
42 atoms, 41 bonds, 7 residues, 1 model selected
> select add #3
12456 atoms, 12765 bonds, 1582 residues, 2 models selected
> select add #1
24828 atoms, 25448 bonds, 5 pseudobonds, 3150 residues, 3 models selected
> select subtract #1
12414 atoms, 12724 bonds, 1575 residues, 1 model selected
Alignment identifier is 3/A
Alignment identifier is 3/B
Alignment identifier is 3/C
> select #3/C:91-92
12 atoms, 11 bonds, 2 residues, 1 model selected
> select #3/C:91-97
42 atoms, 41 bonds, 7 residues, 1 model selected
> select #3/C:91-92
12 atoms, 11 bonds, 2 residues, 1 model selected
> select #3/C:91-100
68 atoms, 69 bonds, 10 residues, 1 model selected
> select #3/C:78
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/C:78-100
157 atoms, 161 bonds, 23 residues, 1 model selected
> select #3/C:80
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #3/C:80-100
141 atoms, 144 bonds, 21 residues, 1 model selected
> close #3
> open
> /Users/pryor/Documents/AlphaFold_Files/fold_kin_20c_lin42b_1xmyrf_1_482_atp_prelimdna/fold_kin_20c_lin42b_1xmyrf_1_482_atp_prelimdna_model_0.cif
Chain information for
fold_kin_20c_lin42b_1xmyrf_1_482_atp_prelimdna_model_0.cif #3
---
Chain | Description
A | .
B | .
C | .
E | .
F | .
> open
> /Users/pryor/Documents/AlphaFold_Files/fold_kin_20c_lin42b_1xmyrf_1_482_atp_prelimdna/fold_kin_20c_lin42b_1xmyrf_1_482_atp_prelimdna_model_1.cif
Chain information for
fold_kin_20c_lin42b_1xmyrf_1_482_atp_prelimdna_model_1.cif #5
---
Chain | Description
A | .
B | .
C | .
E | .
F | .
> hide #5 models
> select add #3
13974 atoms, 14472 bonds, 1651 residues, 1 model selected
> hide sel atoms
> show sel cartoons
Computing secondary structure
> color sel bychain
> select ligand
124 atoms, 132 bonds, 4 residues, 4 models selected
> show sel & #3 atoms
> select add #5
14067 atoms, 14571 bonds, 1654 residues, 4 models selected
> select subtract #5
93 atoms, 99 bonds, 3 residues, 3 models selected
> select add #3
14036 atoms, 14538 bonds, 1653 residues, 3 models selected
> select subtract #3
62 atoms, 66 bonds, 2 residues, 2 models selected
> select add #2
15973 atoms, 16353 bonds, 2025 residues, 2 models selected
> select subtract #2
31 atoms, 33 bonds, 1 residue, 1 model selected
> select add #1
12414 atoms, 12724 bonds, 5 pseudobonds, 1575 residues, 2 models selected
> select subtract #1
Nothing selected
> ui tool show "AlphaFold Error Plot"
Must choose path to predicted aligned file
> alphafold pae #3 file
> /Users/pryor/Documents/AlphaFold_Files/fold_kin_20c_lin42b_1xmyrf_1_482_atp_prelimdna/fold_kin_20c_lin42b_1xmyrf_1_482_atp_prelimdna_full_data_0.json
> color #3/B:488-526 lime
> color #3/C:242-431 magenta
> color #3/B:454-478 lime
> color #3/C:245-431 magenta
> color #3/B:495-526 lime
> color #3/C:242-431 magenta
> color bfactor #3 palette alphafold
13974 atoms, 1651 residues, atom bfactor range 13.3 to 94.5
> alphafold pae #3 colorDomains true
> select add #3
13974 atoms, 14472 bonds, 1651 residues, 1 model selected
> show sel surfaces
> color sel bychain
> ui mousemode right clip
> hide sel surfaces
> show sel surfaces
> hide sel surfaces
> ui mousemode right select
> select clear
> select #3/A
3991 atoms, 4099 bonds, 495 residues, 1 model selected
> hide sel cartoons
> select add #3
13974 atoms, 14472 bonds, 1651 residues, 2 models selected
> show sel surfaces
> hide sel surfaces
> select subtract #3
5 models selected
> select add #3.2
4594 atoms, 597 residues, 1 model selected
> select add #3.3
8392 atoms, 1079 residues, 2 models selected
> show sel surfaces
> hide sel surfaces
> show sel surfaces
> color #3/B:497-524 lime
> color #3/C:242-424 magenta
> select clear
> select add #3.2
4594 atoms, 597 residues, 1 model selected
> select add #3.3
8392 atoms, 1079 residues, 2 models selected
> hide sel surfaces
> color #3/B:493-524 lime
> color #3/C:245-424 magenta
> select clear
> hide #!3 models
> show #2 models
> select add #2
15942 atoms, 16320 bonds, 2024 residues, 1 model selected
> color sel bychain
> show sel surfaces
> hide #2.1 models
> select clear
> hide #2.2 models
> show #2.2 models
> hide #2.3 models
> hide #2.2 models
> show #2.2 models
> show #2.1 models
> hide #2.1 models
> show #2.3 models
> hide #2.3 models
> show #2.3 models
> hide #2.3 models
> hide #2.2 models
> show #2.2 models
> show #2.3 models
> hide #2.3 models
> show #2.3 models
> hide #!2 models
> show #!3 models
> select add #3
13974 atoms, 14472 bonds, 1651 residues, 1 model selected
> show sel surfaces
> hide #3.5 models
> hide #3.4 models
> hide #3.1 models
> select subtract #3.1
9983 atoms, 10373 bonds, 1156 residues, 6 models selected
> select add #3.1
13974 atoms, 10373 bonds, 1651 residues, 5 models selected
> select subtract #3.2
9380 atoms, 5662 bonds, 1054 residues, 6 models selected
> select add #3.2
13974 atoms, 5662 bonds, 1651 residues, 5 models selected
> hide #3.2 models
> hide #3.3 models
> color #3/B:452-481 lime
> color #3/C:239-421 magenta
> show #3.3 models
> color #3/B:397-426 lime
> color #3/C:242-431 magenta
> show #3.1 models
> hide #3.1 models
> hide #3.3 models
> show #3.1 models
> hide #3.1 models
> show #3.1 models
> hide #3.1 models
> show #3.2 models
> hide #3.2 models
> show #3.3 models
> show #3.1 models
> select subtract #3.1
9983 atoms, 5662 bonds, 1156 residues, 6 models selected
> color sel bychain
> select clear
> ui mousemode right clip
> color bfactor #3 palette alphafold
13974 atoms, 1651 residues, 5 surfaces, atom bfactor range 13.3 to 94.5
> undo
> color bfactor #3 palette alphafold
13974 atoms, 1651 residues, 5 surfaces, atom bfactor range 13.3 to 94.5
> undo
> color #3/B:402-521 lime
> color #3/C:242-424 magenta
> select add #3
13974 atoms, 14472 bonds, 1651 residues, 3 models selected
> color sel bychain
> ui mousemode right select
> select clear
> ui mousemode right clip
> select add #3
13974 atoms, 14472 bonds, 1651 residues, 3 models selected
Alignment identifier is 3/A
Alignment identifier is 3/B
Alignment identifier is 3/C
Alignment identifier is 3/E
Alignment identifier is 3/F
> select #3/C:35
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #3/C:35-45
72 atoms, 72 bonds, 11 residues, 1 model selected
> select #3/A:305-306
18 atoms, 18 bonds, 2 residues, 1 model selected
> select #3/A:305-308
37 atoms, 37 bonds, 4 residues, 1 model selected
> select #3/A:306
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #3/A:306-308
29 atoms, 29 bonds, 3 residues, 1 model selected
> select #3/C:35
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #3/C:35-45
72 atoms, 72 bonds, 11 residues, 1 model selected
> save /Users/pryor/DNA_complex_1xMYRF_wireLIN42.jpg width 899 height 768
> supersample 3
> save /Users/pryor/Desktop/DNA_complex_1xMYRF_wireLIN42.jpg width 899 height
> 768 supersample 3
> color bfactor #3 palette alphafold
13974 atoms, 1651 residues, 5 surfaces, atom bfactor range 13.3 to 94.5
> save /Users/pryor/Desktop/DNA_complex_1xMYRF_wireLIN42_PAE.jpg width 899
> height 768 supersample 3
> show #3.2 models
> undo
> show #3.2 models
> hide #3.2 models
> color bfactor #3 palette alphafold
13974 atoms, 1651 residues, 5 surfaces, atom bfactor range 13.3 to 94.5
> show #3.2 models
> hide #3.2 models
> undo
> show #3.2 models
> hide #3.2 models
> color bfactor #3 palette alphafold
13974 atoms, 1651 residues, 5 surfaces, atom bfactor range 13.3 to 94.5
> undo
> color #3/B:398-476 lime
> color #3/E:1
> #3/D:1@O3G,PB,O1B,O2B,O3B,PA,O1A,O2A,O3A,O5',C5',C4',O4',C3',O3',C2',O2',C1',N9,C8,N7,C5,C6,N6,N1,C2,N3,C4
> magenta
> color #3/C:19-41 lime
> color #3/E:1
> #3/D:1@O3G,PB,O1B,O2B,O3B,PA,O1A,O2A,O3A,O5',C5',C4',O4',C3',O3',C2',O2',C1',N9,C8,N7,C5,C6,N6,N1,C2,N3,C4
> magenta
> hide #!3.1 models
> show #3.1 models
> hide #!3.3 models
> show #3.3 models
> hide #3.1 models
> show #3.2 models
> hide #3.2 models
> show #3.2 models
> hide #3.2 models
> show #3.2 models
> hide #3.2 models
> hide #!3.3 models
> color #3/B:395-524 lime
> color #3/C:236-427 magenta
> show #3.1 models
> select add #3.1
4063 atoms, 72 bonds, 506 residues, 2 models selected
> show sel cartoons
> hide sel surfaces
> ui mousemode right select
> select clear
> hide #3.1 models
> show #3.1 models
> hide #3.1 models
> select add #3.1
3991 atoms, 495 residues, 1 model selected
> hide sel cartoons
> show sel cartoons
> color #3/A:135-482 lime
> color #3/B:388-523 magenta
> color #3/A:132-476 lime
> color #3/C:236-427 magenta
> color #3/A:140-484 lime
> color #3/C:13-45 magenta
> color #3/B:398-529 lime
> color #3/C:240-431 magenta
> hide sel cartoons
> show #3.2 models
> show #3.3 models
> hide #3.2 models
> select subtract #3.1
1 model selected
> select add #3.1
3991 atoms, 495 residues, 1 model selected
> show sel surfaces
> show sel cartoons
> hide sel surfaces
> select add #3.3
7789 atoms, 977 residues, 2 models selected
> select subtract #3.1
3798 atoms, 482 residues, 3 models selected
> hide sel surfaces
> select clear
> color #3/C:16-38 lime
> color #3/A:183-473 magenta
> select add #3.2
4594 atoms, 597 residues, 1 model selected
> hide sel cartoons
> hide #!3 models
> select add #3
13974 atoms, 14472 bonds, 1651 residues, 2 models selected
> select subtract #3
5 models selected
> show #5 models
> select add #5
13974 atoms, 14472 bonds, 1651 residues, 1 model selected
> color sel bychain
> hide sel atoms
> show sel cartoons
Computing secondary structure
> select ligand
124 atoms, 132 bonds, 4 residues, 4 models selected
> show sel & #5 atoms
> select add #3
14067 atoms, 14571 bonds, 1654 residues, 4 models selected
> select subtract #3
93 atoms, 99 bonds, 3 residues, 8 models selected
> select add #2
16004 atoms, 16386 bonds, 2026 residues, 3 models selected
> select subtract #2
62 atoms, 66 bonds, 2 residues, 5 models selected
> select add #1
12445 atoms, 12757 bonds, 5 pseudobonds, 1576 residues, 3 models selected
> select subtract #1
31 atoms, 33 bonds, 1 residue, 1 model selected
> select add #5
13974 atoms, 14472 bonds, 1651 residues, 1 model selected
> select subtract #5
Nothing selected
> select add #5
13974 atoms, 14472 bonds, 1651 residues, 1 model selected
> show sel surfaces
> hide #5.2 models
> hide #5.4 models
> hide #5.5 models
> select clear
> hide #5.1 models
> select add #5.1
3991 atoms, 495 residues, 1 model selected
> hide sel cartoons
> select add #5.3
7789 atoms, 977 residues, 2 models selected
> hide sel surfaces
> hide sel cartoons
> select add #5.4
8571 atoms, 1015 residues, 3 models selected
> select add #5.5
9349 atoms, 1053 residues, 4 models selected
> hide sel cartoons
> select clear
Drag select of 31 atoms, 61 residues, 33 bonds
Drag select of 11 residues
Drag select of 31 atoms, 51 residues, 33 bonds
Drag select of 11 residues
Drag select of 31 atoms, 52 residues, 33 bonds
Drag select of 11 residues
Drag select of 5 residues
Drag select of 8 residues
> select add #5/B:407
446 atoms, 40 bonds, 51 residues, 2 models selected
> select add #5/B:411
455 atoms, 48 bonds, 52 residues, 2 models selected
> select add #5/B:413
462 atoms, 54 bonds, 53 residues, 2 models selected
> select add #5/B:417
470 atoms, 61 bonds, 54 residues, 2 models selected
> select add #5/B:464
484 atoms, 76 bonds, 55 residues, 2 models selected
> select add #5/B:462
492 atoms, 83 bonds, 56 residues, 2 models selected
> select add #5/B:461
501 atoms, 91 bonds, 57 residues, 2 models selected
> select add #5/B:459
510 atoms, 99 bonds, 58 residues, 2 models selected
> save /Users/pryor/Desktop/SYQ_LT.jpg width 899 height 768 supersample 3
> show #5.1 models
> show #5.2 models
> hide #5.2 models
> show sel cartoons
> select add #5.1
4501 atoms, 99 bonds, 553 residues, 2 models selected
> select add #5.3
8299 atoms, 99 bonds, 1035 residues, 3 models selected
> show sel cartoons
> select subtract #5.2
7820 atoms, 33 bonds, 978 residues, 4 models selected
> select subtract #5.1
3829 atoms, 33 bonds, 483 residues, 3 models selected
> hide sel cartoons
> alphafold contacts #1
Structure fold_kin_20c_lin_42b_myrf_1_482_atp_model_2.cif #1 does not have PAE
data opened
> alphafold contacts #5
Structure fold_kin_20c_lin42b_1xmyrf_1_482_atp_prelimdna_model_1.cif #5 does
not have PAE data opened
> alphafold contacts #5
Structure fold_kin_20c_lin42b_1xmyrf_1_482_atp_prelimdna_model_1.cif #5 does
not have PAE data opened
> alphafold contacts
Missing or invalid "atoms" argument: empty atom specifier
> alphafold contacts #5/A
Structure fold_kin_20c_lin42b_1xmyrf_1_482_atp_prelimdna_model_1.cif #5 does
not have PAE data opened
> hide #!5 models
> show #!3 models
> hide #!3 models
> show #!5 models
> select add #5
13974 atoms, 14472 bonds, 1651 residues, 2 models selected
Alignment identifier is 5/A
Alignment identifier is 5/B
Alignment identifier is 5/C
Alignment identifier is 5/E
Alignment identifier is 5/F
> select #5/B:399
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/B:399-473
632 atoms, 648 bonds, 75 residues, 1 model selected
Unsupported scale factor (0.000000) detected on Display0
> open
> /Users/pryor/Documents/AlphaFold_Files/fold_kin_20c_lin42b_3xmyrf_1_482_atp_prelimdna/fold_kin_20c_lin42b_3xmyrf_1_482_atp_prelimdna_model_0.cif
Chain information for
fold_kin_20c_lin42b_3xmyrf_1_482_atp_prelimdna_model_0.cif #6
---
Chain | Description
A | .
B | .
C D E | .
G | .
H | .
> hide #!5 models
> select add #5
13974 atoms, 14472 bonds, 1651 residues, 2 models selected
> select subtract #5
5 models selected
> select add #6
21570 atoms, 22234 bonds, 2615 residues, 1 model selected
> show sel cartoons
Computing secondary structure
> style sel stick
Changed 21570 atom styles
> hide sel atoms
> select ligand
155 atoms, 165 bonds, 5 residues, 5 models selected
> show sel & #6 atoms
Drag select of 23 residues
> select clear
> select add #6
21570 atoms, 22234 bonds, 2615 residues, 1 model selected
> color sel bychain
> select clear
> select add #6
21570 atoms, 22234 bonds, 2615 residues, 1 model selected
> show sel surfaces
> hide #6.1 models
> hide #6.2 models
> hide #6.5 models
> hide #6.6 models
> show #6.5 models
> hide #6.7 models
> select clear
> select add #6.3
3798 atoms, 482 residues, 1 model selected
> select add #6.4
7596 atoms, 964 residues, 2 models selected
> select add #6.5
11394 atoms, 1446 residues, 3 models selected
> show #6.1 models
> hide #!6 models
> open
> /Users/pryor/Documents/AlphaFold_Files/fold_kin_20c_lin42b_1xmyrf_1_482_atp_prelimdna/fold_kin_20c_lin42b_1xmyrf_1_482_atp_prelimdna_model_2.cif
Chain information for
fold_kin_20c_lin42b_1xmyrf_1_482_atp_prelimdna_model_2.cif #7
---
Chain | Description
A | .
B | .
C | .
E | .
F | .
> select add #6
21570 atoms, 22234 bonds, 2615 residues, 4 models selected
> select subtract #6
7 models selected
> select add #7
13974 atoms, 14472 bonds, 1651 residues, 1 model selected
> show sel cartoons
Computing secondary structure
> hide sel atoms
> color sel bychain
> show sel surfaces
> hide #!7 models
> show #!3 models
> hide #!3 models
> show #!5 models
> show #5.4 models
> hide #5.4 models
> hide #!5 models
> show #!7 models
> close #7
> open
> /Users/pryor/Documents/AlphaFold_Files/fold_kin_20c_lin42b_1xmyrf_1_482_atp_prelimdna/fold_kin_20c_lin42b_1xmyrf_1_482_atp_prelimdna_model_3.cif
Chain information for
fold_kin_20c_lin42b_1xmyrf_1_482_atp_prelimdna_model_3.cif #7
---
Chain | Description
A | .
B | .
C | .
E | .
F | .
> select add #7
13974 atoms, 14472 bonds, 1651 residues, 1 model selected
> show sel cartoons
Computing secondary structure
> hide sel atoms
> color sel bychain
> show sel surfaces
> hide sel surfaces
> show sel surfaces
> hide sel surfaces
> close #7
> open
> /Users/pryor/Documents/AlphaFold_Files/fold_kin_20c_lin42b_1xmyrf_1_482_atp_prelimdna/fold_kin_20c_lin42b_1xmyrf_1_482_atp_prelimdna_model_4.cif
Chain information for
fold_kin_20c_lin42b_1xmyrf_1_482_atp_prelimdna_model_4.cif #7
---
Chain | Description
A | .
B | .
C | .
E | .
F | .
> select add #7
13974 atoms, 14472 bonds, 1651 residues, 1 model selected
> hide sel cartoons
> show sel cartoons
Computing secondary structure
> hide sel atoms
> show sel surfaces
> color sel bychain
> hide #!7 models
QPainter::begin: Paint device returned engine == 0, type: 2
===== 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
OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M3
OpenGL vendor: Apple
Python: 3.11.4
Locale: 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: Mac15,3
Model Number: Z1C80001DLL/A
Chip: Apple M3
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 11881.61.3
OS Loader Version: 10151.140.19.700.2
Software:
System Software Overview:
System Version: macOS 14.7.2 (23H311)
Kernel Version: Darwin 23.6.0
Time since boot: 19 days, 22 hours, 44 minutes
Graphics/Displays:
Apple M3:
Chipset Model: Apple M3
Type: GPU
Bus: Built-In
Total Number of Cores: 10
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
LG TV SSCR2:
Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
UI Looks like: 1920 x 1080 @ 30.00Hz
Main Display: Yes
Mirror: On
Mirror Status: Master Mirror
Online: Yes
Rotation: Supported
Television: Yes
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Mirror: On
Mirror Status: Hardware Mirror
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
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
Change History (2)
comment:1 by , 9 months ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash on Mac waking from sleep |
comment:2 by , 9 months ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | assigned → closed |
Note:
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Appears Qt was doing a window resize. This is not the usual crash stack trace and did not show the message about this being a Qt multi-display crash. It may be the a crash related to the same problem. But this one is in
QMacCGContext::QMacCGContext(QPainter*)
when it crashes. There more than 100 previous crash reports with this call, most of them in QTabBar:paintEvent().