![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 11 months ago
Closed 11 months ago
#16482 closed defect (duplicate)
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-15.1.1-arm64-arm-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 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 0x00000001f2ef7840 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 315 in event_loop
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1003 in init
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1166 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, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, 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.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, PIL._imagingmath, chimerax.atom_search.ast, chimerax.chem_group._chem_group, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets (total: 58)
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{
"uptime" : 520000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "Mac15,6",
"coalitionID" : 63254,
"osVersion" : {
"train" : "macOS 15.1.1",
"build" : "24B91",
"releaseType" : "User"
},
"captureTime" : "2024-12-16 15:07:35.8320 -0800",
"codeSigningMonitor" : 1,
"incident" : "3D43577B-1EEC-4620-B536-1DB71A76DB3B",
"pid" : 81040,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-12-11 14:51:10.9764 -0800",
"procStartAbsTime" : 8872545059915,
"procExitAbsTime" : 12535118597553,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.8.0","CFBundleVersion":"1.8.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"4BAEC3FB-9ECE-59E7-B6C0-BE1E86EAE642","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "09A485D4-C95A-39C6-48C9-D9A6A1D170E1",
"lowPowerMode" : 1,
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRcuD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkWfg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"bootSessionUUID" : "A59E0546-C07F-498B-A5F1-57077A708681",
"wakeTime" : 7275,
"sleepWakeUUID" : "FD4FB97A-8C73-492F-80E8-82A2B499336C",
"sip" : "enabled",
"vmRegionInfo" : "0x6388d0307e98 is not in any region. Bytes after previous region: 3882922049177 \n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n MALLOC_NANO 6000a0000000-6000c0000000 [512.0M] rw-\/rwx SM=PRV \n---> \n UNUSED SPACE AT END",
"exception" : {"codes":"0x0000000000000001, 0x0000e388d0307e98","rawCodes":[1,250176747896472],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000e388d0307e98 -> 0x00006388d0307e98 (possible pointer authentication failure)"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":81040},
"vmregioninfo" : "0x6388d0307e98 is not in any region. Bytes after previous region: 3882922049177 \n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n MALLOC_NANO 6000a0000000-6000c0000000 [512.0M] rw-\/rwx SM=PRV \n---> \n UNUSED SPACE AT END",
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"faultingThread" : 0,
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===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/vickiebowcut/Library/CloudStorage/OneDrive-
> Personal/Desktop/Shokat Lab/Crystallography/20241024_Beamline/Final
> Structures/Rac1b_G12C_GDC-6036/001_rac1b_g12c_GDC_refine_119.pdb"
Chain information for 001_rac1b_g12c_GDC_refine_119.pdb #1
---
Chain | Description
A | No description available
B | No description available
10 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> select /B
2332 atoms, 2354 bonds, 2 pseudobonds, 156 residues, 2 models selected
> delete atoms (#!1 & sel)
> delete bonds (#!1 & sel)
Drag select of 91 atoms, 84 bonds
> delete atoms sel
> delete bonds sel
> color #1 #8d8dffff
> set bgColor white
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> select ::name="LNK"
76 atoms, 80 bonds, 1 residue, 1 model selected
> color sel magenta
> select ::name="001"::name="HOH"::name="LNK"::name="MG"
304 atoms, 122 bonds, 190 residues, 1 model selected
> color sel byhetero
> select sel @ select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
76 atoms, 80 bonds, 1 residue, 1 model selected
> select sel @ color sel byhetero
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
76 atoms, 80 bonds, 1 residue, 1 model selected
> ui tool show H-Bonds
> hbonds sel color #19cb10 dashes 6 showDist true twoColors true slopColor
> #e9e54e reveal true retainCurrent true
7 hydrogen bonds found
1 strict hydrogen bonds found
> ui tool show Contacts
> contacts sel overlapCutoff -0.1 resSeparation 5 ignoreHiddenModels true
> color #020402
26 contacts
> select sel @ ui tool show Matchmaker
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> select ::name="LNK"
76 atoms, 80 bonds, 1 residue, 1 model selected
> ui tool show H-Bonds
> hbonds sel color #19cb10 dashes 6 showDist true twoColors true slopColor
> #e9e54e reveal true retainCurrent true
7 hydrogen bonds found
1 strict hydrogen bonds found
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> open "/Users/vickiebowcut/Library/CloudStorage/OneDrive-
> Personal/Desktop/Shokat Lab/Crystallography/20241024_Beamline/Final
> Structures/KRas_G12C_GDC6036_refine23 (4).pdb"
Chain information for KRas_G12C_GDC6036_refine23 (4).pdb #2
---
Chain | Description
A | No description available
21 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> ui tool show Matchmaker
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> matchmaker #!2 to #1
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 001_rac1b_g12c_GDC_refine_119.pdb, chain A (#1) with
KRas_G12C_GDC6036_refine23 (4).pdb, chain A (#2), sequence alignment score =
307.7
RMSD between 117 pruned atom pairs is 0.839 angstroms; (across all 163 pairs:
2.578)
> hide #!1 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
76 atoms, 80 bonds, 1 residue, 1 model selected
> ui tool show H-Bonds
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> hbonds sel color #19cb10 dashes 6 showDist true twoColors true slopColor
> #e9e54e reveal true retainCurrent true
11 hydrogen bonds found
6 strict hydrogen bonds found
> hbonds sel color #19cb10 dashes 6 showDist true twoColors true slopColor
> #e9e54e reveal true retainCurrent true
11 hydrogen bonds found
6 strict hydrogen bonds found
> ui tool show Contacts
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> contacts sel overlapCutoff -0.1 resSeparation 5 ignoreHiddenModels true
> color #020402
18 contacts
> select clear
> lighting simple
> lighting soft
> lighting full
> lighting simple
> ui tool show "Side View"
> lighting simple
> lighting soft
> lighting simple
> color #2 #19cb10ff
> color #2 #71ff4fff
> color #2 #70fb4eff
> color #2 #c9f5c9ff
> color #2 #8ae68bff
> select ::name="GE4"
76 atoms, 80 bonds, 1 residue, 1 model selected
> color sel dark gray
> select
> ::name="001"::name="GDP"::name="GE4"::name="HOH"::name="LNK"::name="MG"
483 atoms, 242 bonds, 20 pseudobonds, 257 residues, 7 models selected
> color sel & #!2 byhetero
> color #3.1 #0c7d0bff models
> color #3 #0c7d0bff models
> color #4 black models
> ui tool show H-Bonds
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> hbonds sel color #d72600 dashes 6 showDist true twoColors true slopColor
> #e9e54e reveal true retainCurrent true
837 hydrogen bonds found
566 strict hydrogen bonds found
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
76 atoms, 80 bonds, 1 residue, 1 model selected
> ui tool show H-Bonds
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> hbonds sel color #d72600 dashes 6 showDist true twoColors true slopColor
> #e9e54e reveal true retainCurrent true
11 hydrogen bonds found
6 strict hydrogen bonds found
> hbonds sel color #d72600 dashes 6 showDist true twoColors true slopColor
> #e9e54e reveal true retainCurrent true
11 hydrogen bonds found
6 strict hydrogen bonds found
> hbonds sel color #cf2600 twoColors true slopColor #ffc900 reveal true
11 hydrogen bonds found
6 strict hydrogen bonds found
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> select sel @ color sel & #!2 byhetero
> select clear
> ui tool show Contacts
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> ui tool show Contacts
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> show #!1 models
> hide #!2 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
76 atoms, 80 bonds, 1 residue, 1 model selected
> ui tool show H-Bonds
> hbonds sel color #cf2600 twoColors true slopColor #ffc900 reveal true
11 hydrogen bonds found
2 strict hydrogen bonds found
> hbonds sel color #cf2600 twoColors true slopColor #ffc900 reveal true
11 hydrogen bonds found
2 strict hydrogen bonds found
> select clear
> hide #1.3 models
> hide #1.1 models
> show #1.1 models
> hide #1.1 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> hide #3 models
> ui mousemode right distance
> distance #1/A:65@OD1 #1/C:301@C7
Distance between 001_rac1b_g12c_GDC_refine_119.pdb #1/A ASP 65 OD1 and /C LNK
301 C7: 3.034Å
> ui mousemode right distance
> distance #1/A:85@HG1 #1/C:301@C6
Distance between 001_rac1b_g12c_GDC_refine_119.pdb #1/A THR 85 HG1 and /C LNK
301 C6: 3.649Å
> ui mousemode right distance
> distance #1/C:301@O1 #1/A:115@HZ3
Distance between 001_rac1b_g12c_GDC_refine_119.pdb #1/C LNK 301 O1 and /A LYS
115 HZ3: 2.326Å
> color #5 #19cb10ff models
> color #5 #0c7d0bff models
> color #5.1 black models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> select #1/C:301@C29
1 atom, 1 residue, 1 model selected
> ui mousemode right distance
> distance #1/C:301@C25 #1/A:92@CD
Distance between 001_rac1b_g12c_GDC_refine_119.pdb #1/C LNK 301 C25 and /A PRO
92 CD: 3.466Å
> ui mousemode right distance
> distance #1/A:123@HE2 #1/C:301@N7
Distance between 001_rac1b_g12c_GDC_refine_119.pdb #1/A HIS 123 HE2 and /C LNK
301 N7: 4.096Å
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> ui mousemode right distance
> distance #1/C:301@N6 #1/A:89@HZ1
Distance between 001_rac1b_g12c_GDC_refine_119.pdb #1/C LNK 301 N6 and /A LYS
89 HZ1: 4.973Å
> ui mousemode right distance
> distance #1/A:86@HG #1/C:301@C25
Distance between 001_rac1b_g12c_GDC_refine_119.pdb #1/A SER 86 HG and /C LNK
301 C25: 3.525Å
> color #3 black models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> color #5 #0c7d0bff models
> hide #4 models
> show #4 models
> hide #3 models
> show #3 models
> show #1.3 models
> hide #1.3 models
> show #1.3 models
> hide #1.3 models
> color #5 black models
> color #3 #0c7d0bff models
> color #3 black models
> color #1.3 #0c7d0bff models
> color #4 #0c7d0bff models
> show #1.3 models
> hide #1.3 models
> show #1.3 models
> hide #1.3 models
> color #5 #0c7d0bff models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #5.1 models
> show #5.1 models
> hide #5.1 models
> show #5.1 models
> color #5.1 black models
> hide #5.1 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> ~distance #1/C:301@O1 #1/A:115@HZ3
> select clear
> show #5.1 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> ui mousemode right distance
> distance #1/A:119@OE1 #1/C:301@F4
Distance between 001_rac1b_g12c_GDC_refine_119.pdb #1/A GLU 119 OE1 and /C LNK
301 F4: 5.138Å
> ui mousemode right distance
> distance #1/C:301@C27 #1/A:92@CD
Distance between 001_rac1b_g12c_GDC_refine_119.pdb #1/C LNK 301 C27 and /A PRO
92 CD: 3.259Å
> ui mousemode right distance
> distance #1/A:86@HG #1/C:301@C27
Distance between 001_rac1b_g12c_GDC_refine_119.pdb #1/A SER 86 HG and /C LNK
301 C27: 4.154Å
Unsupported scale factor (0.000000) detected on Display0
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> ui tool show "Dock Prep"
Populating font family aliases took 167 ms. Replace uses of missing font
family "Times" with one that exists to avoid this cost.
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> select #1/A:123@HD1
1 atom, 1 residue, 1 model selected
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> select #1/A:122
17 atoms, 17 bonds, 1 residue, 1 model selected
> select #1/A:123@HD1
1 atom, 1 residue, 1 model selected
> distance #1/C:301@C25 #1/A:123@HD1
Distance between 001_rac1b_g12c_GDC_refine_119.pdb #1/C LNK 301 C25 and /A HIS
123 HD1: 5.512Å
> ~distance #1/C:301@C25 #1/A:123@HD1
> ui mousemode right select
> select #1/A:123@HD1
1 atom, 1 residue, 1 model selected
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> select #1/A:123@HD1
1 atom, 1 residue, 1 model selected
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> delete bonds sel
> select #1/A:123@HD1
1 atom, 1 residue, 1 model selected
> select #1/A:123@HD1
1 atom, 1 residue, 1 model selected
> select #1/A:123@HD1
1 atom, 1 residue, 1 model selected
> select #1/A:123@HD1
1 atom, 1 residue, 1 model selected
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> select #1/A:123@HD1
1 atom, 1 residue, 1 model selected
> select #1/A:123@HD1
1 atom, 1 residue, 1 model selected
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> select #1/A:123@HD1
1 atom, 1 residue, 1 model selected
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> select #1/A:123
18 atoms, 17 bonds, 1 residue, 1 model selected
> select clear
> select #1/A:123@HD1
1 atom, 1 residue, 1 model selected
> select #1/A:123@HD1
1 atom, 1 residue, 1 model selected
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> select #1/A:123@HD1
1 atom, 1 residue, 1 model selected
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> hide sel atoms
> show #!2 models
> hide #!1 models
> hide #!2 models
> show #!1 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> ui tool show "Build Structure"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> select #1/C:301@H29
1 atom, 1 residue, 1 model selected
> select #1/C:301@C25
1 atom, 1 residue, 1 model selected
> build start fragment #1 imidazole
> select #1/het:1@C2
1 atom, 1 residue, 1 model selected
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> select #1/het:1@C2
1 atom, 1 residue, 1 model selected
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> select #1/het:1@C2
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 9 bonds, 1 residue, 1 model selected
> select down
1 bond, 1 model selected
> select down
1 bond, 1 model selected
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
9 atoms, 9 bonds, 1 residue, 1 model selected
> select #1/C:301@C25
1 atom, 1 residue, 1 model selected
> select #1/het:1@C3
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 9 bonds, 1 residue, 1 model selected
> select up
3183 atoms, 3032 bonds, 381 residues, 1 model selected
> select down
9 atoms, 9 bonds, 1 residue, 1 model selected
> select #1/het:1@C3
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 9 bonds, 1 residue, 1 model selected
> select down
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 9 bonds, 1 residue, 1 model selected
> select #1/het:1@C3
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 9 bonds, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> select #1/C:301@N7
1 atom, 1 residue, 1 model selected
> select up
76 atoms, 80 bonds, 1 residue, 1 model selected
> select down
1 atom, 1 residue, 1 model selected
> select #1/C:301@N7
1 atom, 1 residue, 1 model selected
> select #1/C:301@N7
1 atom, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> build start fragment #1 imidazole
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
9 atoms, 9 bonds, 1 residue, 1 model selected
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
9 atoms, 9 bonds, 1 residue, 1 model selected
> select down
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
9 atoms, 9 bonds, 1 residue, 1 model selected
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> delete atoms sel
> delete bonds sel
> select #1/C:301@C24
1 atom, 1 residue, 1 model selected
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> open /Users/vickiebowcut/Downloads/pdb_extract_coord_706356.cif
Summary of feedback from opening
/Users/vickiebowcut/Downloads/pdb_extract_coord_706356.cif
---
warnings | Unknown polymer entity '1' on line 168
Unknown polymer entity '2' on line 3038
Unable to fetch template for 'lnk': will connect using distance criteria
Atom H1 is not in the residue template for 001 /D:201
Atom H1 is not in the residue template for 001 /C:201
Missing or incomplete sequence information. Inferred polymer connectivity.
Chain information for pdb_extract_coord_706356.cif #6
---
Chain | Description
A | No description available
B | No description available
10 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> select add #6
5633 atoms, 5499 bonds, 3 pseudobonds, 550 residues, 3 models selected
> select add #1
8804 atoms, 8518 bonds, 42 pseudobonds, 930 residues, 7 models selected
> select subtract #1
5633 atoms, 5498 bonds, 3 pseudobonds, 550 residues, 2 models selected
> hide #5.1 models
> hide #!5 models
> hide #4 models
> hide #3 models
> hide #!1 models
> select #6/B:167
15 atoms, 14 bonds, 1 residue, 1 model selected
> select up
171 atoms, 172 bonds, 11 residues, 1 model selected
> select up
1617 atoms, 1634 bonds, 105 residues, 1 model selected
> select up
1641 atoms, 1657 bonds, 107 residues, 1 model selected
> select up
1911 atoms, 1931 bonds, 126 residues, 1 model selected
> select up
1976 atoms, 1997 bonds, 131 residues, 1 model selected
> select up
2332 atoms, 2354 bonds, 156 residues, 1 model selected
> select up
5633 atoms, 5498 bonds, 550 residues, 1 model selected
> select down
2332 atoms, 2354 bonds, 156 residues, 1 model selected
> delete atoms sel
> delete bonds sel
Drag select of 74 atoms, 68 bonds
Drag select of 90 atoms, 84 bonds
Drag select of 91 atoms, 84 bonds
> delete atoms sel
> delete bonds sel
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> select #6/A:123
18 atoms, 18 bonds, 1 residue, 1 model selected
> select up
149 atoms, 154 bonds, 8 residues, 1 model selected
> select up
1782 atoms, 1800 bonds, 115 residues, 1 model selected
> select #6/A:98
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #6/C:301@C1
1 atom, 1 residue, 1 model selected
> select up
76 atoms, 80 bonds, 1 residue, 1 model selected
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> select ~sel & ##selected
3097 atoms, 2943 bonds, 1 pseudobond, 378 residues, 2 models selected
> delete atoms (#!6 & sel)
> delete bonds (#!6 & sel)
> select #6/C:301@C25
1 atom, 1 residue, 1 model selected
> build start fragment #6 imidazole
> select clear
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
9 atoms, 9 bonds, 1 residue, 1 model selected
> select #6/het:1@C1
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 9 bonds, 1 residue, 1 model selected
> select up
85 atoms, 89 bonds, 2 residues, 1 model selected
> select down
9 atoms, 9 bonds, 1 residue, 1 model selected
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
9 atoms, 9 bonds, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> select #6/C:301@N7
1 atom, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> select #6/C:301@C24
1 atom, 1 residue, 1 model selected
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> build modify #6/C:301@C24 C 4 geometry tetrahedral resName UNL
> undo
> select #6/C:301@C24
1 atom, 1 residue, 1 model selected
> select #6/C:301@C24
1 atom, 1 residue, 1 model selected
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> build start fragment #6 imidazole
> select #6/het:1@C2
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 9 bonds, 1 residue, 1 model selected
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
9 atoms, 9 bonds, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> build start fragment #6 imidazole
> select #6/het:1@C2
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 9 bonds, 1 residue, 1 model selected
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
9 atoms, 9 bonds, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> open
> C=CC(N(CC1)C[C@H](C)N1C2=NC(OC[C@H]3N(C)CCC3)=NC4=C(F)C(C5=NC(N)=C6C(N=CN6)=C5C(F)(F)F)=C(Cl)C=C42)=O
> fromDatabase smiles
Translated SMILES to 3D structure via NCI web service (SMILES:
C=CC(N(CC1)C[C@H](C)N1C2=NC(OC[C@H]3N(C)CCC3)=NC4=C(F)C(C5=NC(N)=C6C(N=CN6)=C5C(F)(F)F)=C(Cl)C=C42)=O)
> ui tool show Matchmaker
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> matchmaker #7 to #6
No matrix compatible with both reference structure and all match structures
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
75 atoms, 80 bonds, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> select clear
> hide #!6 models
> show #!6 models
> select #6/C:301@C24
1 atom, 1 residue, 1 model selected
> select #6/C:301@C24
1 atom, 1 residue, 1 model selected
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
You must select exactly one atom to modify.
> select #6/C:301@C24
1 atom, 1 residue, 1 model selected
> select #6/C:301@C24
1 atom, 1 residue, 1 model selected
> select clear
> select #6/C:301@C24
1 atom, 1 residue, 1 model selected
> select #6/C:301@C24
1 atom, 1 residue, 1 model selected
> select #6/C:301@C24
1 atom, 1 residue, 1 model selected
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> select down
1 bond, 1 model selected
> select down
1 bond, 1 model selected
> select #6/C:301@C25
1 atom, 1 residue, 1 model selected
> build modify #6/C:301@C25 C 4 geometry tetrahedral connectBack false
> select #6/C:301@C25
1 atom, 1 residue, 1 model selected
> select #6/C:301@C25
1 atom, 1 residue, 1 model selected
> select #6/C:301@C25
1 atom, 1 residue, 1 model selected
You must select exactly one atom to modify.
> select #6/C:301@C25
1 atom, 1 residue, 1 model selected
> select #6/C:301@C25
1 atom, 1 residue, 1 model selected
You must select exactly one atom to modify.
> build start fragment #6 imidazole
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
9 atoms, 9 bonds, 1 residue, 1 model selected
> select clear
> select #6/het:1@C1
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 9 bonds, 1 residue, 1 model selected
> select up
85 atoms, 89 bonds, 2 residues, 1 model selected
> select down
9 atoms, 9 bonds, 1 residue, 1 model selected
> select #6/het:1@C1
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 9 bonds, 1 residue, 1 model selected
> toolshed show
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> select #6/het:1@C3
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 9 bonds, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> bond sel
Must specify two or more atoms
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> open "/Users/vickiebowcut/Library/CloudStorage/OneDrive-
> Personal/Desktop/Shokat Lab/Inventories/Drug_Inventory/001C7.pdb"
Summary of feedback from opening
/Users/vickiebowcut/Library/CloudStorage/OneDrive-Personal/Desktop/Shokat
Lab/Inventories/Drug_Inventory/001C7.pdb
---
warnings | Ignored bad PDB record found on line 2
ATOM 1 H6 001C7 A 1 -2.476 -2.618 2.527 1.00 20.00 H
Ignored bad PDB record found on line 3
ATOM 2 H7 001C7 A 1 -2.127 -4.140 2.339 1.00 20.00 H
Ignored bad PDB record found on line 4
ATOM 3 H29 001C7 A 1 -3.176 6.677 2.041 1.00 20.00 H
Ignored bad PDB record found on line 5
ATOM 4 C4 001C7 A 1 -2.307 -3.311 1.865 1.00 20.00 C
Ignored bad PDB record found on line 6
ATOM 5 H28 001C7 A 1 -2.962 8.135 1.652 1.00 20.00 H
72 messages similar to the above omitted
> open "/Users/vickiebowcut/Library/CloudStorage/OneDrive-
> Personal/Desktop/Shokat Lab/Inventories/Drug_Inventory/001C7.pdb"
Summary of feedback from opening
/Users/vickiebowcut/Library/CloudStorage/OneDrive-Personal/Desktop/Shokat
Lab/Inventories/Drug_Inventory/001C7.pdb
---
warnings | Ignored bad PDB record found on line 2
ATOM 1 H6 001C7 A 1 -2.476 -2.618 2.527 1.00 20.00 H
Ignored bad PDB record found on line 3
ATOM 2 H7 001C7 A 1 -2.127 -4.140 2.339 1.00 20.00 H
Ignored bad PDB record found on line 4
ATOM 3 H29 001C7 A 1 -3.176 6.677 2.041 1.00 20.00 H
Ignored bad PDB record found on line 5
ATOM 4 C4 001C7 A 1 -2.307 -3.311 1.865 1.00 20.00 C
Ignored bad PDB record found on line 6
ATOM 5 H28 001C7 A 1 -2.962 8.135 1.652 1.00 20.00 H
72 messages similar to the above omitted
> open "/Users/vickiebowcut/Library/CloudStorage/OneDrive-
> Personal/Desktop/Shokat Lab/Inventories/Drug_Inventory/001C7.pdb"
Summary of feedback from opening
/Users/vickiebowcut/Library/CloudStorage/OneDrive-Personal/Desktop/Shokat
Lab/Inventories/Drug_Inventory/001C7.pdb
---
warnings | Ignored bad PDB record found on line 2
ATOM 1 H6 001C7 A 1 -2.476 -2.618 2.527 1.00 20.00 H
Ignored bad PDB record found on line 3
ATOM 2 H7 001C7 A 1 -2.127 -4.140 2.339 1.00 20.00 H
Ignored bad PDB record found on line 4
ATOM 3 H29 001C7 A 1 -3.176 6.677 2.041 1.00 20.00 H
Ignored bad PDB record found on line 5
ATOM 4 C4 001C7 A 1 -2.307 -3.311 1.865 1.00 20.00 C
Ignored bad PDB record found on line 6
ATOM 5 H28 001C7 A 1 -2.962 8.135 1.652 1.00 20.00 H
72 messages similar to the above omitted
> open "/Users/vickiebowcut/Library/CloudStorage/OneDrive-
> Personal/Desktop/Shokat Lab/Inventories/Drug_Inventory/001C7.pdb"
Summary of feedback from opening
/Users/vickiebowcut/Library/CloudStorage/OneDrive-Personal/Desktop/Shokat
Lab/Inventories/Drug_Inventory/001C7.pdb
---
warnings | Ignored bad PDB record found on line 2
ATOM 1 H6 001C7 A 1 -2.476 -2.618 2.527 1.00 20.00 H
Ignored bad PDB record found on line 3
ATOM 2 H7 001C7 A 1 -2.127 -4.140 2.339 1.00 20.00 H
Ignored bad PDB record found on line 4
ATOM 3 H29 001C7 A 1 -3.176 6.677 2.041 1.00 20.00 H
Ignored bad PDB record found on line 5
ATOM 4 C4 001C7 A 1 -2.307 -3.311 1.865 1.00 20.00 C
Ignored bad PDB record found on line 6
ATOM 5 H28 001C7 A 1 -2.962 8.135 1.652 1.00 20.00 H
72 messages similar to the above omitted
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> open "/Users/vickiebowcut/Library/CloudStorage/OneDrive-
> Personal/Desktop/Shokat Lab/Inventories/Drug_Inventory/001C7.pdb"
Summary of feedback from opening
/Users/vickiebowcut/Library/CloudStorage/OneDrive-Personal/Desktop/Shokat
Lab/Inventories/Drug_Inventory/001C7.pdb
---
warnings | Ignored bad PDB record found on line 2
ATOM 1 H6 001C7 A 1 -2.476 -2.618 2.527 1.00 20.00 H
Ignored bad PDB record found on line 3
ATOM 2 H7 001C7 A 1 -2.127 -4.140 2.339 1.00 20.00 H
Ignored bad PDB record found on line 4
ATOM 3 H29 001C7 A 1 -3.176 6.677 2.041 1.00 20.00 H
Ignored bad PDB record found on line 5
ATOM 4 C4 001C7 A 1 -2.307 -3.311 1.865 1.00 20.00 C
Ignored bad PDB record found on line 6
ATOM 5 H28 001C7 A 1 -2.962 8.135 1.652 1.00 20.00 H
72 messages similar to the above omitted
> open "/Users/vickiebowcut/Library/CloudStorage/OneDrive-
> Personal/Desktop/Shokat Lab/Inventories/Drug_Inventory/001C7.cif"
Summary of feedback from opening
/Users/vickiebowcut/Library/CloudStorage/OneDrive-Personal/Desktop/Shokat
Lab/Inventories/Drug_Inventory/001C7.cif
---
warnings | Skipping chem_comp category: Missing column 'type' on line 12
No mmCIF models found.
> select clear
> open "/Users/vickiebowcut/Library/CloudStorage/OneDrive-
> Personal/Desktop/Shokat Lab/Inventories/Drug_Inventory/001C7.pdb"
Summary of feedback from opening
/Users/vickiebowcut/Library/CloudStorage/OneDrive-Personal/Desktop/Shokat
Lab/Inventories/Drug_Inventory/001C7.pdb
---
warnings | Ignored bad PDB record found on line 2
ATOM 1 H28 001C7 A 1 2.755 7.535 3.647 1.00 20.00 H
Ignored bad PDB record found on line 3
ATOM 2 H29 001C7 A 1 1.530 6.637 3.528 1.00 20.00 H
Ignored bad PDB record found on line 4
ATOM 3 N7 001C7 A 1 2.364 6.820 3.312 1.00 20.00 N
Ignored bad PDB record found on line 5
ATOM 4 H31 001C7 A 1 5.183 7.965 2.899 1.00 20.00 H
Ignored bad PDB record found on line 6
ATOM 5 C21 001C7 A 1 3.039 6.023 2.480 1.00 20.00 C
72 messages similar to the above omitted
> ui tool show "Build Structure"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> open
> O=C(CC)N(CC1)C[C@H](C)N1C2=NC(OC[C@H]3N(C)CCC3)=NC4=C(F)C(C5=NC(N)=C6C(N=CN6)=C5C(F)(F)F)=C(Cl)C=C42
> fromDatabase smiles
Translated SMILES to 3D structure via NCI web service (SMILES:
O=C(CC)N(CC1)C[C@H](C)N1C2=NC(OC[C@H]3N(C)CCC3)=NC4=C(F)C(C5=NC(N)=C6C(N=CN6)=C5C(F)(F)F)=C(Cl)C=C42)
> ui tool show Matchmaker
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
77 atoms, 82 bonds, 1 residue, 1 model selected
> ui tool show Matchmaker
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> matchmaker #7 to #1/A pairing bs
Reference and/or match model contains no nucleic or amino acid chains.
Use the command-line 'align' command to superimpose small molecules/ligands.
> align
Missing or invalid "atoms" argument: empty atom specifier
> select add #6
153 atoms, 162 bonds, 2 residues, 2 models selected
> select subtract #6
77 atoms, 82 bonds, 1 residue, 1 model selected
> select add #6
153 atoms, 162 bonds, 2 residues, 2 models selected
> select subtract #7
76 atoms, 80 bonds, 1 residue, 1 model selected
> select add #7
153 atoms, 162 bonds, 2 residues, 2 models selected
> select subtract #7
76 atoms, 80 bonds, 1 residue, 1 model selected
> select add #7
153 atoms, 162 bonds, 2 residues, 2 models selected
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> rename #6 GDC-6036.cif
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> rename #7 001_C7
> align 001_C7 toAtoms GDC-6036
Missing or invalid "atoms" argument: invalid atoms specifier
> hide #!6 models
> show #!6 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
77 atoms, 82 bonds, 1 residue, 1 model selected
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> align ULN 1 toAtoms ULN
Missing or invalid "atoms" argument: invalid atoms specifier
> align ULN 1 matchatoms ULN
Missing or invalid "atoms" argument: invalid atoms specifier
> select add #6
153 atoms, 162 bonds, 2 residues, 2 models selected
> align ULN 1 matchatoms ULN
Missing or invalid "atoms" argument: invalid atoms specifier
> align UNL 1 matchatoms UNL
Missing or invalid "atoms" argument: invalid atoms specifier
> align UNL 1 toAtoms UNL
Missing or invalid "atoms" argument: invalid atoms specifier
> align #7/? UNL 1 toAtoms #6/C UNL
Expected a keyword
> align #7/? UNL 1 toAtoms #6/C UNL 301
Expected a keyword
> align #7:UNL 1@C1-22 toAtoms #6: UNL 301 @C1-22
Expected a keyword
> align #7:UNL 1@C1-22 toAtoms #6: UNL 301@C1-22
Expected a keyword
> align #7:UNL 1@C1-22 toAtoms #6: UNL@C1-22
Expected a keyword
> align #7:UNL 1@C1-22 to #6: UNL@C1-22
Expected a keyword
> align #7:UNL 1 to #6: UNL
Expected a keyword
> align 001_C7 to GDC-6036
Missing or invalid "atoms" argument: invalid atoms specifier
> align #1:UNL 1@C1,C2,C3 to #2:UNL@C1,C2,C3
Expected a keyword
> align #7:UNL 1@C1,C2,C3 to #6:UNL@C1,C2,C3
Expected a keyword
> align #7:UNL@C1,C2,C3 toAtoms #6:UNL@C1,C2,C3
RMSD between 3 atom pairs is 0.529 angstroms
> align #7:UNL@C1-C20 to #6:UNL@C1-C20
Missing or invalid "atoms" argument: only initial part "#7:UNL@C1" of atom
specifier valid
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/vickiebowcut/Library/CloudStorage/OneDrive-
> Personal/Desktop/Shokat
> Lab/Crystallography/20241024_Beamline/Processing/Jay_process/Rac1b G12C GDC
> Process/Refine_119/001_rac1b_g12c_GDC_refine_119.pdb" format pdb
Chain information for 001_rac1b_g12c_GDC_refine_119.pdb #1
---
Chain | Description
A | No description available
B | No description available
10 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> select /B
2332 atoms, 2354 bonds, 2 pseudobonds, 156 residues, 2 models selected
> delete atoms (#!1 & sel)
> delete bonds (#!1 & sel)
> select clear
Drag select of 90 atoms, 84 bonds
> delete atoms sel
> delete bonds sel
> select /C:301@C10
1 atom, 1 residue, 1 model selected
> select up
76 atoms, 80 bonds, 1 residue, 1 model selected
> select up
116 atoms, 122 bonds, 2 residues, 1 model selected
> select down
76 atoms, 80 bonds, 1 residue, 1 model selected
> color sel hot pink
> color sel byhetero
> ui tool show "Build Structure"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> open
> O=C(CC)N(CC1)C[C@H](C)N1C2=NC(OC[C@H]3N(C)CCC3)=NC4=C(F)C(C5=NC(N)=C6C(N=CN6)=C5C(F)(F)F)=C(Cl)C=C42
> fromDatabase smiles
Translated SMILES to 3D structure via NCI web service (SMILES:
O=C(CC)N(CC1)C[C@H](C)N1C2=NC(OC[C@H]3N(C)CCC3)=NC4=C(F)C(C5=NC(N)=C6C(N=CN6)=C5C(F)(F)F)=C(Cl)C=C42)
> select #2/?:1@C19
1 atom, 1 residue, 1 model selected
> select #2/?:1@C18
1 atom, 1 residue, 1 model selected
> select #1/A:107
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #2/?:1@C18
1 atom, 1 residue, 1 model selected
> select #1/C:301@C1
1 atom, 1 residue, 1 model selected
> select #2/?:1@C18
1 atom, 1 residue, 1 model selected
> align #1:UNL@C18,C17,C9 toAtoms #2:UNL@C1,C2,C10
Unequal number of atoms to pair, 0 and 3
> align #2:UNL@C18,C17,C10 toAtoms #1:LNK@C1,C2,C3
RMSD between 3 atom pairs is 0.019 angstroms
> align #2:UNL@C18,C17,C10,C11,C3 toAtoms #1:LNK@C1,C2,C3,C4,C16
RMSD between 5 atom pairs is 0.863 angstroms
> align #2:UNL@C18,C17,C10,C11,C3,C12 toAtoms #1:LNK@C1,C2,C3,C4,C16,C5
RMSD between 6 atom pairs is 1.130 angstroms
> align #2:UNL@C18,C17,C10,C11,C3,C12,O2 toAtoms #1:LNK@C1,C2,C3,C4,C16,C5,O1
RMSD between 7 atom pairs is 1.149 angstroms
> align #2:UNL@C18,C17,C10,C11,C3,C12,O2,C7 toAtoms
> #1:LNK@C1,C2,C3,C4,C16,C5,O1,C11
RMSD between 8 atom pairs is 1.316 angstroms
> align #2:UNL@C18,C17,C10,C11,C3,C12,O2,C7,C8 toAtoms
> #1:LNK@C1,C2,C3,C4,C16,C5,O1,C11,C12
RMSD between 9 atom pairs is 1.478 angstroms
> align #2:UNL@C18,C17,C10,C11,C3,C12,O2,C7,C8,C4 toAtoms
> #1:LNK@C1,C2,C3,C4,C16,C5,O1,C11,C12,C13
RMSD between 10 atom pairs is 1.438 angstroms
> align #2:UNL@C18,C17,C10,C11,C3,C12,O2,C7,C8,C4,N1 toAtoms
> #1:LNK@C1,C2,C3,C4,C16,C5,O1,C11,C12,C13,N5
RMSD between 11 atom pairs is 1.386 angstroms
> align #2:UNL@C18,C17,C10,C11,C3,C12,O2,C7,C8,C4,N1,C26 toAtoms
> #1:LNK@C1,C2,C3,C4,C16,C5,O1,C11,C12,C13,N5,C29
RMSD between 12 atom pairs is 1.401 angstroms
> align #2:UNL@C18,C17,C10,C11,C3,C12,O2,C7,C8,C4,N1,C26,C22 toAtoms
> #1:LNK@C1,C2,C3,C4,C16,C5,O1,C11,C12,C13,N5,C29,C25
RMSD between 13 atom pairs is 1.355 angstroms
> align #2:UNL@C18,C17,C10,C11,C3,C12,O2,C7,C8,C4,N1,C26,C22,C13 toAtoms
> #1:LNK@C1,C2,C3,C4,C16,C5,O1,C11,C12,C13,N5,C29,C25,C6
Unequal number of atoms to pair, 14 and 15
> align #2:UNL@C18,C17,C10,C11,C3,C12,O2,C7,C8,C4,N1,C26,C22,C13,N4 toAtoms
> #1:LNK@C1,C2,C3,C4,C16,C5,O1,C11,C12,C13,N5,C29,C25,N2
Unequal number of atoms to pair, 15 and 14
> ui mousemode right distance
> distance #2/?:1@N9 #1/A:123@CD2
Distance between
smiles:O=C(CC)N(CC1)C[C@H](C)N1C2=NC(OC[C@H]3N(C)CCC3)=NC4=C(F)C(C5=NC(N)=C6C(N=CN6)=C5C(F)(F)F)=C(Cl)C=C42
#2/? UNL 1 N9 and 001_rac1b_g12c_GDC_refine_119.pdb #1/A HIS 123 CD2: 2.983Å
OpenGL version: 4.1 Metal - 89.3
OpenGL renderer: Apple M3 Pro
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac15,6
Model Number: Z1AV001HXLL/A
Chip: Apple M3 Pro
Total Number of Cores: 12 (6 performance and 6 efficiency)
Memory: 36 GB
System Firmware Version: 11881.41.5
OS Loader Version: 11881.41.5
Software:
System Software Overview:
System Version: macOS 15.1.1 (24B91)
Kernel Version: Darwin 24.1.0
Time since boot: 10 days, 19 hours, 2 minutes
Graphics/Displays:
Apple M3 Pro:
Chipset Model: Apple M3 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 18
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
DELL P2417H:
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: 0.7.16
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
Babel: 2.15.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.17
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.7
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.57.1
ChimeraX-AtomicLibrary: 14.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.6
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.7
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: 2.2.4
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: 1.8
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.4
ChimeraX-DiffPlot: 1.0
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: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.10
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.2
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: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.1
ChimeraX-MedicalToolbar: 1.0.3
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.17
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-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.5
ChimeraX-PDB: 2.7.5
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: 1.1.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.4.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.0.15
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.5
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: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.39.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.3
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: 1.2.1
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.4
fonttools: 4.53.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.11.0
html2text: 2024.2.26
idna: 3.7
ihm: 1.0
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.3
jedi: 0.19.1
jinja2: 3.1.4
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.11
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.2.1
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.4
matplotlib-inline: 0.1.7
msgpack: 1.0.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.0
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: 10.3.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.2
prompt-toolkit: 3.0.47
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.1.2
pyproject-hooks: 1.1.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.3
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.3
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 26.0.3
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.13.0
setuptools: 69.5.1
setuptools-scm: 8.0.4
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.1
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4.1
traitlets: 5.14.2
typing-extensions: 4.12.2
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.11
Change History (2)
comment:1 by , 11 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 , 11 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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