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Opened 16 months ago
Closed 16 months ago
#15473 closed defect (can't reproduce)
Crash during screen removal
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| 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-14.0-arm64-arm-64bit
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 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 0x00000001e5f1d300 (most recent call first):
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/save_command/dialog.py", line 39 in display
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/save_command/dialog.py", line 127 in show_save_file_dialog
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/save_command/dialog.py", line 116 in
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 275 in event_loop
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 892 in init
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 1043 in
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 197 in _run_module_as_main
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{
"uptime" : 350000,
"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro17,1",
"coalitionID" : 5493,
"osVersion" : {
"train" : "macOS 14.0",
"build" : "23A344",
"releaseType" : "User"
},
"captureTime" : "2024-06-20 17:54:40.8986 -0600",
"codeSigningMonitor" : 1,
"incident" : "BB1B339C-26A5-4E2F-80DB-0F8DA0EDE983",
"pid" : 50887,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-06-19 13:25:34.2006 -0600",
"procStartAbsTime" : 7517059129763,
"procExitAbsTime" : 8617906560807,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.6.1.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.6.1","CFBundleVersion":"1.6.1.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"137D9DDF-D96F-5056-A285-A44D230577EE","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "43CEB50D-8E40-87B1-DC8B-A0FC95EA9B4F",
"lowPowerMode" : 1,
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRXOD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkVHg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"wakeTime" : 7923,
"sleepWakeUUID" : "DB1733C3-DC2F-4A31-86AB-5D426728D378",
"sip" : "enabled",
"vmRegionInfo" : "0x24 is not in any region. Bytes before following region: 105556874362844\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n MALLOC_NANO 6000e0000000-600100000000 [512.0M] rw-\/rwx SM=PRV ",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000024","rawCodes":[1,36],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000024"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":50887},
"ktriageinfo" : "VM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\n",
"vmregioninfo" : "0x24 is not in any region. Bytes before following region: 105556874362844\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n MALLOC_NANO 6000e0000000-600100000000 [512.0M] rw-\/rwx SM=PRV ",
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"faultingThread" : 0,
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===== Log before crash start =====
Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration-
> complex/paper.drafts/integration_paper_2/draft_20240525/supp.figure/SX.Ecoli.Cas12/ecoli-1E-pseudomonas-1F-comparison.cxs
> format session
opened ChimeraX session
> show #!2 models
> show #!5 models
> show #!6 models
> show #!7 models
> hide #!6 models
> hide #!5 models
> hide #!7 models
> select add #2
69728 atoms, 71070 bonds, 231 pseudobonds, 5105 residues, 4 models selected
> select subtract #2
15523 atoms, 16255 bonds, 231 pseudobonds, 1657 residues, 3 models selected
> select add #7
15523 atoms, 16255 bonds, 231 pseudobonds, 1657 residues, 3 models selected
> select subtract #7
Nothing selected
> tile
2 models tiled
> select add #2
54205 atoms, 54815 bonds, 3448 residues, 1 model selected
> show #!7 models
> select subtract #2
6 models selected
> open 7ei1
Summary of feedback from opening 7ei1 fetched from pdb
---
warnings | Atom H1 is not in the residue template for MET /Q:1
Atom H1 is not in the residue template for MET /R:1
Atom H1 is not in the residue template for MET /S:1
Atom H1 is not in the residue template for MET /T:1
Atom H1 is not in the residue template for MET /U:1
3 messages similar to the above omitted
note | Fetching compressed mmCIF 7ei1 from
http://files.rcsb.org/download/7ei1.cif
7ei1 title:
Structure of Pyrococcus furiosus Cas1Cas2 complex [more info...]
Chain information for 7ei1 #3
---
Chain | Description | UniProt
A B C D E F G H I J K L M N O P | CRISPR-associated endonuclease Cas1 |
I6TWX9_9EURY 1-322
Q R S T U V W X | CRISPR-associated endoribonuclease Cas2 | I6V1H0_9EURY 1-85
7ei1 mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
3| author_defined_assembly
4| author_defined_assembly
> sym #3 assembly 1
Made 1 copies for 7ei1 assembly 1
> view
> ~tile
> hide #!7 models
> mmaker #4.1 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 4p6i, chain D (#1) with 7ei1, chain A (#4.1), sequence alignment
score = 297.5
RMSD between 119 pruned atom pairs is 1.271 angstroms; (across all 266 pairs:
7.050)
> mmaker #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 4p6i, chain F (#1) with apo-Refinement17-chains-corrected-
renamed.cif, chain E (#2), sequence alignment score = 422.2
RMSD between 135 pruned atom pairs is 1.201 angstroms; (across all 266 pairs:
5.970)
> hide #!2 models
> select add #1
9925 atoms, 10115 bonds, 3 pseudobonds, 1291 residues, 2 models selected
> show #!3 models
> close #3
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.99255,-0.015265,-0.12088,186.71,0.1034,0.4193,-0.90194,163.19,0.064453,-0.90772,-0.4146,268.65
> view matrix models
> #1,-0.98859,-0.093934,-0.11774,192.31,0.071497,0.39536,-0.91574,166,0.13257,-0.91371,-0.38414,266.82
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.98859,-0.093934,-0.11774,188.56,0.071497,0.39536,-0.91574,175.47,0.13257,-0.91371,-0.38414,268.41
> mmaker #4 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 4p6i, chain D (#1) with 7ei1, chain A (#4.1), sequence alignment
score = 297.5
RMSD between 119 pruned atom pairs is 1.271 angstroms; (across all 266 pairs:
7.050)
> view matrix models
> #1,-0.98859,-0.093934,-0.11774,261.89,0.071497,0.39536,-0.91574,158.38,0.13257,-0.91371,-0.38414,338.97
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.008205,0.96713,0.25413,152.5,0.39377,-0.23673,0.8882,160.99,0.91917,0.092782,-0.38277,246.06
> view matrix models
> #1,0.22181,0.93253,0.28493,149.21,0.55141,-0.36096,0.7521,168.93,0.8042,-0.0097089,-0.59428,260.57
> view matrix models
> #1,0.23316,0.9639,0.12855,149.73,0.53241,-0.23715,0.81259,159.14,0.81375,-0.12102,-0.56848,267.97
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.23316,0.9639,0.12855,70.434,0.53241,-0.23715,0.81259,180.55,0.81375,-0.12102,-0.56848,206.48
> view matrix models
> #1,0.23316,0.9639,0.12855,121.24,0.53241,-0.23715,0.81259,132.74,0.81375,-0.12102,-0.56848,92.59
> view matrix models
> #1,0.23316,0.9639,0.12855,63.006,0.53241,-0.23715,0.81259,184.48,0.81375,-0.12102,-0.56848,205.37
> show #!5 models
> show #!6 models
> show sel cartoons
> show sel atoms
> show sel surfaces
> select add #5
17017 atoms, 17386 bonds, 3 pseudobonds, 2179 residues, 9 models selected
> select add #6
24109 atoms, 24657 bonds, 3 pseudobonds, 3067 residues, 11 models selected
> select subtract #1
14184 atoms, 14542 bonds, 1776 residues, 10 models selected
> color (#!5-6 & sel) #758ec4ff
> hide sel surfaces
> hide sel atoms
> select subtract #5
7092 atoms, 7271 bonds, 888 residues, 3 models selected
> select subtract #6
1 model selected
> hide #!5 models
> hide #!6 models
> hide #!4 models
> hide #!4.1 models
> select #1/A
792 atoms, 807 bonds, 101 residues, 1 model selected
> select #1/A-B
1547 atoms, 1576 bonds, 198 residues, 1 model selected
> show sel atoms
> show sel cartoons
> show sel surfaces
> color (#!1 & sel) #ce9bc2ff
> select #1/D-F
6298 atoms, 6419 bonds, 3 pseudobonds, 823 residues, 2 models selected
> select #1/D,F
4319 atoms, 4405 bonds, 2 pseudobonds, 564 residues, 2 models selected
> color (#!1 & sel) #c0b59dff
> select #1/C,E
4059 atoms, 4134 bonds, 1 pseudobond, 529 residues, 2 models selected
> color (#!1 & sel) #98877cff
> select add #1
9925 atoms, 10115 bonds, 3 pseudobonds, 1291 residues, 4 models selected
> select subtract #1
6 models selected
> show #!2 models
> hide #!1 models
> color #2/a:1-94/b:1-94 #d799c4
> color #2/a:95-end/b:95-end #6d8fc9
> color #2/f,e #c2b59bff
> color #2/c,d #9c857a
> show #!1 models
> show #!4 models
> hide #!2 models
> hide #!1 models
> hide #!4 models
> show #!4 models
> show #!4.1 models
> select /4.1/R,Q
Expected an objects specifier or a keyword
> select #4.1/R,Q
2814 atoms, 2836 bonds, 168 residues, 1 model selected
> color sel #ffffffff
> color sel #ce9bc2ff
> select #4.1/A,I
10039 atoms, 10146 bonds, 2 pseudobonds, 623 residues, 2 models selected
> color (#!4.1 & sel) #c0b59dff
> select #4.1/B,J
9865 atoms, 9969 bonds, 4 pseudobonds, 615 residues, 2 models selected
> color (#!4.1 & sel) #98877cff
> select add #4.1
22718 atoms, 22951 bonds, 6 pseudobonds, 1406 residues, 2 models selected
> select add #4
22718 atoms, 22951 bonds, 6 pseudobonds, 1406 residues, 3 models selected
> select subtract #4
Nothing selected
> select add #4.1
22718 atoms, 22951 bonds, 6 pseudobonds, 1406 residues, 2 models selected
> select add #4
22718 atoms, 22951 bonds, 6 pseudobonds, 1406 residues, 3 models selected
> select subtract #4.1
1 model selected
> select add #4
22718 atoms, 22951 bonds, 6 pseudobonds, 1406 residues, 3 models selected
> select subtract #4
Nothing selected
> show #!1 models
> show #!2 models
> hide #!2 models
> mmaker #4/Q,R to #1/A,B
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 4p6i, chain A (#1) with 7ei1, chain Q (#4.1), sequence alignment
score = 82.8
RMSD between 46 pruned atom pairs is 0.841 angstroms; (across all 78 pairs:
13.045)
> hide #!1#!4.1 surfaces
> tile
2 models tiled
> ~tile tile
> tile off tile
Expected a models specifier or a keyword
> ~tile
> mmaker #4/Q,R to #1/A,B
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 4p6i, chain A (#1) with 7ei1, chain Q (#4.1), sequence alignment
score = 82.8
RMSD between 46 pruned atom pairs is 0.841 angstroms; (across all 78 pairs:
13.045)
> mmaker #2/A,B:1-100 to #1/A,B
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 4p6i, chain A (#1) with apo-Refinement17-chains-corrected-
renamed.cif, chain A (#2), sequence alignment score = 63.8
RMSD between 41 pruned atom pairs is 1.076 angstroms; (across all 80 pairs:
7.338)
> show #!2 models
> hide #!1-2#!4.1 surfaces
> hide #!1-2#!4.1 atoms
> preset cartoons/nucleotides cylinders/stubs
Using preset: Cartoons/Nucleotides / Cylinders/Stubs
Changed 102371 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh tube rad 2 sides 24 thick 0.6
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides stubs
> tile
3 models tiled
> undo
> lighting flat
> lighting soft
> lighting shadows true intensity 0.5
> lighting flat
> lighting soft
> tile
3 models tiled
> undo
> ui tool show "Side View"
> ui tool show "Show Sequence Viewer"
> ui tool show "Modeller Comparative"
> ui tool show "Show Sequence Viewer"
> sequence chain #1/A #1/B #7/E #7/F
Alignment identifier is 1
> sequence chain #1/C #1/D #1/E #1/F #7/A #7/B #7/C #7/D
Alignment identifier is 2
> sequence chain #2/A #2/B
Alignment identifier is 3
> sequence chain #2/C #2/D #2/E #2/F
Alignment identifier is 4
> sequence chain #4.1/A #4.1/B #4.1/I #4.1/J
Alignment identifier is 5
> sequence chain #4.1/Q #4.1/R
Alignment identifier is 6
> hide #!1 models
> hide #!4 models
> show #!1 models
> show #!4 models
> hide #!1 models
> hide #!2 models
> select #4/Q,R:16,18,19,22
169 atoms, 163 bonds, 8 residues, 1 model selected
> show #!2 models
> show #!1 models
> select add #1
10094 atoms, 10278 bonds, 3 pseudobonds, 1299 residues, 3 models selected
> select add #2
64299 atoms, 65093 bonds, 3 pseudobonds, 4747 residues, 10 models selected
> select add #4
86848 atoms, 87881 bonds, 9 pseudobonds, 6145 residues, 18 models selected
> show sel surfaces
> hide sel cartoons
> transparency (#!1-2#!4.1 & sel) 10
> transparency (#!1-2#!4.1 & sel) 90
> select subtract #1
76923 atoms, 77766 bonds, 6 pseudobonds, 4854 residues, 22 models selected
> select subtract #2
22718 atoms, 22951 bonds, 6 pseudobonds, 1406 residues, 15 models selected
> select subtract #4
6 models selected
> hide #!2 models
> hide #!1 models
> select #4/Q,R:16,18,19,22
169 atoms, 163 bonds, 8 residues, 1 model selected
> color (#!4.1 & sel) black
> transparency (#!4.1 & sel) 0
> select #4/B,J:192,269,273
136 atoms, 130 bonds, 6 residues, 1 model selected
> color (#!4.1 & sel) black
> transparency (#!4.1 & sel) 0
> select #4/I,A:45,54,68,79
144 atoms, 142 bonds, 8 residues, 1 model selected
> select #4/I,A:45,54
64 atoms, 64 bonds, 4 residues, 1 model selected
> select #4/I,A:45,54,68,79
144 atoms, 142 bonds, 8 residues, 1 model selected
> select #4/B,J:45,54,68,79
144 atoms, 142 bonds, 8 residues, 1 model selected
> select #4/I,A:45,54,68,79
144 atoms, 142 bonds, 8 residues, 1 model selected
> select #4/B,J,I,A:45,54,68,79
288 atoms, 284 bonds, 16 residues, 1 model selected
> select add #4
22718 atoms, 22951 bonds, 6 pseudobonds, 1406 residues, 7 models selected
> select subtract #4
6 models selected
> show #!2 models
> show #!1 models
> hide #!2 models
> hide #!4 models
> select #1/A-B:77,16,78 #1/F,D:41,66 #1/E,C:59,248,245,163,84
220 atoms, 202 bonds, 20 residues, 1 model selected
> color (#!1 & sel) black
> transparency (#!1 & sel) 0
> select add #1
9925 atoms, 10115 bonds, 3 pseudobonds, 1291 residues, 8 models selected
> select subtract #1
6 models selected
> show #!4 models
> hide #!1 models
> select #4/B,J,I,A:45,54,68,79
288 atoms, 284 bonds, 16 residues, 1 model selected
> select add #4
22718 atoms, 22951 bonds, 6 pseudobonds, 1406 residues, 7 models selected
> select subtract #4
6 models selected
> show #!1 models
> hide #!4 models
> show #!2 models
> hide #!1 models
> select #2/G:93,94,99, 91,95,92 #2/H:11,18 #2/A:67,27,32
62 atoms, 59 bonds, 3 residues, 1 model selected
> select #2/A,B:93,94,99, 91,95,92 #2/A,B:11,18 #2/E,F:67,27,32
406 atoms, 392 bonds, 22 residues, 1 model selected
> color (#!2 & sel) black
> transparency (#!2 & sel) 0
> hide #!2 models
> select add #2
54205 atoms, 54815 bonds, 3448 residues, 5 models selected
> select subtract #2
6 models selected
> show #!1 models
> show #!2 models
> show #!4 models
> tile
3 models tiled
> undo
> hide #!2 models
> hide #!4 models
> show #!2 models
> hide #!1 models
> show #!4 models
> hide #!4 models
> select #2/D:1-7
98 atoms, 98 bonds, 7 residues, 1 model selected
> hide sel surfaces
> save /Users/whenriques/wiedenheft/projects/1-f-integration-
> complex/paper.drafts/integration_paper_2/draft_20240525/main.figures/figure1/comparative.cas12.across.systems/chimera.pngs/IF-
> pseudomonas.png width 864 height 670 supersample 3 transparentBackground
> true
> show #!1 models
> hide #!2 models
> save /Users/whenriques/wiedenheft/projects/1-f-integration-
> complex/paper.drafts/integration_paper_2/draft_20240525/main.figures/figure1/comparative.cas12.across.systems/chimera.pngs/IE-
> ecoli.png width 864 height 670 supersample 3 transparentBackground true
> hide #!1 models
> show #!4 models
> save /Users/whenriques/wiedenheft/projects/1-f-integration-
> complex/paper.drafts/integration_paper_2/draft_20240525/main.figures/figure1/comparative.cas12.across.systems/chimera.pngs/IA-
> IG-IIIB-pfuriosis.png width 864 height 670 supersample 3
> transparentBackground true
> show #!7 models
> show #!6 models
> hide #!6 models
> hide #!7 models
> show #!2 models
> hide #!4 models
> save /Users/whenriques/wiedenheft/projects/1-f-integration-
> complex/paper.drafts/integration_paper_2/draft_20240525/main.figures/figure1/comparative.cas12.across.systems/chimera.pngs/dna-
> binding-comparison.cxs includeMaps true
> close session
> open /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration-
> complex/cryoem/cas1-2-3-prespacer-bound/phenix/J1222-local-
> refine/RealSpaceRefine_2/trimmed-8flj-
> AFCas3_real_space_refined_001-coot-0-cas23-joined-chains-
> renamed_real_space_refined_002.pdb
Chain information for trimmed-8flj-
AFCas3_real_space_refined_001-coot-0-cas23-joined-chains-
renamed_real_space_refined_002.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
E | No description available
G | No description available
H | No description available
> color #2/g,h #f69320ff
> color #1,2,3/a:1-94/b:1-94 #d799c4
> color #1,2,3/a:95-end/b:95-end #6d8fc9ff
> color #1,2,3/f,e #c2b59bff
> color #1,2,3/c,d #9c857a
> color #1/g:1-27/h:1-27 #f69320ff
> color #1/g:28-end/h:28-56 #92278f
> color #1/i/h:57-end #939598
> color #1/m,k #d91b5d
> color #1/l,j #a51e23
> color #1/g:1-27/h:1-27 #f69320ff
> set bgColor white
> lighting soft
> select /C
4188 atoms, 4233 bonds, 303 residues, 1 model selected
> show sel surfaces
> select /G
854 atoms, 922 bonds, 27 residues, 1 model selected
> style sel stick
Changed 854 atom styles
> select add #1
21746 atoms, 22179 bonds, 1844 residues, 1 model selected
> select subtract #1
1 model selected
> select /E
4942 atoms, 4994 bonds, 315 residues, 1 model selected
> show sel surfaces
> hbonds sel reveal true
261 hydrogen bonds found
> hbonds sel reveal true
261 hydrogen bonds found
> select add #1
21746 atoms, 22179 bonds, 261 pseudobonds, 1844 residues, 3 models selected
> select subtract #1
2 models selected
> select add #1
21746 atoms, 22179 bonds, 261 pseudobonds, 1844 residues, 2 models selected
> select subtract #1
2 models selected
> hbonds reveal true
1456 hydrogen bonds found
> coulombic
The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:
/C LEU 149
/C GLU 150
/C ASP 151
/C ARG 152
/C VAL 153
/C LEU 154
/C ARG 155
/C ASP 156
/C PHE 159
/C VAL 161
/C ASP 162
/C THR 164
/C LEU 166
/C VAL 168
/C VAL 170
/C GLU 171
/C ASP 172
/C SER 173
/C ARG 175
/C LEU 177
/C GLU 178
/C GLN 179
/C ASN 182
/C HIS 183
/C GLU 184
/C HIS 185
/C LEU 186
/C LEU 187
/C THR 188
/C GLU 189
/C GLU 190
/C ARG 192
/C LEU 193
/C SER 194
/C LYS 195
/C ARG 196
/C LEU 197
/C PHE 198
/C LYS 199
/C LEU 200
/C GLN 203
/C THR 205
/C ARG 206
/C TYR 207
/C GLU 209
/C PHE 210
/C VAL 211
/C ARG 212
/C LYS 214
/C ARG 215
/C SER 217
Using Amber 20 recommended default charges and atom types for standard
residues
Hydrogen /A LYS 100 H bonded to atom that should not have hydrogens (/A LYS
100 C)
> coulombic
The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:
/C LEU 149
/C GLU 150
/C ASP 151
/C ARG 152
/C VAL 153
/C LEU 154
/C ARG 155
/C ASP 156
/C PHE 159
/C VAL 161
/C ASP 162
/C THR 164
/C LEU 166
/C VAL 168
/C VAL 170
/C GLU 171
/C ASP 172
/C SER 173
/C ARG 175
/C LEU 177
/C GLU 178
/C GLN 179
/C ASN 182
/C HIS 183
/C GLU 184
/C HIS 185
/C LEU 186
/C LEU 187
/C THR 188
/C GLU 189
/C GLU 190
/C ARG 192
/C LEU 193
/C SER 194
/C LYS 195
/C ARG 196
/C LEU 197
/C PHE 198
/C LYS 199
/C LEU 200
/C GLN 203
/C THR 205
/C ARG 206
/C TYR 207
/C GLU 209
/C PHE 210
/C VAL 211
/C ARG 212
/C LYS 214
/C ARG 215
/C SER 217
Using Amber 20 recommended default charges and atom types for standard
residues
Hydrogen /A LYS 100 H bonded to atom that should not have hydrogens (/A LYS
100 C)
> select /C
4188 atoms, 4233 bonds, 208 pseudobonds, 303 residues, 2 models selected
> coulombic sel
The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:
/C LEU 149
/C GLU 150
/C ASP 151
/C ARG 152
/C VAL 153
/C LEU 154
/C ARG 155
/C ASP 156
/C PHE 159
/C VAL 161
/C ASP 162
/C THR 164
/C LEU 166
/C VAL 168
/C VAL 170
/C GLU 171
/C ASP 172
/C SER 173
/C ARG 175
/C LEU 177
/C GLU 178
/C GLN 179
/C ASN 182
/C HIS 183
/C GLU 184
/C HIS 185
/C LEU 186
/C LEU 187
/C THR 188
/C GLU 189
/C GLU 190
/C ARG 192
/C LEU 193
/C SER 194
/C LYS 195
/C ARG 196
/C LEU 197
/C PHE 198
/C LYS 199
/C LEU 200
/C GLN 203
/C THR 205
/C ARG 206
/C TYR 207
/C GLU 209
/C PHE 210
/C VAL 211
/C ARG 212
/C LYS 214
/C ARG 215
/C SER 217
Using Amber 20 recommended default charges and atom types for standard
residues
Assigning partial charges to residue HIS (net charge -3) with am1-bcc method
Running ANTECHAMBER command:
/Applications/ChimeraX-1.6.1.app/Contents/bin/amber20/bin/antechamber -ek
qm_theory='AM1', -i
/var/folders/4j/dgkkn5fn7p14vdghmyn16rzh0000gn/T/tmp18wu4sxi/ante.in.mol2 -fi
mol2 -o
/var/folders/4j/dgkkn5fn7p14vdghmyn16rzh0000gn/T/tmp18wu4sxi/ante.out.mol2 -fo
mol2 -c bcc -nc -3 -j 5 -s 2 -dr n
(HIS) ``
(HIS) `Welcome to antechamber 20.0: molecular input file processor.`
(HIS) ``
(HIS) `Info: Finished reading file
(/var/folders/4j/dgkkn5fn7p14vdghmyn16rzh0000gn/T/tmp18wu4sxi/ante.in.mol2);
atoms read (19), bonds read (18).`
(HIS) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(HIS) `Running:
/Applications/ChimeraX-1.6.1.app/Contents/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`
(HIS) ``
(HIS) ``
(HIS) `Running:
/Applications/ChimeraX-1.6.1.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`
(HIS) `Info: Total number of electrons: 78; net charge: -3`
(HIS) ``
(HIS) `Running: /Applications/ChimeraX-1.6.1.app/Contents/bin/amber20/bin/sqm
-O -i sqm.in -o sqm.out`
(HIS) `/Applications/ChimeraX-1.6.1.app/Contents/bin/amber20/bin/antechamber:
Fatal Error!`
(HIS) `Cannot properly run
"/Applications/ChimeraX-1.6.1.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o
sqm.out".`
Contents of sqm.out:
--------------------------------------------------------
AMBER SQM VERSION 19
By
Ross C. Walker, Michael F. Crowley, Scott Brozell,
Tim Giese, Andreas W. Goetz,
Tai-Sung Lee and David A. Case
--------------------------------------------------------
--------------------------------------------------------------------------------
QM CALCULATION INFO
--------------------------------------------------------------------------------
| QMMM: Citation for AMBER QMMM Run:
| QMMM: R.C. Walker, M.F. Crowley and D.A. Case, J. COMP. CHEM. 29:1019, 2008
QMMM: SINGLET STATE CALCULATION
QMMM: RHF CALCULATION, NO. OF DOUBLY OCCUPIED LEVELS = 29
| QMMM: *** Selected Hamiltonian ***
| QMMM: AM1
| QMMM: *** Parameter sets in use ***
| QMMM: N : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
| QMMM: C : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
| QMMM: O : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
| QMMM: H : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
| QMMM: *** SCF convergence criteria ***
| QMMM: Energy change : 0.1D-07 kcal/mol
| QMMM: Error matrix |FP-PF| : 0.1D+00 au
| QMMM: Density matrix change : 0.5D-05
| QMMM: Maximum number of SCF cycles : 1000
| QMMM: *** Diagonalization Routine Information ***
| QMMM: Pseudo diagonalizations are allowed.
| QMMM: Auto diagonalization routine selection is in use.
| QMMM:
| QMMM: Timing diagonalization routines:
| QMMM: norbs = 49
| QMMM: diag iterations used for timing = 20
| QMMM:
| QMMM: Internal diag routine = 0.007674 seconds
| QMMM: Dspev diag routine = 0.008439 seconds
| QMMM: Dspevd diag routine = 0.007529 seconds
| QMMM: Dspevx diag routine = 0.032484 seconds
| QMMM: Dsyev diag routine = 0.009132 seconds
| QMMM: Dsyevd diag routine = 0.008580 seconds
| QMMM: Dsyevr diag routine = 0.009147 seconds
| QMMM:
| QMMM: Pseudo diag routine = 0.001625 seconds
| QMMM:
| QMMM: Using dspevd routine (diag_routine=3).
QMMM: QM Region Cartesian Coordinates (*=link atom)
QMMM: QM_NO. MM_NO. ATOM X Y Z
QMMM: 1 1 N 245.8740 187.3160 181.6970
QMMM: 2 2 C 244.8840 188.2690 182.1990
QMMM: 3 3 C 244.1270 188.9350 181.0550
QMMM: 4 4 O 242.9040 189.1030 181.1230
QMMM: 5 5 C 245.5660 189.3220 183.0700
QMMM: 6 6 H 246.6860 187.4990 181.9310
QMMM: 7 7 H 244.2350 187.8100 182.7590
QMMM: 8 8 C 245.4960 186.2640 180.9570
QMMM: 9 9 C 246.6290 185.3770 180.4390
QMMM: 10 10 H 247.4480 186.0090 180.0650
QMMM: 11 11 H 247.0000 184.7420 181.2570
QMMM: 12 12 H 246.2540 184.7420 179.6230
QMMM: 13 13 N 244.8400 189.3330 179.9990
QMMM: 14 14 C 244.1830 189.9850 178.8700
QMMM: 15 15 H 244.2510 191.0770 178.9860
QMMM: 16 16 H 244.6780 189.6850 177.9350
QMMM: 17 17 H 243.1250 189.6850 178.8380
QMMM: 18 18 O 244.3130 186.0220 180.6900
QMMM: 19 19 H 245.6920 189.2380 179.9160
--------------------------------------------------------------------------------
RESULTS
--------------------------------------------------------------------------------
QMMM: ERROR!
QMMM: Unable to achieve self consistency to the tolerances specified
QMMM: No convergence in SCF after 1000 steps.
QMMM: E = -0.2032E+06 DeltaE = -0.2880E-06 DeltaP = 0.1291E-04
QMMM: Smallest DeltaE = -0.2880E-06 DeltaP = 0.1291E-04 Step = 1000
Failure running ANTECHAMBER for residue HIS Check reply log for details
> addh
Summary of feedback from adding hydrogens to trimmed-8flj-
AFCas3_real_space_refined_001-coot-0-cas23-joined-chains-
renamed_real_space_refined_002.pdb #1
---
warnings | Not adding hydrogens to /C LEU 149 CB because it is missing heavy-
atom bond partners
Not adding hydrogens to /C GLU 150 CB because it is missing heavy-atom bond
partners
Not adding hydrogens to /C ASP 151 CB because it is missing heavy-atom bond
partners
Not adding hydrogens to /C ARG 152 CB because it is missing heavy-atom bond
partners
Not adding hydrogens to /C VAL 153 CB because it is missing heavy-atom bond
partners
48 messages similar to the above omitted
notes | No usable SEQRES records for trimmed-8flj-
AFCas3_real_space_refined_001-coot-0-cas23-joined-chains-
renamed_real_space_refined_002.pdb (#1) chain A; guessing termini instead
No usable SEQRES records for trimmed-8flj-
AFCas3_real_space_refined_001-coot-0-cas23-joined-chains-
renamed_real_space_refined_002.pdb (#1) chain B; guessing termini instead
No usable SEQRES records for trimmed-8flj-
AFCas3_real_space_refined_001-coot-0-cas23-joined-chains-
renamed_real_space_refined_002.pdb (#1) chain C; guessing termini instead
No usable SEQRES records for trimmed-8flj-
AFCas3_real_space_refined_001-coot-0-cas23-joined-chains-
renamed_real_space_refined_002.pdb (#1) chain E; guessing termini instead
No usable SEQRES records for trimmed-8flj-
AFCas3_real_space_refined_001-coot-0-cas23-joined-chains-
renamed_real_space_refined_002.pdb (#1) chain G; guessing termini instead
1 messages similar to the above omitted
Chain-initial residues that are actual N termini: /A MET 1, /B MET 1
Chain-initial residues that are not actual N termini: /C ASN 19, /E GLU 8
Chain-final residues that are actual C termini: /A ASN 1076
Chain-final residues that are not actual C termini: /B ARG 99, /C THR 321, /E
VAL 322
1464 hydrogen bonds
/B ARG 99 is not terminus, removing H atom from 'C'
/C THR 321 is not terminus, removing H atom from 'C'
/E VAL 322 is not terminus, removing H atom from 'C'
7607 hydrogens added
> hbonds sel reveal true
224 hydrogen bonds found
> coulombic sel
The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:
/C LEU 149
/C GLU 150
/C ASP 151
/C ARG 152
/C VAL 153
/C LEU 154
/C ARG 155
/C ASP 156
/C PHE 159
/C VAL 161
/C ASP 162
/C THR 164
/C LEU 166
/C VAL 168
/C VAL 170
/C GLU 171
/C ASP 172
/C SER 173
/C ARG 175
/C LEU 177
/C GLU 178
/C GLN 179
/C ASN 182
/C HIS 183
/C GLU 184
/C HIS 185
/C LEU 186
/C LEU 187
/C THR 188
/C GLU 189
/C GLU 190
/C ARG 192
/C LEU 193
/C SER 194
/C LYS 195
/C ARG 196
/C LEU 197
/C PHE 198
/C LYS 199
/C LEU 200
/C GLN 203
/C THR 205
/C ARG 206
/C TYR 207
/C GLU 209
/C PHE 210
/C VAL 211
/C ARG 212
/C LYS 214
/C ARG 215
/C SER 217
Using Amber 20 recommended default charges and atom types for standard
residues
Assigning partial charges to residue HIS (net charge -3) with am1-bcc method
Running ANTECHAMBER command:
/Applications/ChimeraX-1.6.1.app/Contents/bin/amber20/bin/antechamber -ek
qm_theory='AM1', -i
/var/folders/4j/dgkkn5fn7p14vdghmyn16rzh0000gn/T/tmphwt5bo5n/ante.in.mol2 -fi
mol2 -o
/var/folders/4j/dgkkn5fn7p14vdghmyn16rzh0000gn/T/tmphwt5bo5n/ante.out.mol2 -fo
mol2 -c bcc -nc -3 -j 5 -s 2 -dr n
(HIS) ``
(HIS) `Welcome to antechamber 20.0: molecular input file processor.`
(HIS) ``
(HIS) `Info: Finished reading file
(/var/folders/4j/dgkkn5fn7p14vdghmyn16rzh0000gn/T/tmphwt5bo5n/ante.in.mol2);
atoms read (19), bonds read (18).`
(HIS) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(HIS) `Running:
/Applications/ChimeraX-1.6.1.app/Contents/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`
(HIS) ``
(HIS) ``
(HIS) `Running:
/Applications/ChimeraX-1.6.1.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`
(HIS) `Info: Total number of electrons: 78; net charge: -3`
(HIS) ``
(HIS) `Running: /Applications/ChimeraX-1.6.1.app/Contents/bin/amber20/bin/sqm
-O -i sqm.in -o sqm.out`
(HIS) `/Applications/ChimeraX-1.6.1.app/Contents/bin/amber20/bin/antechamber:
Fatal Error!`
(HIS) `Cannot properly run
"/Applications/ChimeraX-1.6.1.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o
sqm.out".`
Contents of sqm.out:
--------------------------------------------------------
AMBER SQM VERSION 19
By
Ross C. Walker, Michael F. Crowley, Scott Brozell,
Tim Giese, Andreas W. Goetz,
Tai-Sung Lee and David A. Case
--------------------------------------------------------
--------------------------------------------------------------------------------
QM CALCULATION INFO
--------------------------------------------------------------------------------
| QMMM: Citation for AMBER QMMM Run:
| QMMM: R.C. Walker, M.F. Crowley and D.A. Case, J. COMP. CHEM. 29:1019, 2008
QMMM: SINGLET STATE CALCULATION
QMMM: RHF CALCULATION, NO. OF DOUBLY OCCUPIED LEVELS = 29
| QMMM: *** Selected Hamiltonian ***
| QMMM: AM1
| QMMM: *** Parameter sets in use ***
| QMMM: N : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
| QMMM: C : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
| QMMM: O : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
| QMMM: H : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
| QMMM: *** SCF convergence criteria ***
| QMMM: Energy change : 0.1D-07 kcal/mol
| QMMM: Error matrix |FP-PF| : 0.1D+00 au
| QMMM: Density matrix change : 0.5D-05
| QMMM: Maximum number of SCF cycles : 1000
| QMMM: *** Diagonalization Routine Information ***
| QMMM: Pseudo diagonalizations are allowed.
| QMMM: Auto diagonalization routine selection is in use.
| QMMM:
| QMMM: Timing diagonalization routines:
| QMMM: norbs = 49
| QMMM: diag iterations used for timing = 20
| QMMM:
| QMMM: Internal diag routine = 0.007498 seconds
| QMMM: Dspev diag routine = 0.008459 seconds
| QMMM: Dspevd diag routine = 0.007679 seconds
| QMMM: Dspevx diag routine = 0.032344 seconds
| QMMM: Dsyev diag routine = 0.009111 seconds
| QMMM: Dsyevd diag routine = 0.008656 seconds
| QMMM: Dsyevr diag routine = 0.012212 seconds
| QMMM:
| QMMM: Pseudo diag routine = 0.001643 seconds
| QMMM:
| QMMM: Using internal diagonalization routine (diag_routine=1).
QMMM: QM Region Cartesian Coordinates (*=link atom)
QMMM: QM_NO. MM_NO. ATOM X Y Z
QMMM: 1 1 N 245.8740 187.3160 181.6970
QMMM: 2 2 C 244.8840 188.2690 182.1990
QMMM: 3 3 C 244.1270 188.9350 181.0550
QMMM: 4 4 O 242.9040 189.1030 181.1230
QMMM: 5 5 C 245.5660 189.3220 183.0700
QMMM: 6 6 H 246.6860 187.4990 181.9310
QMMM: 7 7 H 244.2350 187.8100 182.7590
QMMM: 8 8 C 245.4960 186.2640 180.9570
QMMM: 9 9 C 246.6290 185.3770 180.4390
QMMM: 10 10 H 247.4480 186.0090 180.0650
QMMM: 11 11 H 247.0000 184.7420 181.2570
QMMM: 12 12 H 246.2540 184.7420 179.6230
QMMM: 13 13 N 244.8400 189.3330 179.9990
QMMM: 14 14 C 244.1830 189.9850 178.8700
QMMM: 15 15 H 244.2510 191.0770 178.9860
QMMM: 16 16 H 244.6780 189.6850 177.9350
QMMM: 17 17 H 243.1250 189.6850 178.8380
QMMM: 18 18 H 245.6920 189.2380 179.9160
QMMM: 19 19 O 244.3130 186.0220 180.6900
--------------------------------------------------------------------------------
RESULTS
--------------------------------------------------------------------------------
QMMM: ERROR!
QMMM: Unable to achieve self consistency to the tolerances specified
QMMM: No convergence in SCF after 1000 steps.
QMMM: E = -0.2032E+06 DeltaE = -0.2880E-06 DeltaP = 0.1291E-04
QMMM: Smallest DeltaE = -0.2880E-06 DeltaP = 0.1291E-04 Step = 1000
Failure running ANTECHAMBER for residue HIS Check reply log for details
> close session
> open /Users/whenriques/Downloads/cryosparc_P28_J1806_006_volume_map.mrc
Opened cryosparc_P28_J1806_006_volume_map.mrc as #1, grid size 336,336,336,
pixel 1.07, shown at level 0.0536, step 2, values float32
> volume #1 step 1
> volume #1 level 0.1578
> volume #1 level 0.154
> volume #1 level 0.245
> volume #1 level 0.2222
> open /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration-
> complex/cryoem/cas1-2-3-apo/phenix/J411-alphafold/cas123-apo-J411-C2.ccp4
Opened cas123-apo-J411-C2.ccp4 as #2, grid size 336,336,336, pixel 1.07, shown
at level 0.039, step 2, values float32
> volume #2 step 1
> volume #2 level 0.238
> volume #1 level 0.1484
> volume flip #1
Opened cryosparc_P28_J1806_006_volume_map.mrc z flip as #3, grid size
336,336,336, pixel 1.07, shown at step 1, values float32
> ui mousemode right "rotate selected models"
> select add #3
2 models selected
> view matrix models
> #3,0.38943,0.91875,-0.065088,-41.224,0.91129,-0.3946,-0.11767,103.87,-0.13379,-0.013489,-0.99092,380.57
> close #1
> fitmap #3 inMap #2
Fit map cryosparc_P28_J1806_006_volume_map.mrc z flip in map
cas123-apo-J411-C2.ccp4 using 74318 points
correlation = 0.9325, correlation about mean = 0.5093, overlap = 4056
steps = 88, shift = 4.77, angle = 8.01 degrees
Position of cryosparc_P28_J1806_006_volume_map.mrc z flip (#3) relative to
cas123-apo-J411-C2.ccp4 (#2) coordinates:
Matrix rotation and translation
0.44950484 0.89327788 0.00016678 -60.69296899
0.89322366 -0.44947548 -0.01110331 101.93481576
-0.00984338 0.00513996 -0.99993834 357.99162458
Axis 0.85132024 0.52463871 -0.00284171
Axis point 0.00000000 68.66591985 179.17893225
Rotation angle (degrees) 179.45338739
Shift along axis 0.79248910
> select subtract #3
Nothing selected
> volume #2 level 0.148
> open /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration-
> complex/cryoem/cas1-2-3-apo/phenix/J411-alphafold/RealSpaceRefine_17_chains_updated/apo-
> Refinement17-chains-corrected-renamed.cif
Summary of feedback from opening
/Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration-
complex/cryoem/cas1-2-3-apo/phenix/J411-alphafold/RealSpaceRefine_17_chains_updated/apo-
Refinement17-chains-corrected-renamed.cif
---
warnings | Atom H1 is not in the residue template for ARG /A:95
Atom H1 is not in the residue template for TYR /C:115
Atom H1 is not in the residue template for TYR /D:115
Atom H1 is not in the residue template for TYR /E:115
Atom H1 is not in the residue template for TYR /F:115
Chain information for apo-Refinement17-chains-corrected-renamed.cif #1
---
Chain | Description
A B | No description available
C D E F | No description available
> fitmap #4 inMap #2
No atoms or maps for #4
> fitmap #1 inMap #2
Fit molecule apo-Refinement17-chains-corrected-renamed.cif (#1) to map
cas123-apo-J411-C2.ccp4 (#2) using 54205 atoms
average map value = 0.05567, steps = 380
shifted from previous position = 23.9
rotated from previous position = 28 degrees
atoms outside contour = 46121, contour level = 0.148
Position of apo-Refinement17-chains-corrected-renamed.cif (#1) relative to
cas123-apo-J411-C2.ccp4 (#2) coordinates:
Matrix rotation and translation
0.94791798 0.10752863 -0.29981510 64.48967402
-0.20827382 0.92142338 -0.32802587 107.60805819
0.24098447 0.37338526 0.89582919 -102.33198106
Axis 0.74594025 -0.57513226 -0.33585119
Axis point 0.00000000 334.76833599 283.94750993
Rotation angle (degrees) 28.04418676
Shift along axis 20.58489514
> select add #1
54205 atoms, 54815 bonds, 3448 residues, 1 model selected
> view matrix models
> #1,0.24362,0.78341,0.57177,-106.17,-0.11127,0.60822,-0.78593,234.93,-0.96347,0.12785,0.23535,266.8
> fitmap #1 inMap #2
Fit molecule apo-Refinement17-chains-corrected-renamed.cif (#1) to map
cas123-apo-J411-C2.ccp4 (#2) using 54205 atoms
average map value = 0.1719, steps = 92
shifted from previous position = 8.52
rotated from previous position = 9.85 degrees
atoms outside contour = 25406, contour level = 0.148
Position of apo-Refinement17-chains-corrected-renamed.cif (#1) relative to
cas123-apo-J411-C2.ccp4 (#2) coordinates:
Matrix rotation and translation
0.11504553 0.80202823 0.58610174 -96.24150302
-0.00313957 0.59030997 -0.80717055 230.66035293
-0.99335526 0.09102125 0.07043055 313.15822399
Axis 0.45194489 0.79473842 -0.40513783
Axis point 65.28499623 0.00000000 272.76301302
Rotation angle (degrees) 96.43678798
Shift along axis 12.94654506
> color #2/g,h #f69320ff
> color #1,2,3/a:1-94/b:1-94 #d799c4
> color #1,2,3/a:95-end/b:95-end #6d8fc9ff
> color #1,2,3/f,e #c2b59bff
> color #1,2,3/c,d #9c857a
> hide sel atoms
> show sel cartoons
> hide #!2 models
> show #!2 models
> hide #!3 models
> set bgColor white
> lighting soft
> ui tool show "Color Zone"
> color zone #2 near #1 distance 3
> show #!3 models
> hide #!3 models
> show #!3 models
> volume #3 level 0.1208
> transparency 50
> hide #!2 models
> volume #3 level 0.1484
> open /Users/whenriques/Downloads/cryosparc_P28_J1670_012_volume_map(1).mrc
Opened cryosparc_P28_J1670_012_volume_map(1).mrc as #4, grid size 336,336,336,
pixel 1.07, shown at level 0.0468, step 2, values float32
> volume #4 step 1
> volume #4 level 0.2464
> volume flip #4
Opened cryosparc_P28_J1670_012_volume_map(1).mrc z flip as #5, grid size
336,336,336, pixel 1.07, shown at step 1, values float32
> fitmap #5 inMap #2
Fit map cryosparc_P28_J1670_012_volume_map(1).mrc z flip in map
cas123-apo-J411-C2.ccp4 using 19800 points
correlation = 0.4882, correlation about mean = 0.05939, overlap = 476.6
steps = 288, shift = 10.6, angle = 16 degrees
Position of cryosparc_P28_J1670_012_volume_map(1).mrc z flip (#5) relative to
cas123-apo-J411-C2.ccp4 (#2) coordinates:
Matrix rotation and translation
0.97763276 -0.11940625 -0.17313676 50.73415836
0.08606282 0.97825520 -0.18870601 24.55697789
0.19190461 0.16958454 0.96665077 -52.71673311
Axis 0.64999410 -0.66224111 0.37275245
Axis point 314.77138663 0.00000000 263.38712117
Rotation angle (degrees) 15.99840650
Shift along axis -2.93602838
> select subtract #1
Nothing selected
> select add #5
2 models selected
> view matrix models
> #5,-0.97547,-0.035221,0.21731,361.41,-0.12706,0.89618,-0.42511,120.84,-0.17978,-0.44229,-0.87867,435.61
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.97547,-0.035221,0.21731,316.37,-0.12706,0.89618,-0.42511,142,-0.17978,-0.44229,-0.87867,450.85
> fitmap #5 inMap #2
Fit map cryosparc_P28_J1670_012_volume_map(1).mrc z flip in map
cas123-apo-J411-C2.ccp4 using 19800 points
correlation = 0.5822, correlation about mean = 0.04315, overlap = 606.2
steps = 124, shift = 10.2, angle = 11 degrees
Position of cryosparc_P28_J1670_012_volume_map(1).mrc z flip (#5) relative to
cas123-apo-J411-C2.ccp4 (#2) coordinates:
Matrix rotation and translation
-0.98080755 -0.07152921 0.18138394 332.08283830
-0.11658827 0.96079882 -0.25154088 89.10053568
-0.15628095 -0.26786043 -0.95069820 428.46616278
Axis -0.04785110 0.99007818 -0.13211913
Axis point 186.86976559 0.00000000 205.74097384
Rotation angle (degrees) 170.18169229
Shift along axis 15.71739182
> view matrix models
> #5,-0.98081,-0.071529,0.18138,333.17,-0.11659,0.9608,-0.25154,90.553,-0.15628,-0.26786,-0.9507,427.8
> view matrix models
> #5,-0.98081,-0.071529,0.18138,314.53,-0.11659,0.9608,-0.25154,104.4,-0.15628,-0.26786,-0.9507,429.49
> fitmap #5 inMap #2
Fit map cryosparc_P28_J1670_012_volume_map(1).mrc z flip in map
cas123-apo-J411-C2.ccp4 using 19800 points
correlation = 0.6087, correlation about mean = 0.0787, overlap = 672.3
steps = 216, shift = 20.9, angle = 34.5 degrees
Position of cryosparc_P28_J1670_012_volume_map(1).mrc z flip (#5) relative to
cas123-apo-J411-C2.ccp4 (#2) coordinates:
Matrix rotation and translation
-0.99809986 0.05125922 -0.03419326 353.47728620
0.03982020 0.96007352 0.27689927 -28.40170049
0.04702169 0.27501153 -0.96029039 295.10923181
Axis -0.02301041 -0.98996381 -0.13943517
Axis point 174.04105738 0.00000000 153.21286536
Rotation angle (degrees) 177.64911614
Shift along axis -21.16560966
> view matrix models
> #5,-0.9981,0.051259,-0.034193,341.68,0.03982,0.96007,0.2769,-32.046,0.047022,0.27501,-0.96029,295.85
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.97719,0.14004,-0.15966,344.72,0.15087,0.98686,-0.057804,-1.2959,0.14947,-0.080574,-0.98548,336.68
> view matrix models
> #5,-0.9829,0.17567,-0.05526,322.29,0.18065,0.97802,-0.10416,2.0929,0.035748,-0.11236,-0.99302,365.84
> view matrix models
> #5,-0.97844,0.18555,-0.090697,325.87,0.19494,0.97477,-0.10873,0.53705,0.068233,-0.12407,-0.98993,360.68
> view matrix models
> #5,-0.88539,0.46296,-0.041951,254.42,0.45049,0.87679,0.16824,-82.307,0.11467,0.13006,-0.98485,309.76
> view matrix models
> #5,-0.89253,0.44504,-0.072982,264.03,0.42445,0.88364,0.19756,-83.21,0.15241,0.14535,-0.97757,298.51
> view matrix models
> #5,-0.89253,0.44504,-0.072982,266.36,0.42445,0.88364,0.19756,-87.173,0.15241,0.14535,-0.97757,301.07
> fitmap #5 inMap #2
Fit map cryosparc_P28_J1670_012_volume_map(1).mrc z flip in map
cas123-apo-J411-C2.ccp4 using 19800 points
correlation = 0.9412, correlation about mean = 0.4323, overlap = 1974
steps = 140, shift = 7.19, angle = 13.1 degrees
Position of cryosparc_P28_J1670_012_volume_map(1).mrc z flip (#5) relative to
cas123-apo-J411-C2.ccp4 (#2) coordinates:
Matrix rotation and translation
-0.86110360 0.50840669 0.00482061 242.48923124
0.50840603 0.86111626 -0.00145346 -66.17175483
-0.00489005 0.00119925 -0.99998733 357.65546782
Axis 0.26351887 0.96465424 -0.00006565
Axis point 130.74936482 0.00000000 178.50918917
Rotation angle (degrees) 179.71161577
Shift along axis 0.04414403
> volume #4 level 0.217
> volume #5 level 0.1352
> view matrix models
> #5,-0.099665,0.74318,0.66163,-54.49,0.73613,0.50245,-0.45349,27.331,-0.66946,0.44185,-0.59715,342.42
> undo
> volume #5 level 0.2006
> hide #!3 models
> volume #5 level 0.1384
> volume #5 level 0.1123
> volume #5 level 0.1286
> transparency sel 50
> select subtract #5
Nothing selected
> volume #5 level 0.2104
> open /Users/whenriques/Downloads/cryosparc_P17_J760_002_volume_map.mrc
Opened cryosparc_P17_J760_002_volume_map.mrc as #6, grid size 200,200,200,
pixel 2.3, shown at level 0.0742, step 1, values float32
> open /Users/whenriques/Downloads/cryosparc_P17_J759_002_volume_map.mrc
Opened cryosparc_P17_J759_002_volume_map.mrc as #7, grid size 200,200,200,
pixel 2.3, shown at level 0.0756, step 1, values float32
> open /Users/whenriques/Downloads/cryosparc_P17_J758_002_volume_map.mrc
Opened cryosparc_P17_J758_002_volume_map.mrc as #8, grid size 200,200,200,
pixel 2.3, shown at level 0.0551, step 1, values float32
> undo
> close #1
> close #2
> close #3-5
> volume #8 level 0.1751
> volume #8 level 0.09729
> volume flip *
Missing or invalid "volumes" argument: invalid density maps specifier
> volume flip #6-8
Opened cryosparc_P17_J760_002_volume_map.mrc z flip as #1, grid size
200,200,200, pixel 2.3, shown at step 1, values float32
Opened cryosparc_P17_J759_002_volume_map.mrc z flip as #2, grid size
200,200,200, pixel 2.3, shown at step 1, values float32
Opened cryosparc_P17_J758_002_volume_map.mrc z flip as #3, grid size
200,200,200, pixel 2.3, shown at step 1, values float32
> tile
3 models tiled
> volume #8 level 0.1881
> volume #8 level 0.2399
> undo
> show #!6 models
> hide #!8 models
> hide #!6 models
> close #6-8
> volume #3 level 0.214
> volume #1 level 0.2878
> volume #2 level 0.138
> volume #1 level 0.33
> volume #2 level 0.3
> volume #3 level 0.3
> volume #3 level 0.1087
> volume #3 level 0.3389
> lighting soft
> volume #2 level 0.2844
> close session
> open /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration-
> complex/cryoem/integration_complex/spermidine.Mn.data.collection.2022.10/pam_prespacer/cryosparc/P17/J758-J764-NURefines/cryosparc_P17_J764_002_volume_map.mrc
> /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration-
> complex/cryoem/integration_complex/spermidine.Mn.data.collection.2022.10/pam_prespacer/cryosparc/P17/J758-J764-NURefines/cryosparc_P17_J763_003_volume_map.mrc
> /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration-
> complex/cryoem/integration_complex/spermidine.Mn.data.collection.2022.10/pam_prespacer/cryosparc/P17/J758-J764-NURefines/cryosparc_P17_J762_002_volume_map.mrc
> /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration-
> complex/cryoem/integration_complex/spermidine.Mn.data.collection.2022.10/pam_prespacer/cryosparc/P17/J758-J764-NURefines/cryosparc_P17_J761_002_volume_map.mrc
> /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration-
> complex/cryoem/integration_complex/spermidine.Mn.data.collection.2022.10/pam_prespacer/cryosparc/P17/J758-J764-NURefines/cryosparc_P17_J760_002_volume_map.mrc
> /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration-
> complex/cryoem/integration_complex/spermidine.Mn.data.collection.2022.10/pam_prespacer/cryosparc/P17/J758-J764-NURefines/cryosparc_P17_J759_002_volume_map.mrc
> /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration-
> complex/cryoem/integration_complex/spermidine.Mn.data.collection.2022.10/pam_prespacer/cryosparc/P17/J758-J764-NURefines/cryosparc_P17_J758_002_volume_map.mrc
Opened cryosparc_P17_J764_002_volume_map.mrc as #1.1, grid size 200,200,200,
pixel 2.3, shown at level 0.044, step 1, values float32
Opened cryosparc_P17_J763_003_volume_map.mrc as #1.2, grid size 200,200,200,
pixel 2.3, shown at level 0.0354, step 1, values float32
Opened cryosparc_P17_J762_002_volume_map.mrc as #1.3, grid size 200,200,200,
pixel 2.3, shown at level 0.0364, step 1, values float32
Opened cryosparc_P17_J761_002_volume_map.mrc as #1.4, grid size 200,200,200,
pixel 2.3, shown at level 0.0479, step 1, values float32
Opened cryosparc_P17_J760_002_volume_map.mrc as #1.5, grid size 200,200,200,
pixel 2.3, shown at level 0.0742, step 1, values float32
Opened cryosparc_P17_J759_002_volume_map.mrc as #1.6, grid size 200,200,200,
pixel 2.3, shown at level 0.0756, step 1, values float32
Opened cryosparc_P17_J758_002_volume_map.mrc as #1.7, grid size 200,200,200,
pixel 2.3, shown at level 0.0551, step 1, values float32
> volume flip #1
Opened cryosparc_P17_J764_002_volume_map.mrc z flip as #2, grid size
200,200,200, pixel 2.3, shown at step 1, values float32
Opened cryosparc_P17_J763_003_volume_map.mrc z flip as #3, grid size
200,200,200, pixel 2.3, shown at step 1, values float32
Opened cryosparc_P17_J762_002_volume_map.mrc z flip as #4, grid size
200,200,200, pixel 2.3, shown at step 1, values float32
Opened cryosparc_P17_J761_002_volume_map.mrc z flip as #5, grid size
200,200,200, pixel 2.3, shown at step 1, values float32
Opened cryosparc_P17_J760_002_volume_map.mrc z flip as #6, grid size
200,200,200, pixel 2.3, shown at step 1, values float32
Opened cryosparc_P17_J759_002_volume_map.mrc z flip as #7, grid size
200,200,200, pixel 2.3, shown at step 1, values float32
Opened cryosparc_P17_J758_002_volume_map.mrc z flip as #8, grid size
200,200,200, pixel 2.3, shown at step 1, values float32
> close #1#1.1-7
> set bgColor white
> lighting soft
> volume #2 level 0.3
> volume #4 level 0.3
> volume #3 level 0.3
> volume #5 level 0.3
> volume #6 level 0.3
> volume #7 level 0.3
> volume #8 level 0.3
> tile
7 models tiled
> volume #6 level 0.2
> volume #7 level 0.2
> volume #8 level 0.2
> volume #5 level 0.2
> volume #4 level 0.2
> volume #3 level 0.2
> volume #2 level 0.2
> volume #7 level 0.3404
> vop level 0.1
> vop level 0.3
> save /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration-
> complex/cryoem/integration_complex/spermidine.Mn.data.collection.2022.10/pam_prespacer/cryosparc/P17/J758-J764-NURefines/volumes_flipped.cxs
> includeMaps true
===== Log before crash end =====
Log:
Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 86
OpenGL renderer: Apple M1
OpenGL vendor: Apple
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro17,1
Model Number: MJ123LL/A
Chip: Apple M1
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 10151.1.1
OS Loader Version: 10151.1.1
Software:
System Software Overview:
System Version: macOS 14.0 (23A344)
Kernel Version: Darwin 23.0.0
Time since boot: 13 days, 22 hours, 54 minutes
Graphics/Displays:
Apple M1:
Chipset Model: Apple M1
Type: GPU
Bus: Built-In
Total Number of Cores: 8
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
BenQ GW2760HS:
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: 0.7.13
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.2.1
Babel: 2.12.1
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
build: 0.10.0
certifi: 2021.10.8
cftime: 1.6.2
charset-normalizer: 3.1.0
ChimeraX-AddCharge: 1.5.9.1
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.3.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.9.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.43.10
ChimeraX-AtomicLibrary: 10.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.8
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3.1
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-Clipper: 0.21.0
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.3
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.6.1
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.1
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: 1.2.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ISOLDE: 1.6.0
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-Label: 1.1.7
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
ChimeraX-Map: 1.1.4
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.0.12
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.9
ChimeraX-ModelPanel: 1.3.7
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.0
ChimeraX-NRRD: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.10.1
ChimeraX-PDB: 2.7.2
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 3.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.1
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.8.3
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.10.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Topography: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.28.4
ChimeraX-uniprot: 2.2.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.1
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.1.3
contourpy: 1.0.7
cxservices: 1.2.2
cycler: 0.11.0
Cython: 0.29.33
debugpy: 1.6.7
decorator: 5.1.1
docutils: 0.19
executing: 1.2.0
filelock: 3.9.0
fonttools: 4.39.3
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.8.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.35
imagecodecs: 2022.2.22
imagesize: 1.4.1
importlib-metadata: 6.6.0
ipykernel: 6.21.1
ipython: 8.10.0
ipython-genutils: 0.2.0
ipywidgets: 8.0.6
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.0.2
jupyter-core: 5.3.0
jupyterlab-widgets: 3.0.7
kiwisolver: 1.4.4
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.2
matplotlib: 3.6.3
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.2
networkx: 2.8.8
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.4
numpy: 1.23.5
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.3.0
pkginfo: 1.9.6
platformdirs: 3.5.0
prompt-toolkit: 3.0.38
psutil: 5.9.4
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.14.0
pynrrd: 1.0.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.4.2
PyQt6-Qt6: 6.4.3
PyQt6-sip: 13.4.1
PyQt6-WebEngine-commercial: 6.4.0
PyQt6-WebEngine-Qt6: 6.4.3
python-dateutil: 2.8.2
pytz: 2023.3
pyzmq: 25.0.2
qtconsole: 5.4.0
QtPy: 2.3.1
RandomWords: 0.4.0
requests: 2.28.2
scipy: 1.9.3
setuptools: 67.4.0
setuptools-scm: 7.0.5
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.4.1
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.4
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.1
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tcia-utils: 1.2.0
tifffile: 2022.10.10
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.3.1
traitlets: 5.9.0
typing-extensions: 4.5.0
tzdata: 2023.3
urllib3: 1.26.15
wcwidth: 0.2.6
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.7
zipp: 3.15.0
Change History (2)
comment:1 by , 16 months ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash during screen removal |
comment:2 by , 16 months ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
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