![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 2 years ago
Closed 2 years ago
#9997 closed defect (duplicate)
Crashed in QTabBar::paintEvent()
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-13.5.2-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 0x00000001e68ca080 (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/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" : 110000,
"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "Mac14,2",
"coalitionID" : 644,
"osVersion" : {
"train" : "macOS 13.5.2",
"build" : "22G91",
"releaseType" : "User"
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"captureTime" : "2023-10-16 09:48:55.9439 -0400",
"incident" : "933E375C-2799-4BC7-803E-9518E81DF46A",
"pid" : 22434,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2023-10-15 18:51:06.0276 -0400",
"procStartAbsTime" : 2054701025143,
"procExitAbsTime" : 2753838759917,
"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":"F2A0B2FA-B61F-5734-BA89-599109DA1F98","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "04CBAFB6-075B-CE76-D44A-FD9D049AF824",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 0,
"wakeTime" : 4,
"sleepWakeUUID" : "D0AFCF5F-02AA-4150-8413-D7F8791E327F",
"sip" : "enabled",
"vmRegionInfo" : "0x18 is not in any region. Bytes before following region: 105562108854248\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n MALLOC_NANO 600218000000-600220000000 [128.0M] rw-\/rwx SM=PRV ",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000018","rawCodes":[1,24],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000018"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":22434},
"vmregioninfo" : "0x18 is not in any region. Bytes before following region: 105562108854248\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n MALLOC_NANO 600218000000-600220000000 [128.0M] rw-\/rwx SM=PRV ",
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"faultingThread" : 0,
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===== Log before crash start =====
Startup Messages
---
warnings | Unable to find icon for toolbar provider 'Dump Bead Data' in bundle
'ChimeraX-GenomeTools'
Unable to find icon for toolbar provider 'Highlight' in bundle 'ChimeraX-
GenomeTools'
Unable to find icon for toolbar provider 'Bed Models' in bundle 'ChimeraX-
GenomeTools'
Unable to find icon for toolbar provider 'Bead Overlap' in bundle 'ChimeraX-
GenomeTools'
Unable to find icon for toolbar provider 'Genome Distance' in bundle
'ChimeraX-GenomeTools'
1 messages similar to the above omitted
> camera ortho
> cofr centerOfView
> mousemode rightMode clip
> mousemode alt rightMode "contour level"
> mousemode alt leftMode "move picked models"
> alias cofron cofr centerofview showpivot true
> alias cofroff cofr centerofview showpivot false
> alias symclip cofr centerofview; clip near -$1 far $1 position cofr
> alias cootmode surface cap false; surface style solid; lighting flat;
> graphics silhouettes false; style stick; ~rib; color ##num_residues gold;
> color byhet ; disp; ~disp @H*; style solvent ball; size ballscale 0.1; size
> stickradius 0.07; transparency 70; cofr centerofview; clip near -10 far 10
> position cofr; color ##~num_residues cornflower blue
> alias cootmode_mesh surface cap false; surface style mesh; lighting flat;
> graphics silhouettes false; style stick; ~rib; color ##num_residues gold;
> color byhet ; disp; ~disp @H*; style solvent ball; size ballscale 0.1; size
> stickradius 0.07; cofr centerofview; clip near -10 far 10 position cofr;
> color ##~num_residues #3d60ffff; transparency 50
> alias ca_and_sidechains ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1;
> disp @P&nucleic&$1; style $1 stick; disp sidechain&$1; disp
> ~backbone&nucleic&$1; size stickradius 0.1; size pseudobondradius 0.1
> alias ca_trace ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1; disp
> @P&nucleic&$1; style $1 stick; size stickradius 0.1; size pseudobondradius
> 0.1
> alias map_sphere_15 surface unzone ##~num_residues; sel; close #10000;
> marker #10000 position cofr; sel ~sel; surface zone ##~num_residues
> nearAtoms sel distance 15; close #10000
> alias map_unsphere surface unzone ##~num_residues
> alias default_mol_display ~disp; rib; rainbow chain palette RdYlBu-5;
> lighting soft
> alias hidemaps surface unzone ##~num_residues; sel; close #10000; marker
> #10000 position cofr; sel ~sel; surface zone ##~num_residues nearAtoms sel
> distance 0; close #10000
> alias showmaps surface unzone ##~num_residues
> buttonpanel Shortcuts rows 3 columns 4
> buttonpanel Shortcuts add Vol_Viewer command "tool show 'Volume Viewer'"
> buttonpanel Shortcuts add Model_Panel command "tool show Models"
> buttonpanel Shortcuts add Log command "tool show Log"
> buttonpanel Shortcuts add default_disp command default_mol_display
> buttonpanel Shortcuts add map_sphere command map_sphere_15
> buttonpanel Shortcuts add map_unsphere command map_unsphere
> buttonpanel Shortcuts add cofron command cofron
> buttonpanel Shortcuts add cofroff command cofroff
> buttonpanel Shortcuts add cootmode command cootmode
> buttonpanel Shortcuts add mark_cofr command "marker #10000 position cofr"
> buttonpanel Shortcuts add hidemaps command hidemaps
> buttonpanel Shortcuts add showmaps command showmaps
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/patrick/Documents/Research/scs7p/New/compact/compact_af/Production_162/run1/frame_30ns.pdb
frame_30ns.pdb title:
MDANALYSIS FRAMES FROM 0, STEP 1: Created by PDBWriter [more info...]
Chain information for frame_30ns.pdb #1
---
Chain | Description
X | No description available
Non-standard residues in frame_30ns.pdb #1
---
FE2P — (FE2P)
HEME — (heme)
HSD — (HSD)
> set bgColor white
> cartoon style helix width 2.5 thickness 0.3
> show surfaces
> color silver target s
> transparency 80 target s
> graphics silhouettes true
> transparency 30 target c
> hide surfaces
> color light gray target a
> color byhetero target a
> lighting gentle
> hide H
> hide target c
> hide @c,n,o
> hide #1.4 models
> ui mousemode right coordinationbond
> select ::name="HEME"
73 atoms, 76 bonds, 4 pseudobonds, 1 residue, 2 models selected
> hide sel
> select clear
> ui mousemode right select
Drag select of 26 atoms, 23 bonds
> select clear
Drag select of 85 atoms, 73 bonds
> hide sel
> select clear
> ui mousemode right coordinationbond
> ui tool show Distances
> ui mousemode right select
> select /X:349@NE2
1 atom, 1 residue, 1 model selected
> select add /X:386@FE2P
2 atoms, 2 residues, 2 models selected
> distance /X:349@NE2 /X:386@FE2P
Distance between /X HSD 349 NE2 and FE2P 386 FE2P: 2.132Å
> distance style decimalPlaces 2
> distance style decimalPlaces 1
> select add /X:271@NE2
3 atoms, 3 residues, 2 models selected
> select subtract /X:386@FE2P
2 atoms, 2 residues, 2 models selected
> select clear
> select add /X:271@NE2
1 atom, 1 residue, 1 model selected
> select add /X:386@FE2P
2 atoms, 2 residues, 2 models selected
> distance /X:271@NE2 /X:386@FE2P
Distance between /X HSD 271 NE2 and FE2P 386 FE2P: 2.1Å
> select clear
> select add /X:330@NE2
1 atom, 1 residue, 1 model selected
> select add /X:386@FE2P
2 atoms, 2 residues, 1 model selected
> distance /X:330@NE2 /X:386@FE2P
Distance between /X HSD 330 NE2 and FE2P 386 FE2P: 2.2Å
> select clear
> select add /X:345@NE2
1 atom, 1 residue, 1 model selected
> select add /X:386@FE2P
2 atoms, 2 residues, 2 models selected
> distance /X:345@NE2 /X:386@FE2P
Distance between /X HSD 345 NE2 and FE2P 386 FE2P: 2.1Å
> select clear
> select add /X:326@NE2
1 atom, 1 residue, 1 model selected
> select add /X:386@FE2P
2 atoms, 2 residues, 2 models selected
> distance /X:326@NE2 /X:386@FE2P
Distance between /X HSD 326 NE2 and FE2P 386 FE2P: 2.2Å
> select clear
> select /X:268@NE2
1 atom, 1 residue, 1 model selected
> select add /X:387@FE2P
2 atoms, 2 residues, 2 models selected
> distance /X:268@NE2 /X:387@FE2P
Distance between /X HSD 268 NE2 and FE2P 387 FE2P: 2.1Å
> select clear
> select /X:249@NE2
1 atom, 1 residue, 1 model selected
> select add /X:387@FE2P
2 atoms, 2 residues, 1 model selected
> distance /X:249@NE2 /X:387@FE2P
Distance between /X HSD 249 NE2 and FE2P 387 FE2P: 2.1Å
> select clear
> select add /X:348@NE2
1 atom, 1 residue, 1 model selected
> select add /X:387@FE2P
2 atoms, 2 residues, 2 models selected
> distance /X:348@NE2 /X:387@FE2P
Distance between /X HSD 348 NE2 and FE2P 387 FE2P: 2.2Å
> select clear
> select add /X:272@NE2
1 atom, 1 residue, 1 model selected
> select add /X:387@FE2P
2 atoms, 2 residues, 2 models selected
> distance /X:272@NE2 /X:387@FE2P
Distance between /X HSD 272 NE2 and FE2P 387 FE2P: 2.1Å
> select clear
> select add /X:244@NE2
1 atom, 1 residue, 1 model selected
> select add /X:387@FE2P
2 atoms, 2 residues, 2 models selected
> distance /X:244@NE2 /X:387@FE2P
Distance between /X HSD 244 NE2 and FE2P 387 FE2P: 2.1Å
> select clear
> 2dlabels text 2.1Å bold true size 24
> ui mousemode right "move label"
> 2dlabels #3.1 xpos 0.547 ypos 0.536
> ~2dlabels #3.1
> 2dlabels text 2.1Å bold true size 20
> 2dlabels #4.1 xpos 0.556 ypos 0.545
> ~2dlabels #4.1
> 2dlabels text 2.1 bold true size 20
> 2dlabels #5.1 xpos 0.569 ypos 0.559
> ~distance /X:268@NE2 /X:387@FE2P
> 2dlabels text 2.1 bold true size 20
> 2dlabels #5.2 xpos 0.394 ypos 0.346
> ~distance /X:345@NE2 /X:386@FE2P
> 2dlabels text 2.2 bold true size 20
> ~distance /X:326@NE2 /X:386@FE2P
> 2dlabels #5.3 xpos 0.299 ypos 0.314
> 2dlabels text 2.2 bold true size 20
> ~distance /X:330@NE2 /X:386@FE2P
> 2dlabels #5.4 xpos 0.271 ypos 0.417
> 2dlabels text 2.1 bold true size 20
> ~distance /X:271@NE2 /X:386@FE2P
> 2dlabels #5.5 xpos 0.300 ypos 0.490
> 2dlabels text 2.1 bold true size 20
> ~distance /X:349@NE2 /X:386@FE2P
> 2dlabels #5.6 xpos 0.378 ypos 0.452
> 2dlabels text 2.1 bold true size 20
> 2dlabels #5.7 xpos 0.609 ypos 0.492
> ~distance /X:244@NE2 /X:387@FE2P
> 2dlabels text 2.2 bold true size 20
Exactly two atoms must be selected!
> ~distance /X:348@NE2 /X:387@FE2P
> 2dlabels #5.8 xpos 0.682 ypos 0.574
> 2dlabels text 2.1 bold true size 20
> ~distance /X:272@NE2 /X:387@FE2P
> 2dlabels #5.9 xpos 0.626 ypos 0.669
> 2dlabels text 2.1 bold true size 20
> ~distance /X:249@NE2 /X:387@FE2P
> 2dlabels #5.10 xpos 0.694 ypos 0.622
> 2dlabels #5.9 xpos 0.582 ypos 0.646
> 2dlabels #5.10 xpos 0.659 ypos 0.654
> 2dlabels text H326 bold true size 25
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> 2dlabels text H345 bold true size 25
> 2dlabels #5.12 xpos 0.507 ypos 0.272
> 2dlabels text H330 bold true size 25
> 2dlabels #5.13 xpos 0.108 ypos 0.282
> 2dlabels text H271 bold true size 25
> 2dlabels #5.14 xpos 0.154 ypos 0.668
> 2dlabels text H349 bold true size 25
> 2dlabels #5.15 xpos 0.324 ypos 0.650
> 2dlabels text H268 bold true size 25
> 2dlabels #5.16 xpos 0.358 ypos 0.807
> 2dlabels text H272 bold true size 25
> 2dlabels #5.17 xpos 0.564 ypos 0.818
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> 2dlabels #5.18 xpos 0.809 ypos 0.659
> 2dlabels text H348 bold true size 25
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> 2dlabels text H244 bold true size 25
> 2dlabels #5.20 xpos 0.598 ypos 0.353
> 2dlabels text "Catalytic Competent" bold true size 25 color #b22222
> 2dlabels #5.21 xpos 0.609 ypos 0.052
> 2dlabels text FE1 bold true size 22 color #e25822
> 2dlabels #5.22 xpos 0.388 ypos 0.404
> 2dlabels text FE2 bold true size 22 color #e25822
> 2dlabels #5.23 xpos 0.556 ypos 0.522
> 2dlabels #5.23 xpos 0.555 ypos 0.518
> 2dlabels #5.23 xpos 0.611 ypos 0.579
> ~2dlabels #5.23
> ~2dlabels #5.22
> 2dlabels text FE2 bold true size 22 color silver
> 2dlabels #5.22 xpos 0.612 ypos 0.579
> 2dlabels text FE1 bold true size 22 color white
> 2dlabels #5.23 xpos 0.319 ypos 0.399
> ~2dlabels #5.22
> 2dlabels text FE2 bold true size 22 color white
> 2dlabels #5.22 xpos 0.610 ypos 0.580
> save /Users/patrick/Desktop/image198.png supersample 3
> ~2dlabels #5.1-23
> open /Users/patrick/4zr1.cif
4zr1.cif title:
Hydroxylase domain of scs7p [more info...]
Chain information for 4zr1.cif #2
---
Chain | Description | UniProt
A B | Ceramide very long chain fatty acid hydroxylase SCS7 | SCS7_YEAST 96-384
Non-standard residues in 4zr1.cif #2
---
BOG — octyl beta-D-glucopyranoside
TRD — tridecane (lipid fragment)
ZN — zinc ion
4zr1.cif mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
> hide #!1 models
> view #2
> select #2/B
2424 atoms, 2510 bonds, 10 pseudobonds, 285 residues, 2 models selected
> delete sel
> select ::name="BOG"
120 atoms, 120 bonds, 6 residues, 1 model selected
> delete sel
> select ::name="TRD"
26 atoms, 24 bonds, 2 residues, 1 model selected
> delete sel
> hide #!2 cartoons
Drag select of 55 atoms, 51 bonds
> hide sel
Drag select of 20 atoms, 16 bonds
> hide sel
Drag select of 29 atoms, 31 bonds
> hide sel
Drag select of 35 atoms, 34 bonds
> hide sel
Drag select of 1 atoms
> hide sel
Drag select of 6 atoms, 5 bonds
> hide sel
Drag select of 19 atoms, 18 bonds
> hide sel
Drag select of 15 atoms, 16 bonds
> hide sel
> hide @c,n,o
> hide #2.2 models
Drag select of 5 atoms, 4 bonds
> hide sel
> select clear
Drag select of 72 atoms, 10 pseudobonds, 70 bonds
> select subtract #2/A:401@ZN
71 atoms, 70 bonds, 5 pseudobonds, 11 residues, 2 models selected
> select subtract #2/A:402@ZN
70 atoms, 70 bonds, 10 residues, 1 model selected
> name frozen exp sel
> select clear
> show #!1 models
> view #1
Drag select of 15 atoms, 3 pseudobonds, 19 bonds
> select clear
Drag select of 72 atoms, 10 pseudobonds, 70 bonds
> select subtract #1/X:386@FE2P
71 atoms, 70 bonds, 5 pseudobonds, 11 residues, 3 models selected
> select subtract #1/X:387@FE2P
70 atoms, 70 bonds, 10 residues, 2 models selected
> name frozen comp sel
> select clear
> matchmaker exp to comp
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 frame_30ns.pdb, chain X (#1) with 4zr1.cif, chain A (#2), sequence
alignment score = 6.8
RMSD between 10 pruned atom pairs is 0.598 angstroms; (across all 10 pairs:
0.598)
> lighting simple
> open
> /Users/patrick/Documents/Research/scs7p/New/open/Production_187/run1/frame_30nso.pdb
frame_30nso.pdb title:
MDANALYSIS FRAMES FROM 0, STEP 1: Created by PDBWriter [more info...]
Chain information for frame_30nso.pdb #3
---
Chain | Description
X | No description available
Non-standard residues in frame_30nso.pdb #3
---
FE2P — (FE2P)
HEME — (heme)
HSD — (HSD)
> hide #!2 models
> hide #!1 models
> hide target c
Drag select of 210 atoms, 6 pseudobonds, 206 bonds
> hide sel
> hide H
> hide @c,n,o
> hide #3.3 models
> ui mousemode right coordinationbond
> ui mousemode right select
Drag select of 72 atoms, 70 bonds
> select clear
> ui mousemode right coordinationbond
Drag select of 12 atoms, 13 bonds
> select clear
Drag select of 72 atoms, 10 pseudobonds, 70 bonds
> select #3/X:386@FE2P
1 atom, 1 residue, 1 model selected
> select clear
Drag select of 60 atoms, 10 pseudobonds, 58 bonds
> select clear
Drag select of 72 atoms, 10 pseudobonds, 70 bonds
> select subtract #3/X:386@FE2P
71 atoms, 70 bonds, 5 pseudobonds, 11 residues, 2 models selected
> select subtract #3/X:387@FE2P
70 atoms, 70 bonds, 10 residues, 1 model selected
> name frozen open sel
> select clear
> show #!2 models
> show #!1 models
> matchmaker open to exp
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 4zr1.cif, chain A (#2) with frame_30nso.pdb, chain X (#3), sequence
alignment score = 6.8
RMSD between 10 pruned atom pairs is 0.723 angstroms; (across all 10 pairs:
0.723)
> center #1
Unknown command: center #1
> hide #!3 models
> hide #!2 models
> show #!2 models
> show #!3 models
> hide #!3 models
> hide #!2 models
> show #!2 models
> show #!3 models
> hide #!3 models
> hide #!2 models
> 2dlabels text H244 bold true size 25
> ui mousemode right "move label"
> 2dlabels #4.1 xpos 0.700 ypos 0.236
> 2dlabels text H348 bold true size 25
> 2dlabels #4.2 xpos 0.814 ypos 0.408
> 2dlabels text H249 bold true size 25
> 2dlabels #4.3 xpos 0.808 ypos 0.619
> 2dlabels #4.3 xpos 0.852 ypos 0.616
> 2dlabels text H272 bold true size 25
> 2dlabels #4.4 xpos 0.603 ypos 0.855
> 2dlabels text H268 bold true size 25
> 2dlabels #4.5 xpos 0.429 ypos 0.736
> 2dlabels text H349 bold true size 25
> 2dlabels #4.6 xpos 0.442 ypos 0.478
> 2dlabels text H345 bold true size 25
> 2dlabels #4.7 xpos 0.400 ypos 0.204
> 2dlabels text H326 bold true size 25
> 2dlabels #4.8 xpos 0.173 ypos 0.207
> 2dlabels text H330 bold true size 25
> 2dlabels #4.9 xpos 0.094 ypos 0.456
> 2dlabels text H271 bold true size 25
> 2dlabels #4.10 xpos 0.202 ypos 0.748
> 2dlabels text 2.1 size 20
> 2dlabels #4.11 xpos 0.326 ypos 0.521
> 2dlabels text 2.1 size 20
> 2dlabels #4.12 xpos 0.391 ypos 0.474
> 2dlabels text 2.1 size 20
> 2dlabels #4.13 xpos 0.396 ypos 0.376
> 2dlabels text 2.2 size 20
> 2dlabels #4.14 xpos 0.314 ypos 0.356
> 2dlabels text 2.2 size 20
> 2dlabels #4.15 xpos 0.285 ypos 0.455
> 2dlabels text 2.2 size 20
> 2dlabels #4.16 xpos 0.710 ypos 0.557
> 2dlabels text 2.1 size 20
> 2dlabels #4.17 xpos 0.697 ypos 0.638
> 2dlabels text 2.1 size 20
> 2dlabels #4.18 xpos 0.626 ypos 0.498
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> 2dlabels text 2.1 size 20
> 2dlabels #4.19 xpos 0.601 ypos 0.569
> 2dlabels text 2.1 size 20
> 2dlabels #4.20 xpos 0.662 ypos 0.665
> 2dlabels #4.17 xpos 0.708 ypos 0.643
> 2dlabels text FE2 bold true size 22 color #e25822
> 2dlabels #4.21 xpos 0.586 ypos 0.520
> 2dlabels text FE1 bold true size 22 color #e25822
> 2dlabels #4.22 xpos 0.391 ypos 0.425
> save /Users/patrick/Desktop/image199.png supersample 3
> ~2dlabels #4.11-20
> show #!2 models
> hide #!1 models
> 2dlabels #4.2 xpos 0.786 ypos 0.417
> 2dlabels #4.3 xpos 0.838 ypos 0.617
> 2dlabels #4.5 xpos 0.402 ypos 0.727
> 2dlabels #4.10 xpos 0.230 ypos 0.749
> 2dlabels #4.8 xpos 0.180 ypos 0.207
> 2dlabels #4.22 xpos 0.418 ypos 0.430
> 2dlabels #4.6 xpos 0.456 ypos 0.488
> 2dlabels #4.21 xpos 0.573 ypos 0.513
> hide #4.21 models
> hide #4.22 models
> ui tool show Distances
> ui mousemode right select
> select #2/A:345@NE2
1 atom, 1 residue, 1 model selected
> select add #2/A:401@ZN
2 atoms, 2 residues, 1 model selected
> distance #2/A:345@NE2 #2/A:401@ZN
Distance between 4zr1.cif #2/A HIS 345 NE2 and ZN 401 ZN: 2.2Å
> select clear
> select #2/A:326@NE2
1 atom, 1 residue, 1 model selected
> select add #2/A:401@ZN
2 atoms, 2 residues, 1 model selected
> distance #2/A:326@NE2 #2/A:401@ZN
Distance between 4zr1.cif #2/A HIS 326 NE2 and ZN 401 ZN: 2.3Å
> select clear
> select add #2/A:330@NE2
1 atom, 1 residue, 1 model selected
> select add #2/A:401@ZN
2 atoms, 2 residues, 1 model selected
> distance #2/A:330@NE2 #2/A:401@ZN
Distance between 4zr1.cif #2/A HIS 330 NE2 and ZN 401 ZN: 2.1Å
> select clear
> select add #2/A:271@NE2
1 atom, 1 residue, 1 model selected
> select add #2/A:401@ZN
2 atoms, 2 residues, 1 model selected
> distance #2/A:271@NE2 #2/A:401@ZN
Distance between 4zr1.cif #2/A HIS 271 NE2 and ZN 401 ZN: 2.3Å
> select clear
> select add #2/A:349@NE2
1 atom, 1 residue, 1 model selected
> select add #2/A:401@ZN
2 atoms, 2 residues, 1 model selected
> distance #2/A:349@NE2 #2/A:401@ZN
Distance between 4zr1.cif #2/A HIS 349 NE2 and ZN 401 ZN: 2.0Å
> select clear
> select add #2/A:268@NE2
1 atom, 1 residue, 1 model selected
> select add #2/A:402@ZN
2 atoms, 2 residues, 1 model selected
> distance #2/A:268@NE2 #2/A:402@ZN
Distance between 4zr1.cif #2/A HIS 268 NE2 and ZN 402 ZN: 2.2Å
> select clear
> select add #2/A:272@NE2
1 atom, 1 residue, 1 model selected
> select add #2/A:402@ZN
2 atoms, 2 residues, 1 model selected
> distance #2/A:272@NE2 #2/A:402@ZN
Distance between 4zr1.cif #2/A HIS 272 NE2 and ZN 402 ZN: 2.3Å
> select clear
> select add #2/A:249@NE2
1 atom, 1 residue, 1 model selected
> select add #2/A:402@ZN
2 atoms, 2 residues, 1 model selected
> distance #2/A:249@NE2 #2/A:402@ZN
Distance between 4zr1.cif #2/A HIS 249 NE2 and ZN 402 ZN: 2.1Å
> select clear
> select add #2/A:348@NE2
1 atom, 1 residue, 1 model selected
> select add #2/A:402@ZN
2 atoms, 2 residues, 1 model selected
> distance #2/A:348@NE2 #2/A:402@ZN
Distance between 4zr1.cif #2/A HIS 348 NE2 and ZN 402 ZN: 2.2Å
> select clear
> select add #2/A:244@NE2
1 atom, 1 residue, 1 model selected
> select add #2/A:402@ZN
2 atoms, 2 residues, 1 model selected
> distance #2/A:244@NE2 #2/A:402@ZN
Distance between 4zr1.cif #2/A HIS 244 NE2 and ZN 402 ZN: 2.3Å
> select clear
> 2dlabels text 2.3 size 20
> ui mousemode right "move label"
> 2dlabels #4.11 xpos 0.367 ypos 0.583
> ~distance #2/A:271@NE2 #2/A:401@ZN
> 2dlabels #4.11 xpos 0.352 ypos 0.538
> 2dlabels text 2.3 size 20
> 2dlabels #4.12 xpos 0.350 ypos 0.377
> ~distance #2/A:326@NE2 #2/A:401@ZN
> 2dlabels text 2.1 size 20
> ~distance #2/A:330@NE2 #2/A:401@ZN
> 2dlabels #4.13 xpos 0.319 ypos 0.480
> 2dlabels text 2.2 size 20
> ~distance #2/A:345@NE2 #2/A:401@ZN
> 2dlabels #4.14 xpos 0.420 ypos 0.374
> 2dlabels text 2.1 size 20
> ~distance #2/A:249@NE2 #2/A:402@ZN
> 2dlabels #4.15 xpos 0.690 ypos 0.636
> 2dlabels text 2.2 size 20
> 2dlabels #4.16 xpos 0.570 ypos 0.560
> ~distance #2/A:268@NE2 #2/A:402@ZN
> 2dlabels text 2.0 size 20
> ~distance #2/A:349@NE2 #2/A:401@ZN
> 2dlabels #4.17 xpos 0.408 ypos 0.475
> 2dlabels #4.11 xpos 0.340 ypos 0.558
> 2dlabels text 2.3 size 20
> ~distance #2/A:272@NE2 #2/A:402@ZN
> 2dlabels #4.18 xpos 0.632 ypos 0.677
> 2dlabels text 2.3 size 20
> 2dlabels #4.19 xpos 0.617 ypos 0.445
> ~distance #2/A:244@NE2 #2/A:402@ZN
> 2dlabels text 2.2 size 20
> ~distance #2/A:348@NE2 #2/A:402@ZN
> 2dlabels #4.20 xpos 0.697 ypos 0.551
> 2dlabels text ZN1 bold true size 22 color #6082b6
> 2dlabels #4.23 xpos 0.417 ypos 0.431
> 2dlabels text ZN2 bold true size 22 color #6082b6
> 2dlabels #4.24 xpos 0.584 ypos 0.515
> save /Users/patrick/Desktop/image200.png supersample 3
> show #!3 models
> hide #!2 models
> hide #4.11 models
> hide #4.12 models
> hide #4.13 models
> hide #4.14 models
> hide #4.15 models
> hide #4.16 models
> hide #4.17 models
> hide #4.18 models
> hide #4.19 models
> hide #4.20 models
> hide #4.23 models
> hide #4.24 models
> 2dlabels #4.4 xpos 0.618 ypos 0.884
> 2dlabels #4.5 xpos 0.402 ypos 0.764
> 2dlabels #4.6 xpos 0.460 ypos 0.497
> 2dlabels #4.10 xpos 0.210 ypos 0.753
> 2dlabels #4.9 xpos 0.093 ypos 0.441
> 2dlabels #4.8 xpos 0.160 ypos 0.143
> 2dlabels #4.7 xpos 0.385 ypos 0.211
> 2dlabels #4.1 xpos 0.695 ypos 0.235
> 2dlabels #4.2 xpos 0.782 ypos 0.402
> ui mousemode right select
> select add #3/X:345@NE2
1 atom, 1 residue, 1 model selected
> select add #3/X:386@FE2P
2 atoms, 2 residues, 1 model selected
> distance #3/X:345@NE2 #3/X:386@FE2P
Distance between frame_30nso.pdb #3/X HSD 345 NE2 and FE2P 386 FE2P: 2.2Å
> select add #3/X:349@NE2
3 atoms, 3 residues, 1 model selected
> select clear
> select add #3/X:349@NE2
1 atom, 1 residue, 1 model selected
> select add #3/X:386@FE2P
2 atoms, 2 residues, 1 model selected
> distance #3/X:349@NE2 #3/X:386@FE2P
Distance between frame_30nso.pdb #3/X HSD 349 NE2 and FE2P 386 FE2P: 2.1Å
> select clear
> select add #3/X:271@NE2
1 atom, 1 residue, 1 model selected
> select add #3/X:386@FE2P
2 atoms, 2 residues, 1 model selected
> distance #3/X:271@NE2 #3/X:386@FE2P
Distance between frame_30nso.pdb #3/X HSD 271 NE2 and FE2P 386 FE2P: 2.1Å
> select clear
> select add #3/X:330@NE2
1 atom, 1 residue, 1 model selected
> select add #3/X:386@FE2P
2 atoms, 2 residues, 1 model selected
> distance #3/X:330@NE2 #3/X:386@FE2P
Distance between frame_30nso.pdb #3/X HSD 330 NE2 and FE2P 386 FE2P: 2.1Å
> select clear
> select add #3/X:326@NE2
1 atom, 1 residue, 1 model selected
> select add #3/X:386@FE2P
2 atoms, 2 residues, 1 model selected
> distance #3/X:326@NE2 #3/X:386@FE2P
Distance between frame_30nso.pdb #3/X HSD 326 NE2 and FE2P 386 FE2P: 2.3Å
> select clear
> select add #3/X:268@NE2
1 atom, 1 residue, 1 model selected
> select add #3/X:387@FE2P
2 atoms, 2 residues, 1 model selected
> distance #3/X:268@NE2 #3/X:387@FE2P
Distance between frame_30nso.pdb #3/X HSD 268 NE2 and FE2P 387 FE2P: 2.1Å
> select clear
> select add #3/X:272@NE2
1 atom, 1 residue, 1 model selected
> select add #3/X:387@FE2P
2 atoms, 2 residues, 1 model selected
> distance #3/X:272@NE2 #3/X:387@FE2P
Distance between frame_30nso.pdb #3/X HSD 272 NE2 and FE2P 387 FE2P: 2.2Å
> select clear
> select add #3/X:249@NE2
1 atom, 1 residue, 1 model selected
> select add #3/X:387@FE2P
2 atoms, 2 residues, 1 model selected
> distance #3/X:249@NE2 #3/X:387@FE2P
Distance between frame_30nso.pdb #3/X HSD 249 NE2 and FE2P 387 FE2P: 2.1Å
> select clear
> select add #3/X:348@NE2
1 atom, 1 residue, 1 model selected
> select add #3/X:387@FE2P
2 atoms, 2 residues, 1 model selected
> distance #3/X:348@NE2 #3/X:387@FE2P
Distance between frame_30nso.pdb #3/X HSD 348 NE2 and FE2P 387 FE2P: 2.4Å
> select clear
> select add #3/X:244@NE2
1 atom, 1 residue, 1 model selected
> select add #3/X:387@FE2P
2 atoms, 2 residues, 1 model selected
> distance #3/X:244@NE2 #3/X:387@FE2P
Distance between frame_30nso.pdb #3/X HSD 244 NE2 and FE2P 387 FE2P: 2.2Å
> select clear
> 2dlabels text 2.2 size 20
> ui mousemode right "move label"
> 2dlabels #4.25 xpos 0.417 ypos 0.358
> ~distance #3/X:345@NE2 #3/X:386@FE2P
> 2dlabels text 2.1 size 20
> 2dlabels #4.26 xpos 0.294 ypos 0.439
> ~distance #3/X:330@NE2 #3/X:386@FE2P
> 2dlabels text 2.1 size 20
> ~distance #3/X:271@NE2 #3/X:386@FE2P
> 2dlabels #4.6 xpos 0.484 ypos 0.539
> 2dlabels #4.27 xpos 0.307 ypos 0.533
> 2dlabels text 2.1 size 20
> 2dlabels #4.28 xpos 0.400 ypos 0.486
> ~distance #3/X:349@NE2 #3/X:386@FE2P
> 2dlabels #4.28 xpos 0.402 ypos 0.488
> 2dlabels text 2.1 size 20
> 2dlabels #4.29 xpos 0.567 ypos 0.465
> ~distance #3/X:249@NE2 #3/X:387@FE2P
> 2dlabels #4.25 xpos 0.417 ypos 0.358
> 2dlabels #4.29 xpos 0.733 ypos 0.661
> 2dlabels text 2.2 size 20
> 2dlabels #4.30 xpos 0.677 ypos 0.706
> ~distance #3/X:272@NE2 #3/X:387@FE2P
> 2dlabels text 2.1 size 20
> ~distance #3/X:268@NE2 #3/X:387@FE2P
> 2dlabels #4.31 xpos 0.617 ypos 0.581
> ~distance #3/X:326@NE2 #3/X:386@FE2P
> 2dlabels text 2.2 size 20
> 2dlabels #4.32 xpos 0.309 ypos 0.341
> 2dlabels #4.28 xpos 0.400 ypos 0.486
> 2dlabels #4.25 xpos 0.413 ypos 0.359
> 2dlabels text 2.2 size 20
> 2dlabels #4.33 xpos 0.659 ypos 0.474
> ~distance #3/X:244@NE2 #3/X:387@FE2P
> ~distance #3/X:348@NE2 #3/X:387@FE2P
> 2dlabels text 2.3 size 20
> 2dlabels #4.34 xpos 0.729 ypos 0.572
> show #4.21 models
> show #4.22 models
> 2dlabels #4.22 xpos 0.395 ypos 0.429
> 2dlabels #4.21 xpos 0.616 ypos 0.530
> 2dlabels #4.6 xpos 0.464 ypos 0.495
> 2dlabels #4.6 xpos 0.461 ypos 0.495
> 2dlabels #4.26 xpos 0.297 ypos 0.452
> save /Users/patrick/Desktop/image201.png supersample 3
> hide #4.34 models
> hide #4.33 models
> hide #4.32 models
> hide #4.31 models
> hide #4.30 models
> hide #4.29 models
> hide #4.28 models
> hide #4.27 models
> hide #4.26 models
> hide #4.25 models
> hide #4.22 models
> hide #4.21 models
> show #!1 models
> hide #!3 models
> show #!2 models
> matchmaker comp to exp
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 4zr1.cif, chain A (#2) with frame_30ns.pdb, chain X (#1), sequence
alignment score = 6.8
RMSD between 10 pruned atom pairs is 0.598 angstroms; (across all 10 pairs:
0.598)
> 2dlabels #4.5 xpos 0.375 ypos 0.753
> 2dlabels #4.4 xpos 0.583 ypos 0.889
> 2dlabels #4.3 xpos 0.833 ypos 0.597
> 2dlabels #4.2 xpos 0.783 ypos 0.396
> 2dlabels #4.3 xpos 0.840 ypos 0.614
> 2dlabels #4.1 xpos 0.687 ypos 0.223
> 2dlabels #4.7 xpos 0.397 ypos 0.200
> 2dlabels #4.8 xpos 0.160 ypos 0.152
> 2dlabels #4.9 xpos 0.087 ypos 0.454
> 2dlabels #4.10 xpos 0.197 ypos 0.736
> 2dlabels #4.5 xpos 0.383 ypos 0.753
> 2dlabels #4.6 xpos 0.456 ypos 0.477
> save /Users/patrick/Desktop/image202.png supersample 3
> hide #!1 models
> show #!3 models
> matchmaker open to exp
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 4zr1.cif, chain A (#2) with frame_30nso.pdb, chain X (#3), sequence
alignment score = 6.8
RMSD between 10 pruned atom pairs is 0.723 angstroms; (across all 10 pairs:
0.723)
> 2dlabels #4.4 xpos 0.598 ypos 0.915
> 2dlabels #4.2 xpos 0.785 ypos 0.401
> 2dlabels #4.7 xpos 0.401 ypos 0.200
> 2dlabels #4.8 xpos 0.160 ypos 0.176
> 2dlabels #4.9 xpos 0.097 ypos 0.458
> 2dlabels #4.10 xpos 0.192 ypos 0.719
> 2dlabels #4.5 xpos 0.389 ypos 0.749
> 2dlabels #4.6 xpos 0.443 ypos 0.478
> save /Users/patrick/Desktop/image203.png supersample 3
> show #!1 models
> matchmaker open to comp
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 frame_30ns.pdb, chain X (#1) with frame_30nso.pdb, chain X (#3),
sequence alignment score = 9.8
RMSD between 10 pruned atom pairs is 0.397 angstroms; (across all 10 pairs:
0.397)
> save /Users/patrick/Desktop/image204.png supersample 3
Unsupported scale factor (0.000000) detected on Display0
QPainter::begin: Paint device returned engine == 0, type: 3
===== Log before crash end =====
Log:
Startup Messages
---
warnings | Unable to find icon for toolbar provider 'Dump Bead Data' in bundle
'ChimeraX-GenomeTools'
Unable to find icon for toolbar provider 'Highlight' in bundle 'ChimeraX-
GenomeTools'
Unable to find icon for toolbar provider 'Bed Models' in bundle 'ChimeraX-
GenomeTools'
Unable to find icon for toolbar provider 'Bead Overlap' in bundle 'ChimeraX-
GenomeTools'
Unable to find icon for toolbar provider 'Genome Distance' in bundle
'ChimeraX-GenomeTools'
1 messages similar to the above omitted
> camera ortho
> cofr centerOfView
> mousemode rightMode clip
> mousemode alt rightMode "contour level"
> mousemode alt leftMode "move picked models"
> alias cofron cofr centerofview showpivot true
> alias cofroff cofr centerofview showpivot false
> alias symclip cofr centerofview; clip near -$1 far $1 position cofr
> alias cootmode surface cap false; surface style solid; lighting flat;
> graphics silhouettes false; style stick; ~rib; color ##num_residues gold;
> color byhet ; disp; ~disp @H*; style solvent ball; size ballscale 0.1; size
> stickradius 0.07; transparency 70; cofr centerofview; clip near -10 far 10
> position cofr; color ##~num_residues cornflower blue
> alias cootmode_mesh surface cap false; surface style mesh; lighting flat;
> graphics silhouettes false; style stick; ~rib; color ##num_residues gold;
> color byhet ; disp; ~disp @H*; style solvent ball; size ballscale 0.1; size
> stickradius 0.07; cofr centerofview; clip near -10 far 10 position cofr;
> color ##~num_residues #3d60ffff; transparency 50
> alias ca_and_sidechains ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1;
> disp @P&nucleic&$1; style $1 stick; disp sidechain&$1; disp
> ~backbone&nucleic&$1; size stickradius 0.1; size pseudobondradius 0.1
> alias ca_trace ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1; disp
> @P&nucleic&$1; style $1 stick; size stickradius 0.1; size pseudobondradius
> 0.1
> alias map_sphere_15 surface unzone ##~num_residues; sel; close #10000;
> marker #10000 position cofr; sel ~sel; surface zone ##~num_residues
> nearAtoms sel distance 15; close #10000
> alias map_unsphere surface unzone ##~num_residues
> alias default_mol_display ~disp; rib; rainbow chain palette RdYlBu-5;
> lighting soft
> alias hidemaps surface unzone ##~num_residues; sel; close #10000; marker
> #10000 position cofr; sel ~sel; surface zone ##~num_residues nearAtoms sel
> distance 0; close #10000
> alias showmaps surface unzone ##~num_residues
> buttonpanel Shortcuts rows 3 columns 4
> buttonpanel Shortcuts add Vol_Viewer command "tool show 'Volume Viewer'"
> buttonpanel Shortcuts add Model_Panel command "tool show Models"
> buttonpanel Shortcuts add Log command "tool show Log"
> buttonpanel Shortcuts add default_disp command default_mol_display
> buttonpanel Shortcuts add map_sphere command map_sphere_15
> buttonpanel Shortcuts add map_unsphere command map_unsphere
> buttonpanel Shortcuts add cofron command cofron
> buttonpanel Shortcuts add cofroff command cofroff
> buttonpanel Shortcuts add cootmode command cootmode
> buttonpanel Shortcuts add mark_cofr command "marker #10000 position cofr"
> buttonpanel Shortcuts add hidemaps command hidemaps
> buttonpanel Shortcuts add showmaps command showmaps
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/patrick/Documents/Research/scs7p/New/compact/compact_af/Production_162/run1/frame_0nsc.pdb
frame_0nsc.pdb title:
MDANALYSIS FRAMES FROM 0, STEP 1: Created by PDBWriter [more info...]
Chain information for frame_0nsc.pdb #1
---
Chain | Description
X | No description available
Non-standard residues in frame_0nsc.pdb #1
---
FE2P — (FE2P)
HEME — (heme)
HSD — (HSD)
OpenGL version: 4.1 Metal - 83.1
OpenGL renderer: Apple M2
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 Air
Model Identifier: Mac14,2
Model Number: Z160000AKLL/A
Chip: Apple M2
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 8 GB
System Firmware Version: 8422.141.2
OS Loader Version: 8422.141.2
Software:
System Software Overview:
System Version: macOS 13.5.2 (22G91)
Kernel Version: Darwin 22.6.0
Time since boot: 3 days, 1 hour, 52 minutes
Graphics/Displays:
Apple M2:
Chipset Model: Apple M2
Type: GPU
Bus: Built-In
Total Number of Cores: 8
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina Display
Resolution: 2560 x 1664 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
DELL U2417H:
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-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-GenomeTools: 0.9
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-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-OpenCommands: 1.1
ChimeraX-PDB: 2.7.2
ChimeraX-PDBBio: 1.0
ChimeraX-PDBImages: 1.2
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-QScore: 1.0
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-RMF: 0.14
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
MolecularDynamicsViewer: 1.4
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
pip: 23.0
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
Send2Trash: 1.8.2
SEQCROW: 1.8.3
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 , 2 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Window Toolkit |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crashed in QTabBar::paintEvent() |
comment:2 by , 2 years ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
Note:
See TracTickets
for help on using tickets.
Thanks for reporting this problem. This is a bug in the Qt windowing toolkit that ChimeraX uses that has to do with waking from sleep on a Mac when multiple displays are connected. In the daily build we have switched to a different version of the Qt toolkit that does not have that problem, so if you use the daily build then you won't get these crashes anymore.