Opened 3 years ago

Closed 3 years ago

#8890 closed defect (can't reproduce)

Crash after saving movie

Reported by: chimerax-bug-report@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Input/Output Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.6rc202304202331 (2023-04-20 23:31:10 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
{"app_name":"ChimeraX","timestamp":"2023-04-24 14:30:16.00 -0400","app_version":"","slice_uuid":"5df621ee-554e-36a8-b448-93b2334e5480","build_version":"","platform":1,"share_with_app_devs":1,"is_first_party":1,"bug_type":"309","os_version":"macOS 13.0.1 (22A400)","roots_installed":0,"incident_id":"66A93111-5A8C-43B6-B796-1443301B80CB","name":"ChimeraX"}
{
  "uptime" : 22000,
  "procRole" : "Background",
  "version" : 2,
  "userID" : 501,
  "deployVersion" : 210,
  "modelCode" : "MacBookAir8,2",
  "coalitionID" : 1737,
  "osVersion" : {
    "train" : "macOS 13.0.1",
    "build" : "22A400",
    "releaseType" : "User"
  },
  "captureTime" : "2023-04-24 14:30:15.7193 -0400",
  "incident" : "66A93111-5A8C-43B6-B796-1443301B80CB",
  "pid" : 2733,
  "cpuType" : "X86-64",
  "roots_installed" : 0,
  "bug_type" : "309",
  "procLaunch" : "2023-04-23 13:10:27.6320 -0400",
  "procStartAbsTime" : 8304977362898,
  "procExitAbsTime" : 22603160586236,
  "procName" : "ChimeraX",
  "procPath" : "\/private\/var\/folders\/*\/ChimeraX-1.5.app\/Contents\/MacOS\/ChimeraX",
  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "9A35D7C2-E5C8-B0AA-6B77-B67DB413D8D9",
  "wakeTime" : 82,
  "bridgeVersion" : {"build":"20P420","train":"7.0"},
  "sleepWakeUUID" : "73294720-AA6E-48C9-9237-AED45071726B",
  "sip" : "enabled",
  "vmRegionInfo" : "0x10b17af30 is in 0x10afa7000-0x10b210000;  bytes after start: 1916720  bytes before end: 610511\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      shared memory               10af98000-10afa7000    [   60K] r--\/r-- SM=SHM  \n--->  mapped file                 10afa7000-10b210000    [ 2468K] r-x\/rwx SM=COW  ...t_id=342d9b09\n      mapped file                 10b210000-10b24a000    [  232K] rw-\/rwx SM=COW  ...t_id=36343009",
  "exception" : {"codes":"0x000000000000000a, 0x000000010b17af30","rawCodes":[10,4481068848],"type":"EXC_BAD_ACCESS","signal":"SIGILL","subtype":"KERN_MEMORY_ERROR at 0x000000010b17af30"},
  "termination" : {"flags":0,"code":4,"namespace":"SIGNAL","indicator":"Illegal instruction: 4","byProc":"ChimeraX","byPid":2733},
  "ktriageinfo" : "VM - Object has no pager\nVM - Filesystem pagein returned an error in vnode_pagein\nVM - Page has error bit set\nVM - Filesystem pagein returned an error in vnode_pagein\nVM - Page has error bit set\n",
  "vmregioninfo" : "0x10b17af30 is in 0x10afa7000-0x10b210000;  bytes after start: 1916720  bytes before end: 610511\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      shared memory               10af98000-10afa7000    [   60K] r--\/r-- SM=SHM  \n--->  mapped file                 10afa7000-10b210000    [ 2468K] r-x\/rwx SM=COW  ...t_id=342d9b09\n      mapped file                 10b210000-10b24a000    [  232K] rw-\/rwx SM=COW  ...t_id=36343009",
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  "faultingThread" : 0,
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    }
  ]
},
  "reportNotes" : [
  "dyld_process_snapshot_create_for_process failed with 5"
]
}
===== Log before crash start =====
You can double click a model's Name or ID in the model panel to edit those
fields  
UCSF ChimeraX version: 1.5 (2022-11-24)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> ui tool show AlphaFold

> alphafold predict
> RHIFLIRHSQYHVDGSLEKDRTLTPLGREQAELTGLRLASLGLKFNKIVHSSMTRAIETTDIISRHLPGVCKVSTDLLREGCRALQFPPEGWLRLSLNNGSITHLVIRPNGRVALRTLGDTGFMPPDKITRSAPIEPDPPVSHWKPEAVQYYEDGARIEAAFRNYIHRADARQEEDSYEIFICHANVIRYIV

Please cite ColabFold: Making protein folding accessible to all. Nature
Methods (2022) if you use these predictions.  
Running AlphaFold prediction  

> open 1ujc

1ujc title:  
Structure of the protein histidine phosphatase SixA complexed with tungstate
[more info...]  
  
Chain information for 1ujc #1  
---  
Chain | Description | UniProt  
A | Phosphohistidine phosphatase sixA | SIXA_ECOLI  
  
Non-standard residues in 1ujc #1  
---  
CA — calcium ion  
WO4 — tungstate(VI)ion  
  

> open 2hur

2hur title:  
Escherichia coli nucleoside diphosphate kinase [more info...]  
  
Chain information for 2hur #2  
---  
Chain | Description | UniProt  
A B C D E F | NUCLEOSIDE DIPHOSPHATE KINASE | NDK_ECOLI  
  
Non-standard residues in 2hur #2  
---  
SO4 — sulfate ion  
  
2hur mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_defined_assembly  
3| software_defined_assembly  
4| software_defined_assembly  
5| software_defined_assembly  
  

> style stick

Changed 8644 atom styles  

> style stick

Changed 8644 atom styles  

> rainbow

> hide #!1 models

> show #!1 models

> show cartoons

> hide atoms

> color #2 #ff2907ff

> color #2 #9f9cffff

> color #1 #2ddb5bff

> color #1 #28db42ff

> mmaker

> matchmaker

Missing or invalid "matchAtoms" argument: empty atom specifier  

> mmaker 1ujc 2hur

> matchmaker 1ujc 2hur

Missing or invalid "matchAtoms" argument: invalid atoms specifier  

> mmaker 1ujc

> matchmaker 1ujc

Missing or invalid "matchAtoms" argument: invalid atoms specifier  

> ui tool show Matchmaker

> matchmaker #2 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 1ujc, chain A (#1) with 2hur, chain D (#2), sequence alignment
score = 42.4  
RMSD between 6 pruned atom pairs is 1.289 angstroms; (across all 69 pairs:
15.519)  
  

> select #2/A:2-143

1082 atoms, 1103 bonds, 142 residues, 1 model selected  

> select #2/B:2-143

1082 atoms, 1103 bonds, 142 residues, 1 model selected  

> select #2/C:2-143

1082 atoms, 1103 bonds, 142 residues, 1 model selected  

> select #2/D:2-143

1082 atoms, 1103 bonds, 142 residues, 1 model selected  

> select add #2

7239 atoms, 6642 bonds, 1575 residues, 1 model selected  

> select subtract #2

Nothing selected  

> select add #2

7239 atoms, 6642 bonds, 1575 residues, 1 model selected  

> select subtract #2

Nothing selected  
AlphaFold prediction finished  
Results in /Users/akash/Downloads/ChimeraX/AlphaFold/prediction_3  

> open /Users/akash/Downloads/ChimeraX/AlphaFold/prediction_3/best_model.pdb

Chain information for best_model.pdb #3  
---  
Chain | Description  
A | No description available  
  

> hide #3 models

> select #2/A:2-143

1082 atoms, 1103 bonds, 142 residues, 1 model selected  

> hide sel atoms

> select #2/A:2-143

1082 atoms, 1103 bonds, 142 residues, 1 model selected  

> select #2/A:2-143

1082 atoms, 1103 bonds, 142 residues, 1 model selected  

> hide sel cartoons

> select #2/B:2-143

1082 atoms, 1103 bonds, 142 residues, 1 model selected  

> hide sel cartoons

> select #2/C:2-143

1082 atoms, 1103 bonds, 142 residues, 1 model selected  

> hide sel cartoons

> select #2/D:2-143

1082 atoms, 1103 bonds, 142 residues, 1 model selected  

> select #2/E:2-143

1082 atoms, 1103 bonds, 142 residues, 1 model selected  

> hide sel cartoons

> select #2/F:2-143

1082 atoms, 1103 bonds, 142 residues, 1 model selected  

> hide sel cartoons

> hide #2 models

> show #2 models

> hide #2 models

> show #3 models

> ui tool show Matchmaker

> matchmaker #3 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 1ujc, chain A (#1) with best_model.pdb, chain A (#3), sequence
alignment score = 146.8  
RMSD between 61 pruned atom pairs is 0.852 angstroms; (across all 127 pairs:
12.283)  
  

> show #2 models

> lighting simple

> graphics silhouettes true

> graphics silhouettes false

> lighting shadows true

> ui tool show "Side View"

> view orient

> hide #3 models

> hide #2 models

> show #2 models

> hide #2 models

> show #2 models

> hide #2 models

> show #2 models

> hide #2 models

> show #2 models

> hide #2 models

> show #2 models

> hide #2 models

> show #3 models

> hide #3 models

> show #3 models

> hide #3 models

> show #3 models

> hide #3 models

> show #2 models

> hide #2 models

> show #2 models

> hide #2 models

> show #2 models

> hide #2 models

> show #2 models

> hide #2 models

> show #2 models

> hide #2 models

> open 3mxo

Summary of feedback from opening 3mxo fetched from pdb  
---  
notes | Fetching compressed mmCIF 3mxo from
http://files.rcsb.org/download/3mxo.cif  
Fetching CCD EDO from http://ligand-expo.rcsb.org/reports/E/EDO/EDO.cif  
Fetching CCD PG4 from http://ligand-expo.rcsb.org/reports/P/PG4/PG4.cif  
Fetching CCD CL from http://ligand-expo.rcsb.org/reports/C/CL/CL.cif  
Fetching CCD PGE from http://ligand-expo.rcsb.org/reports/P/PGE/PGE.cif  
Fetching CCD PEG from http://ligand-expo.rcsb.org/reports/P/PEG/PEG.cif  
  
3mxo title:  
Crystal structure oh human phosphoglycerate mutase family member 5 (PGAM5)
[more info...]  
  
Chain information for 3mxo #4  
---  
Chain | Description | UniProt  
A B | Serine/threonine-protein phosphatase PGAM5, mitochondrial | PGAM5_HUMAN  
  
Non-standard residues in 3mxo #4  
---  
CL — chloride ion  
EDO — 1,2-ethanediol (ethylene glycol)  
PEG — di(hydroxyethyl)ether  
PG4 — tetraethylene glycol  
PGE — triethylene glycol  
  
3mxo mmCIF Assemblies  
---  
1| author_defined_assembly  
2| software_defined_assembly  
  

> hide #!1,4 atoms

> ui tool show Matchmaker

> matchmaker #!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 1ujc, chain A (#1) with 3mxo, chain B (#4), sequence alignment
score = 214.1  
RMSD between 94 pruned atom pairs is 0.950 angstroms; (across all 152 pairs:
7.474)  
  

> select #4/A:88-289

1500 atoms, 1530 bonds, 1 pseudobond, 188 residues, 2 models selected  

> hide sel cartoons

> show #3 models

> color #4 #eeaf73ff

> color #4 #ee9045ff

> color #4 #ee614dff

> color #4 #ee4fe0ff

> color #4 #ecee30ff

> color #4 #ee9e1aff

> hide #!4 models

> show #2 models

> hide #2 models

> show #!4 models

Populating font family aliases took 467 ms. Replace uses of missing font
family "Consolas" with one that exists to avoid this cost.  

> alphafold predict
> MAFRQALQLAACGLAGGSAAVLFSAVAVGKPRAGGDAEPRPAEPPAWAGGARPGPGVWDPNWDRREPLSLINVRKRLDHYKAKATRHIFLIRHSQYHVDGSLEKDRTLTPLGREQAELTGLRLASLGLKFNKIVHSSMTRAIETTDIISRHLPGVCKVSTDLLREGAPIEPDPPVSHWKPEAVQYYEDGARIEAAFRNYIHRADARQEEDSYEIFICHANVIRYIVCRALQFPPEGWLRLSLNNGSITHLVIRPNGRVALRTLGDTGFMPPDKITRS

Running AlphaFold prediction  

> hide #!1 models

> hide #3 models

> show #3 models

> hide #!4 models

> hide #3 models

> show #!4 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

AlphaFold prediction finished  
Results in /Users/akash/Downloads/ChimeraX/AlphaFold/prediction_4  

> open /Users/akash/Downloads/ChimeraX/AlphaFold/prediction_4/best_model.pdb

Chain information for best_model.pdb #5  
---  
Chain | Description  
A | No description available  
  

> ui tool show Matchmaker

> matchmaker #5 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 1ujc, chain A (#1) with best_model.pdb, chain A (#5), sequence
alignment score = 194.4  
RMSD between 94 pruned atom pairs is 0.918 angstroms; (across all 153 pairs:
8.270)  
  

> show #!1 models

> hide #!4 models

> hide #5 models

> select his 8

Expected an objects specifier or a keyword  

> select 1ujc, his8

Expected an objects specifier or a keyword  

> select ::name="HIS"

630 atoms, 630 bonds, 63 residues, 5 models selected  

> show sel & #!1 atoms

> rainbow sel & #!1

> show #!4 models

> hide #!1 models

> show sel & #!4 atoms

> show #!1 models

> show #5 models

> hide #!1 models

> hide #!4 models

> nucleotides sel & #5 atoms

> style nucleic & sel & #5 stick

Changed 0 atom styles  

> show sel & #5 atoms

> rainbow sel & #5

> show #!4 models

> show #!1 models

> hide #!4 models

> hide #!1 models

> show #!1 models

> hide #5 models

> show #5 models

> show #!4 models

> hide #!1 models

> hide #!4 models

> show #!1 models

> hide #!1 models

> show #!4 models

> hide #!4 models

> show #!4 models

> color sel & #5#!4 bychain

> select
> ::name="CA"::name="CL"::name="EDO"::name="HOH"::name="PEG"::name="PG4"::name="PGE"::name="SO4"::name="WO4"

1386 atoms, 100 bonds, 5 pseudobonds, 1286 residues, 4 models selected  

> select #1/A

1405 atoms, 1190 bonds, 7 pseudobonds, 392 residues, 2 models selected  

> show #3 models

> hide #3,5#!4 atoms

> color #3,5#!4 byhetero

> show #3,5#!4 surfaces

> show #!3-5 surfaces

> alphafold predict
> VESGEEELASKLDHYKAKATRHIFLIRHSQYHVDGSLEKDRTLTPLGREQAELTGLRLASLGLKFNKIVHSSMTRAIETTDIISRHLPGVCKVSTDLLREGAPIEPDPPVSHWKPEAVQYYEDGARIEAAFRNYIHRADARQEEDSYEIFICHANVIRYIVCRALQFPPEGWLRLSLNNGSITHLVIRPNGRVALRTLGDTGFMPPDKITRS

Running AlphaFold prediction  

> hide #!3-5 surfaces

> hide #!4 models

> hide #!3 models

AlphaFold prediction finished  
Results in /Users/akash/Downloads/ChimeraX/AlphaFold/prediction_5  

> open /Users/akash/Downloads/ChimeraX/AlphaFold/prediction_5/best_model.pdb

Chain information for best_model.pdb #6  
---  
Chain | Description  
A | No description available  
  

> select subtract #1

Nothing selected  

> hide #!5 models

> show #!5 models

> ui tool show Matchmaker

> matchmaker #6 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 1ujc, chain A (#1) with best_model.pdb, chain A (#6), sequence
alignment score = 194.4  
RMSD between 94 pruned atom pairs is 0.915 angstroms; (across all 153 pairs:
8.313)  
  

> show #!4 models

> hide #!5 models

> show #!5 models

> hide #6 models

> show #6 models

> hide #!5 models

> show #!1 models

> show #!5 models

> hide #6 models

> hide #!4 models

> show #!1,5 surfaces

> hide #!1,5 surfaces

> hide #!1 models

> show #!5 surfaces

> show #!4 models

> hide #!4-5 surfaces

> hide #!4 models

> hide #!5 models

> show #2 models

> show #!1 models

> hide #2 models

> show #!5 models

> turn y 1 360

> set bgColor white

> movie record

> turn y 1 360

> wait

> movie encode

Movie saved to /Users/akash/Desktop/movie.mp4  
  

> hide #!5 models

> show #!4 models

> hide #!1 models

> rainbow #!4

> show #!4 cartoons

> select #4/B:88-289

1514 atoms, 1544 bonds, 1 pseudobond, 191 residues, 2 models selected  

> show #!1 models

> select #4/B:88-289

1514 atoms, 1544 bonds, 1 pseudobond, 191 residues, 2 models selected  

> select #4/B:88-289

1514 atoms, 1544 bonds, 1 pseudobond, 191 residues, 2 models selected  

> select #4/B:88-289

1514 atoms, 1544 bonds, 1 pseudobond, 191 residues, 2 models selected  

> select #4/A:88-289

1500 atoms, 1530 bonds, 1 pseudobond, 188 residues, 2 models selected  

> hide sel cartoons

> hide #!4 models

> show #!4 models

> hide #!1 models

> color (#!4 & sel) byhetero

> color (#!4 & sel) #cdffd6ff

> color (#!4 & sel) #cffff0ff

> color (#!4 & sel) #b6daffff

> color (#!4 & sel) #7990ffff

> color (#!4 & sel) #667bffff

> color (#!4 & sel) #6174ffff

> color (#!4 & sel) #5e73ffff

> color (#!4 & sel) #516affff

> color (#!4 & sel) #4a63ffff

> color (#!4 & sel) #4963ffff

> color (#!4 & sel) #4962ffff

> color (#!4 & sel) #4a62ffff

> color (#!4 & sel) #5060ffff

> color (#!4 & sel) #585bffff

> color (#!4 & sel) #5d5bffff

> color (#!4 & sel) #5e5cffff

> select add #4

3413 atoms, 3146 bonds, 2 pseudobonds, 706 residues, 3 models selected  

> color (#!4 & sel) byhetero

> color (#!4 & sel) blue

> color (#!4 & sel) light sea green

> color (#!4 & sel) cornflower blue

> select subtract #4

2 models selected  

> show #!1 models

> movie record

> turn y 1 360

> wait

> movie encode

Movie saved to /Users/akash/Desktop/movie.mp4  
  

> hide #!1 models

> show #!3 models

> hide #!3 models

> show #!5 models

> hide #!4 models

> show #6 models

> hide #!5 models

> show #!1 models

> movie record

> turn y 1 360

> wait

> movie encode

Movie saved to /Users/akash/Desktop/movie.mp4  
  

> show #!5 models

> hide #6 models

> movie record

> turn y 1 360

> wait

> movie encode

Movie saved to /Users/akash/Desktop/movie.mp4  
  


===== Log before crash end =====

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.6rc202304202331 (2023-04-20)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.1 INTEL-20.2.44
OpenGL renderer: Intel(R) UHD Graphics 617
OpenGL vendor: Intel Inc.

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: MacBookAir8,2
      Processor Name: Dual-Core Intel Core i5
      Processor Speed: 1.6 GHz
      Number of Processors: 1
      Total Number of Cores: 2
      L2 Cache (per Core): 256 KB
      L3 Cache: 4 MB
      Hyper-Threading Technology: Enabled
      Memory: 8 GB
      System Firmware Version: 1916.40.8.0.0 (iBridge: 20.16.420.0.0,0)
      OS Loader Version: 564.40.4~27

Software:

    System Software Overview:

      System Version: macOS 13.0.1 (22A400)
      Kernel Version: Darwin 22.1.0
      Time since boot: 22 minutes, 33 seconds

Graphics/Displays:

    Intel UHD Graphics 617:

      Chipset Model: Intel UHD Graphics 617
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x87c0
      Revision ID: 0x0002
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


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
    ChimeraX-AddH: 2.2.4
    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: 1.6rc202304202331
    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-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
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 3.2.0
    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 Eric Pettersen, 3 years ago

Component: Unassigned → Input/Output
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Crash after saving movie

comment:2 by Eric Pettersen, 3 years ago

Resolution: → can't reproduce
Status: assigned → closed
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