Opened 23 months ago

Closed 23 months ago

Last modified 23 months ago

#10304 closed defect (can't reproduce)

Crash after computing/showing surface

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

Description

The following bug report has been submitted:
Platform:        macOS-13.1-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.
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{
  "uptime" : 1100000,
  "procRole" : "Foreground",
  "version" : 2,
  "userID" : 501,
  "deployVersion" : 210,
  "modelCode" : "Mac14,7",
  "coalitionID" : 83171,
  "osVersion" : {
    "train" : "macOS 13.1",
    "build" : "22C65",
    "releaseType" : "User"
  },
  "captureTime" : "2023-12-07 17:00:19.1673 -0500",
  "incident" : "128DDBDC-E72A-4619-81BB-26CF1933A072",
  "pid" : 73752,
  "translated" : false,
  "cpuType" : "ARM-64",
  "roots_installed" : 0,
  "bug_type" : "309",
  "procLaunch" : "2023-11-30 12:26:41.2318 -0500",
  "procStartAbsTime" : 21060059750723,
  "procExitAbsTime" : 27411267734280,
  "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":"30E58AB6-21DF-5778-97D8-5CEB28F56115","thirdParty":true},
  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "7B494321-7AC5-A034-C77A-3B3421D35ADB",
  "throttleTimeout" : 2147483647,
  "wakeTime" : 6,
  "sleepWakeUUID" : "7A103E86-DAD5-4E20-A8EB-64E9122F3E73",
  "sip" : "enabled",
  "exception" : {"codes":"0x0000000000000001, 0x00000001879f68f8","rawCodes":[1,6570338552],"type":"EXC_BREAKPOINT","signal":"SIGTRAP"},
  "termination" : {"flags":0,"code":5,"namespace":"SIGNAL","indicator":"Trace\/BPT trap: 5","byProc":"exc handler","byPid":73752},
  "os_fault" : {"process":"ChimeraX"},
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  "faultingThread" : 30,
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    "name" : "libopenblas64_.0.dylib"
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},
  "trialInfo" : {
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  "reportNotes" : [
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}
===== Log before crash start =====
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
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/lamiawahba/Downloads/AF-P90786-F1-model_v4.pdb format pdb

AF-P90786-F1-model_v4.pdb title:  
Alphafold monomer V2.0 prediction for piwi-like protein (P90786) [more
info...]  
  
Chain information for AF-P90786-F1-model_v4.pdb #1  
---  
Chain | Description | UniProt  
A | piwi-like protein | P90786_CAEEL 1-824  
  

> style sphere

Changed 6589 atom styles  

> show atoms

> hide atoms

> show atoms

> hide atoms

> label #1 text "{0.name} {0.number}{0.insertion_code}"

> ~label #1 residues

> select

6589 atoms, 6721 bonds, 824 residues, 1 model selected  

> help help:user/menu.html#selectzone

> style sel stick

Changed 6589 atom styles  

> style sel stick

Changed 6589 atom styles  

> style sel sphere

Changed 6589 atom styles  

> select nucleic-acid

Nothing selected  

> nucleotides atoms

> style nucleic stick

Changed 0 atom styles  

> volume style surface

No volumes specified  

> volume step 1

No volumes specified  

> ui mousemode right select

> ui mousemode right rotate

> ui mousemode right label

Alignment identifier is 1/A  

> select
> /A:31-33,82-90,92-98,147-163,183-185,220-230,235-246,284-292,324-326,334-338,340-348,354-370,372-381,416-421,441-461,478-492,509-522,532-534,539-541,548-562,619-640,658-660,662-687,767-780,793-809,815-817

2263 atoms, 2278 bonds, 277 residues, 1 model selected  

> select /A:315

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:315-376

507 atoms, 515 bonds, 62 residues, 1 model selected  

> select /A:311

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:311-415

851 atoms, 868 bonds, 105 residues, 1 model selected  

> select /A:215-216

18 atoms, 17 bonds, 2 residues, 1 model selected  

> select /A:215-217

27 atoms, 26 bonds, 3 residues, 1 model selected  

> select /A:217

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:217-269

455 atoms, 463 bonds, 53 residues, 1 model selected  

> select /A:217

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:217-354

1134 atoms, 1159 bonds, 138 residues, 1 model selected  

> select /A:217

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:217-354

1134 atoms, 1159 bonds, 138 residues, 1 model selected  

> select /A:217-354

1134 atoms, 1159 bonds, 138 residues, 1 model selected  

> select
> /A:48-54,56-61,67-76,108-111,119-124,131-143,167-169,172-174,180-182,187-200,203-216,250-253,258-261,264-266,274-277,280-283,303-307,319-322,327-329,383-385,390-396,401-403,407-409,433-438,469-473,499-504,527-531,577-586,594-601,609-616,648-654,695-702,709-711,726-728,738-743,755-762

1767 atoms, 1773 bonds, 213 residues, 1 model selected  

> select /A:217-354

1134 atoms, 1159 bonds, 138 residues, 1 model selected  

> select
> /A:48-54,56-61,67-76,108-111,119-124,131-143,167-169,172-174,180-182,187-200,203-216,250-253,258-261,264-266,274-277,280-283,303-307,319-322,327-329,383-385,390-396,401-403,407-409,433-438,469-473,499-504,527-531,577-586,594-601,609-616,648-654,695-702,709-711,726-728,738-743,755-762

1767 atoms, 1773 bonds, 213 residues, 1 model selected  

> select /A:217-354

1134 atoms, 1159 bonds, 138 residues, 1 model selected  

> color sel red

> select /A:489

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:489

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select
> /A:48-54,56-61,67-76,108-111,119-124,131-143,167-169,172-174,180-182,187-200,203-216,250-253,258-261,264-266,274-277,280-283,303-307,319-322,327-329,383-385,390-396,401-403,407-409,433-438,469-473,499-504,527-531,577-586,594-601,609-616,648-654,695-702,709-711,726-728,738-743,755-762

1767 atoms, 1773 bonds, 213 residues, 1 model selected  

> ui mousemode right select

> ui mousemode right rotate

> ui mousemode right zoom

> ui mousemode right translate

> ui mousemode right select

> select
> /A:31-33,82-90,92-98,147-163,183-185,220-230,235-246,284-292,324-326,334-338,340-348,354-370,372-381,416-421,441-461,478-492,509-522,532-534,539-541,548-562,619-640,658-660,662-687,767-780,793-809,815-817

2263 atoms, 2278 bonds, 277 residues, 1 model selected  

> select /A:498

10 atoms, 10 bonds, 1 residue, 1 model selected  

> select /A:498-822

2560 atoms, 2610 bonds, 325 residues, 1 model selected  

> color sel blue

> select
> /A:48-54,56-61,67-76,108-111,119-124,131-143,167-169,172-174,180-182,187-200,203-216,250-253,258-261,264-266,274-277,280-283,303-307,319-322,327-329,383-385,390-396,401-403,407-409,433-438,469-473,499-504,527-531,577-586,594-601,609-616,648-654,695-702,709-711,726-728,738-743,755-762

1767 atoms, 1773 bonds, 213 residues, 1 model selected  

> select
> /A:31-33,82-90,92-98,147-163,183-185,220-230,235-246,284-292,324-326,334-338,340-348,354-370,372-381,416-421,441-461,478-492,509-522,532-534,539-541,548-562,619-640,658-660,662-687,767-780,793-809,815-817

2263 atoms, 2278 bonds, 277 residues, 1 model selected  

> style sel sphere

Changed 2263 atom styles  

> color sel bychain

> save /Users/lamiawahba/Desktop/prg-1.cxs

> color sel bychain

> style sel sphere

Changed 2263 atom styles  

> hide target m

> show target m

> view clip false

> view orient

> view clip false

> show target m

> log metadata #1

Metadata for AF-P90786-F1-model_v4.pdb #1  
---  
Title | Alphafold monomer V2.0 prediction for piwi-like protein (P90786)  
Source (natural) | Caenorhabditis elegans  
  
> log chains #1

Chain information for AF-P90786-F1-model_v4.pdb #1  
---  
Chain | Description | UniProt  
A | piwi-like protein | P90786_CAEEL 1-824  
  

> ui tool show "Show Sequence Viewer"

> sequence chain /A

Alignment identifier is 1/A  

> select
> /A:48-54,56-61,67-76,108-111,119-124,131-143,167-169,172-174,180-182,187-200,203-216,250-253,258-261,264-266,274-277,280-283,303-307,319-322,327-329,383-385,390-396,401-403,407-409,433-438,469-473,499-504,527-531,577-586,594-601,609-616,648-654,695-702,709-711,726-728,738-743,755-762

1767 atoms, 1773 bonds, 213 residues, 1 model selected  

> select /A:13

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select /A:13-51

289 atoms, 292 bonds, 39 residues, 1 model selected  

> select
> /A:31-33,82-90,92-98,147-163,183-185,220-230,235-246,284-292,324-326,334-338,340-348,354-370,372-381,416-421,441-461,478-492,509-522,532-534,539-541,548-562,619-640,658-660,662-687,767-780,793-809,815-817

2263 atoms, 2278 bonds, 277 residues, 1 model selected  

> select /A:220

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:220-228

83 atoms, 85 bonds, 9 residues, 1 model selected  

> select /A:312-313

16 atoms, 16 bonds, 2 residues, 1 model selected  

> select /A:312-319

59 atoms, 61 bonds, 8 residues, 1 model selected  

> select /A:367-403

296 atoms, 300 bonds, 37 residues, 1 model selected  

> select /A:367-407

325 atoms, 329 bonds, 41 residues, 1 model selected  

> select /A:311

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:311-402

742 atoms, 756 bonds, 92 residues, 1 model selected  

> color #1 #ebe0d1ff

> color #1 #ebe4d2ff

> ui tool show AlphaFold

> color sel byelement

> select /A:217

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:217-394

1458 atoms, 1487 bonds, 178 residues, 1 model selected  

> select /A:217

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:217-360

1187 atoms, 1212 bonds, 144 residues, 1 model selected  

> select /A:217

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:217-354

1134 atoms, 1159 bonds, 138 residues, 1 model selected  

> color sel red

> select sequence EESMY

44 atoms, 44 bonds, 5 residues, 1 model selected  

> select /A:498

10 atoms, 10 bonds, 1 residue, 1 model selected  

> select /A:498-821

2549 atoms, 2598 bonds, 324 residues, 1 model selected  

> color sel medium blue

> save /Users/lamiawahba/Desktop/prg-1.cxs

> select ::name="LYS"

540 atoms, 482 bonds, 60 residues, 1 model selected  

> color sel yellow

> color sel bychain

> select
> /A:48-54,56-61,67-76,108-111,119-124,131-143,167-169,172-174,180-182,187-200,203-216,250-253,258-261,264-266,274-277,280-283,303-307,319-322,327-329,383-385,390-396,401-403,407-409,433-438,469-473,499-504,527-531,577-586,594-601,609-616,648-654,695-702,709-711,726-728,738-743,755-762

1767 atoms, 1773 bonds, 213 residues, 1 model selected  

> select /A:498-821

2549 atoms, 2598 bonds, 324 residues, 1 model selected  

> view clip false

> log metadata #1

Metadata for AF-P90786-F1-model_v4.pdb #1  
---  
Title | Alphafold monomer V2.0 prediction for piwi-like protein (P90786)  
Source (natural) | Caenorhabditis elegans  
  
> log chains #1

Chain information for AF-P90786-F1-model_v4.pdb #1  
---  
Chain | Description | UniProt  
A | piwi-like protein | P90786_CAEEL 1-824  
  

> view clip false

> select /A:636

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:636

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select
> /A:48-54,56-61,67-76,108-111,119-124,131-143,167-169,172-174,180-182,187-200,203-216,250-253,258-261,264-266,274-277,280-283,303-307,319-322,327-329,383-385,390-396,401-403,407-409,433-438,469-473,499-504,527-531,577-586,594-601,609-616,648-654,695-702,709-711,726-728,738-743,755-762

1767 atoms, 1773 bonds, 213 residues, 1 model selected  

> select /A:537-538

13 atoms, 12 bonds, 2 residues, 1 model selected  

> select /A:537-538

13 atoms, 12 bonds, 2 residues, 1 model selected  

> select /A:583-584

16 atoms, 15 bonds, 2 residues, 1 model selected  

> select /A:583-584

16 atoms, 15 bonds, 2 residues, 1 model selected  

> style sel stick

Changed 16 atom styles  

> style sel stick

Changed 16 atom styles  

> style sel ball

Changed 16 atom styles  

> nucleotides sel atoms

> style nucleic & sel stick

Changed 0 atom styles  

> nucleotides sel fill

> style nucleic & sel stick

Changed 0 atom styles  

> style sel ball

Changed 16 atom styles  

> rainbow sel

> style sel ball

Changed 16 atom styles  

> style sel stick

Changed 16 atom styles  

> style sel sphere

Changed 16 atom styles  

> color sel bychain

> color sel byhetero

> color sel bypolymer

> rainbow sel

> coulombic sel

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for AF-P90786-F1-model_v4.pdb_A SES surface #1.1: minimum,
-19.72, mean 0.46, maximum 16.36  
To also show corresponding color key, enter the above coulombic command and
add key true  

> color sel bynucleotide

> color sel byhetero

> color bfactor sel

16 atoms, 2 residues, 1 surfaces, atom bfactor range 89.8 to 94.4  

> interfaces select & ~solvent

Missing or invalid "atoms" argument: invalid atoms specifier  
Destroying pre-existing alignment with identifier 1/A  
Alignment identifier is 1/A  

> style sel sphere

Changed 16 atom styles  

> select /A:824

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A

6589 atoms, 6721 bonds, 824 residues, 1 model selected  

> style sel sphere

Changed 6589 atom styles  

> lighting full

> set bgColor black

> set bgColor white

> set bgColor black

> show sel surfaces

> show sel cartoons

> show sel atoms

> show sel cartoons

> hide sel atoms

> hide sel cartoons

> hide sel surfaces

> show sel surfaces

> show sel cartoons

> hide sel surfaces

> hide sel cartoons

> show sel cartoons

> show sel atoms

> hide sel cartoons

> show sel cartoons

> hide sel cartoons

> show sel cartoons

> hide sel cartoons

> show sel cartoons

> hide sel surfaces

> hide sel cartoons

> hide sel atoms

> show sel atoms

> show sel surfaces

> hide sel surfaces

> save /Users/lamiawahba/Desktop/image1.png supersample 3

> ui tool show "Side View"

> view orient

> view

> view sel

> ui mousemode right "rotate selected models"

> ui mousemode right rotate

> save /Users/lamiawahba/Desktop/image2.png supersample 3

> save /Users/lamiawahba/Desktop/image3.png supersample 3

> hide sel surfaces

> hide sel cartoons

> hide sel atoms

> show sel atoms

> style sel stick

Changed 6589 atom styles  

> style sel ball

Changed 6589 atom styles  

> show sel cartoons

> select /A

6589 atoms, 6721 bonds, 824 residues, 1 model selected  

> select /A:824

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:824

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:824

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:596-642

380 atoms, 389 bonds, 47 residues, 1 model selected  

> select /A:596-643

389 atoms, 398 bonds, 48 residues, 1 model selected  

> select /A

6589 atoms, 6721 bonds, 824 residues, 1 model selected  

> select /A:462

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:462-507

346 atoms, 350 bonds, 46 residues, 1 model selected  

> select /A

6589 atoms, 6721 bonds, 824 residues, 1 model selected  

> select /A:641

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:641-642

16 atoms, 15 bonds, 2 residues, 1 model selected  

> style sel stick

Changed 16 atom styles  

> style sel ball

Changed 16 atom styles  

> style sel ball

Changed 16 atom styles  

> hide sel atoms

> show sel atoms

> show sel cartoons

> show sel surfaces

> style sel stick

Changed 16 atom styles  

> nucleotides sel fill

> style nucleic & sel stick

Changed 0 atom styles  

> nucleotides sel atoms

> style nucleic & sel stick

Changed 0 atom styles  

> nucleotides sel tube/slab shape box

> select /A

6589 atoms, 6721 bonds, 824 residues, 1 model selected  

> style sel ball

Changed 6589 atom styles  

> style sel ball

Changed 6589 atom styles  

> style sel sphere

Changed 6589 atom styles  

> style sel sphere

Changed 6589 atom styles  

> style sel stick

Changed 6589 atom styles  

> nucleotides sel tube/slab shape box

> nucleotides sel atoms

> style nucleic & sel stick

Changed 0 atom styles  

> nucleotides sel atoms

> style nucleic & sel stick

Changed 0 atom styles  

> nucleotides sel atoms

> style nucleic & sel stick

Changed 0 atom styles  

> nucleotides sel fill

> style nucleic & sel stick

Changed 0 atom styles  

> hide sel atoms

> select /A:824

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:823-824

20 atoms, 20 bonds, 2 residues, 1 model selected  

> select /A:639

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:639-640

14 atoms, 13 bonds, 2 residues, 1 model selected  

> select /A

6589 atoms, 6721 bonds, 824 residues, 1 model selected  

> select /A:643-644

16 atoms, 15 bonds, 2 residues, 1 model selected  

> select /A:642-644

24 atoms, 23 bonds, 3 residues, 1 model selected  

> show sel surfaces

> hide sel surfaces

> select /A:641

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:641

8 atoms, 7 bonds, 1 residue, 1 model selected  

> hide sel surfaces

> interfaces select & ~solvent

Missing or invalid "atoms" argument: invalid atoms specifier  

> show sel surfaces

> hide sel surfaces

> select /A:561

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select /A:561

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select /A:824

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A

6589 atoms, 6721 bonds, 824 residues, 1 model selected  

> show sel surfaces

> select /A:24

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:24

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:42

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:42

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:51

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:51

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:82

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:82-83

14 atoms, 13 bonds, 2 residues, 1 model selected  

> select /A:81-82

15 atoms, 14 bonds, 2 residues, 1 model selected  

> select /A:81-82

15 atoms, 14 bonds, 2 residues, 1 model selected  

> select /A:82-83

14 atoms, 13 bonds, 2 residues, 1 model selected  

> select /A:83

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select /A:82

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:82

9 atoms, 8 bonds, 1 residue, 1 model selected  

> hide sel surfaces

> show sel surfaces

> select /A:87

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:87

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:112

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:112

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:137-138

18 atoms, 17 bonds, 2 residues, 1 model selected  

> select /A:137-138

18 atoms, 17 bonds, 2 residues, 1 model selected  

> select /A:213

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:213

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:226

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:226

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:241

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:241

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:258

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:258

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:277

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:277

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:285

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:285

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:289

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:289

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:309

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:309

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:311

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:311

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:338

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:338

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:341

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:341

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:348

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:348

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:370

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:370

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:373

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:373

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:379

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:379

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:398

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:398

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:405

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:405

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:406

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:406

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:411

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:411

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:420

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:420

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:449

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:449

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:459

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:459

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:490-491

18 atoms, 17 bonds, 2 residues, 1 model selected  

> select /A:490-491

18 atoms, 17 bonds, 2 residues, 1 model selected  

> select /A:509

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:509

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:516

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:516-517

18 atoms, 17 bonds, 2 residues, 1 model selected  

> select /A:538

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:538-539

15 atoms, 14 bonds, 2 residues, 1 model selected  

> select /A:540

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:540

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:546

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:546

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:554

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:554

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:562

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:562

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A

6589 atoms, 6721 bonds, 824 residues, 1 model selected  

> select /A:569

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:569

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:575

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:575

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:591

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:591

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:593

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:593

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:632

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:632

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:665

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:665

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:670

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:670

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:682

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:682

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:689

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:689

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:695

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:695

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:703

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:703

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:711

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:711

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:770

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:770

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:777

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:777

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:800

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:800

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:820

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:820

9 atoms, 8 bonds, 1 residue, 1 model selected  

> open "/Users/lamiawahba/Library/Containers/com.apple.mail/Data/Library/Mail
> Downloads/753B9663-26C1-4821-942F-2BD094A26B5E/Undefined.pdb"

Chain information for Undefined.pdb #2  
---  
Chain | Description  
? | No description available  
  

> open "/Users/lamiawahba/Library/Containers/com.apple.mail/Data/Library/Mail
> Downloads/753B9663-26C1-4821-942F-2BD094A26B5E/Undefined.pdb"

Chain information for Undefined.pdb #3  
---  
Chain | Description  
? | No description available  
  

> show #2 target m

> select add #2

6376 atoms, 6505 bonds, 793 residues, 3 models selected  

> show #2 target m

> hide #!1 models

> show #!1 models

> hide #!1 models

> log metadata #2

The model has no metadata

> log chains #2

Chain information for Undefined.pdb #2  
---  
Chain | Description  
? | No description available  
  

> ui tool show "Show Sequence Viewer"

> sequence chain #2/? #3/?

Alignment identifier is 1  

> select #2/*:84 #3/*:84

16 atoms, 14 bonds, 2 residues, 2 models selected  

> select #2/*:84-134 #3/*:84-134

866 atoms, 882 bonds, 102 residues, 2 models selected  
1 [ID: 1] region 2 chains [52-102] RMSD: 0.000  
  

> select #2/*:33 #3/*:33

16 atoms, 14 bonds, 2 residues, 2 models selected  

> select #2/*:33-37 #3/*:33-37

94 atoms, 94 bonds, 10 residues, 2 models selected  
1 [ID: 1] region 2 chains [1-5] RMSD: 0.000  
  

> select add #1

6683 atoms, 6815 bonds, 834 residues, 3 models selected  

> select add #3

13003 atoms, 13265 bonds, 1621 residues, 4 models selected  

> close #3

> select add #2

12956 atoms, 13218 bonds, 1616 residues, 3 models selected  

> show #!1 models

> hide #2 models

> select ::name="LYS"

1062 atoms, 948 bonds, 118 residues, 2 models selected  

> select #1/A:779-824

376 atoms, 388 bonds, 46 residues, 1 model selected  

> select #1/A

6589 atoms, 6721 bonds, 824 residues, 1 model selected  

> select #1/A:310

7 atoms, 7 bonds, 1 residue, 1 model selected  

> select #1/A:309-310

16 atoms, 16 bonds, 2 residues, 1 model selected  

> select #1/A

6589 atoms, 6721 bonds, 824 residues, 1 model selected  

> select #1/A:309

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #1/A:309-310

16 atoms, 16 bonds, 2 residues, 1 model selected  

> select #1/A:311

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #1/A:310

7 atoms, 7 bonds, 1 residue, 1 model selected  

> select #1/A:309-310

16 atoms, 16 bonds, 2 residues, 1 model selected  

> select #1/A:309

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #1/A:309

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #1/A:309

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #1/A:309-311

25 atoms, 25 bonds, 3 residues, 1 model selected  

> coulombic sel

Coulombic values for AF-P90786-F1-model_v4.pdb_A SES surface #1.1: minimum,
-19.72, mean 0.46, maximum 16.36  
To also show corresponding color key, enter the above coulombic command and
add key true  

> coulombic sel

Coulombic values for AF-P90786-F1-model_v4.pdb_A SES surface #1.1: minimum,
-19.72, mean 0.46, maximum 16.36  
To also show corresponding color key, enter the above coulombic command and
add key true  

> coulombic sel

Coulombic values for AF-P90786-F1-model_v4.pdb_A SES surface #1.1: minimum,
-19.72, mean 0.46, maximum 16.36  
To also show corresponding color key, enter the above coulombic command and
add key true  

> coulombic sel

Coulombic values for AF-P90786-F1-model_v4.pdb_A SES surface #1.1: minimum,
-19.72, mean 0.46, maximum 16.36  
To also show corresponding color key, enter the above coulombic command and
add key true  

> coulombic sel

Coulombic values for AF-P90786-F1-model_v4.pdb_A SES surface #1.1: minimum,
-19.72, mean 0.46, maximum 16.36  
To also show corresponding color key, enter the above coulombic command and
add key true  

> mlp sel

Map values for surface "AF-P90786-F1-model_v4.pdb_A SES surface": minimum
-29.33, mean -5.891, maximum 22.8  
To also show corresponding color key, enter the above mlp command and add key
true  

> mlp sel

Map values for surface "AF-P90786-F1-model_v4.pdb_A SES surface": minimum
-29.33, mean -5.891, maximum 22.8  
To also show corresponding color key, enter the above mlp command and add key
true  

> color bfactor sel

25 atoms, 3 residues, 1 surfaces, atom bfactor range 73.4 to 79.5  

> rainbow sel

> color sel bypolymer

> rainbow sel

> color sel byhetero

> coulombic sel

Coulombic values for AF-P90786-F1-model_v4.pdb_A SES surface #1.1: minimum,
-19.72, mean 0.46, maximum 16.36  
To also show corresponding color key, enter the above coulombic command and
add key true  

> coulombic sel

Coulombic values for AF-P90786-F1-model_v4.pdb_A SES surface #1.1: minimum,
-19.72, mean 0.46, maximum 16.36  
To also show corresponding color key, enter the above coulombic command and
add key true  

> select #1/A

6589 atoms, 6721 bonds, 824 residues, 1 model selected  

> coulombic sel

Coulombic values for AF-P90786-F1-model_v4.pdb_A SES surface #1.1: minimum,
-19.72, mean 0.46, maximum 16.36  
To also show corresponding color key, enter the above coulombic command and
add key true  

> color sel bychain

> select #1/A:217

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #1/A:217-337

992 atoms, 1014 bonds, 121 residues, 1 model selected  

> select #1/A:217

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #1/A:217-354

1134 atoms, 1159 bonds, 138 residues, 1 model selected  

> color (#!1 & sel) forest green

> select #1/A:498

10 atoms, 10 bonds, 1 residue, 1 model selected  

> select #1/A:498-808

2448 atoms, 2496 bonds, 311 residues, 1 model selected  

> color (#!1 & sel) red

> select #1/A

6589 atoms, 6721 bonds, 824 residues, 1 model selected  

> interfaces select & ~solvent

Missing or invalid "atoms" argument: invalid atoms specifier  

> select #1/A:3-4

10 atoms, 9 bonds, 2 residues, 1 model selected  

> select #1/A:3-4

10 atoms, 9 bonds, 2 residues, 1 model selected  

> select #1/A

6589 atoms, 6721 bonds, 824 residues, 1 model selected  

> select #1/A:309

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #1/A:309

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #1/A

6589 atoms, 6721 bonds, 824 residues, 1 model selected  

> select #1/A:309

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #1/A:309-311

25 atoms, 25 bonds, 3 residues, 1 model selected  

> select #1/A:309

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #1/A:309

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #1/A:311

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #1/A:311

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #1/A:309

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #1/A:309

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #1/A:311

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #1/A:311-312

18 atoms, 17 bonds, 2 residues, 1 model selected  

> select #1/A

6589 atoms, 6721 bonds, 824 residues, 1 model selected  

> select #1/A:311

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #1/A:311

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #1/A:309

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #1/A:309

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #1/A:311

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #1/A:311

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #1/A:309

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #1/A:309-311

25 atoms, 25 bonds, 3 residues, 1 model selected  

> select #1/A

6589 atoms, 6721 bonds, 824 residues, 1 model selected  

> select #1/A:824

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #1/A:824

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #1/A

6589 atoms, 6721 bonds, 824 residues, 1 model selected  

> select #1/A:823-824

20 atoms, 20 bonds, 2 residues, 1 model selected  

> select #1/A:823-824

20 atoms, 20 bonds, 2 residues, 1 model selected  

> show target m

> log metadata #1

Metadata for AF-P90786-F1-model_v4.pdb #1  
---  
Title | Alphafold monomer V2.0 prediction for piwi-like protein (P90786)  
Source (natural) | Caenorhabditis elegans  
  
> log chains #1

Chain information for AF-P90786-F1-model_v4.pdb #1  
---  
Chain | Description | UniProt  
A | piwi-like protein | P90786_CAEEL 1-824  
  

> log metadata #2

The model has no metadata

> log chains #2

Chain information for Undefined.pdb #2  
---  
Chain | Description  
? | No description available  
  

> log metadata #1

Metadata for AF-P90786-F1-model_v4.pdb #1  
---  
Title | Alphafold monomer V2.0 prediction for piwi-like protein (P90786)  
Source (natural) | Caenorhabditis elegans  
  
> log chains #1

Chain information for AF-P90786-F1-model_v4.pdb #1  
---  
Chain | Description | UniProt  
A | piwi-like protein | P90786_CAEEL 1-824  
  

> log metadata #2

The model has no metadata

> log chains #2

Chain information for Undefined.pdb #2  
---  
Chain | Description  
? | No description available  
  

> nucleotides sel atoms

> style nucleic & sel stick

Changed 0 atom styles  

> nucleotides sel fill

> style nucleic & sel stick

Changed 0 atom styles  

> select #1/A

6589 atoms, 6721 bonds, 824 residues, 1 model selected  

Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 2 atomic models, 0 maps.  

> surface (#!1 & sel)

> surface hidePatches (#!1 & sel)

> hide #2 models

> select #1/A:97

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #1/A:97-98

17 atoms, 16 bonds, 2 residues, 1 model selected  

> select #1/A

6589 atoms, 6721 bonds, 824 residues, 1 model selected  

> select #1/A:48

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #1/A:48-49

16 atoms, 16 bonds, 2 residues, 1 model selected  

> surface (#!1 & sel)

> select #1/A

6589 atoms, 6721 bonds, 824 residues, 1 model selected  

> surface (#!1 & sel)


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

Log:
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 - 83
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 Pro
      Model Identifier: Mac14,7
      Model Number: Z16R0005YLL/A
      Chip: Apple M2
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 24 GB
      System Firmware Version: 8419.60.44
      OS Loader Version: 8419.60.44

Software:

    System Software Overview:

      System Version: macOS 13.1 (22C65)
      Kernel Version: Darwin 22.2.0
      Time since boot: 44 days, 7 hours, 34 minutes

Graphics/Displays:

    Apple M2:

      Chipset Model: Apple M2
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 10
      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
        DELL SE2722HX:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 75.00Hz
          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-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: 3.5.0
    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 (3)

comment:1 by Eric Pettersen, 23 months ago

Cc: Eric Pettersen added
Component: UnassignedSurface
Owner: set to Tom Goddard
Platform: all
Project: ChimeraX
Status: newassigned
Summary: ChimeraX bug report submissionCrash after computing/showing surface

comment:2 by Eric Pettersen, 23 months ago

Resolution: can't reproduce
Status: assignedclosed

comment:3 by Tom Goddard, 23 months ago

Says faultingThread:30 with EXC_BREAKPOINT. The traceback for thread 30 was uninformative.

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