ChimeraX bug report submission

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-15.5-x86_64-i386-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
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{
  "uptime" : 740000,
  "procRole" : "Background",
  "version" : 2,
  "userID" : 502,
  "deployVersion" : 210,
  "modelCode" : "MacBookPro18,1",
  "coalitionID" : 59378,
  "osVersion" : {
    "train" : "macOS 15.5",
    "build" : "24F74",
    "releaseType" : "User"
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  "captureTime" : "2025-06-12 14:25:08.7253 -0500",
  "codeSigningMonitor" : 1,
  "incident" : "C0BB6E78-B868-48AE-9281-5C9383577F47",
  "pid" : 4604,
  "translated" : true,
  "cpuType" : "X86-64",
  "roots_installed" : 0,
  "bug_type" : "309",
  "procLaunch" : "2025-06-12 11:56:00.6224 -0500",
  "procStartAbsTime" : 17728452628389,
  "procExitAbsTime" : 17870254610613,
  "procName" : "ChimeraX",
  "procPath" : "\/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
  "bundleInfo" : {"CFBundleShortVersionString":"1.8.0","CFBundleVersion":"1.8.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
  "storeInfo" : {"deviceIdentifierForVendor":"ACF28FB2-42FE-58C2-8DE5-A9B04FE55DAD","thirdParty":true},
  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "5CD00815-A492-345C-021D-25B424AB78F6",
  "appleIntelligenceStatus" : {"state":"unavailable","reasons":["siriAssetIsNotReady","assetIsNotReady","notOptedIn"]},
  "codeSigningID" : "edu.ucsf.cgl.ChimeraX",
  "codeSigningTeamID" : "LWV8X224YF",
  "codeSigningFlags" : 570491649,
  "codeSigningValidationCategory" : 6,
  "codeSigningTrustLevel" : 4294967295,
  "codeSigningAuxiliaryInfo" : 0,
  "bootSessionUUID" : "D0F15393-EBAE-4F26-B3FA-2E72EE20C036",
  "wakeTime" : 764,
  "sleepWakeUUID" : "36BCA6E1-1E54-45F0-BEFE-7BF0A8816228",
  "sip" : "enabled",
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  "termination" : {"flags":0,"code":5,"namespace":"SIGNAL","indicator":"Trace\/BPT trap: 5","byProc":"exc handler","byPid":4604},
  "os_fault" : {"process":"ChimeraX"},
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===== Log before crash start =====
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/rnkirchdoerf/Downloads/apply_ncs.pdb

Summary of feedback from opening /Users/rnkirchdoerf/Downloads/apply_ncs.pdb  
---  
warnings | Ignored bad PDB record found on line 4111  
  
  
Ignored bad PDB record found on line 7744  
  
  
Ignored bad PDB record found on line 11628  
  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
4103 messages similar to the above omitted  
Ignored bad PDB record found on line 15738  
  
  
Duplicate atom serial number found: 4109  
Duplicate atom serial number found: 4110  
Duplicate atom serial number found: 4111  
Duplicate atom serial number found: 4112  
Duplicate atom serial number found: 4113  
3626 messages similar to the above omitted  
Ignored bad PDB record found on line 19371  
  
  
Duplicate atom serial number found: 7740  
Duplicate atom serial number found: 7741  
Duplicate atom serial number found: 7742  
Duplicate atom serial number found: 7743  
Duplicate atom serial number found: 7744  
3877 messages similar to the above omitted  
Ignored bad PDB record found on line 23255  
  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
4103 messages similar to the above omitted  
Ignored bad PDB record found on line 27365  
  
  
Duplicate atom serial number found: 4109  
Duplicate atom serial number found: 4110  
Duplicate atom serial number found: 4111  
Duplicate atom serial number found: 4112  
Duplicate atom serial number found: 4113  
3626 messages similar to the above omitted  
Ignored bad PDB record found on line 30998  
  
  
Duplicate atom serial number found: 7740  
Duplicate atom serial number found: 7741  
Duplicate atom serial number found: 7742  
Duplicate atom serial number found: 7743  
Duplicate atom serial number found: 7744  
3877 messages similar to the above omitted  
Ignored bad PDB record found on line 34882  
  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
4103 messages similar to the above omitted  
Ignored bad PDB record found on line 38992  
  
  
Duplicate atom serial number found: 4109  
Duplicate atom serial number found: 4110  
Duplicate atom serial number found: 4111  
Duplicate atom serial number found: 4112  
Duplicate atom serial number found: 4113  
3626 messages similar to the above omitted  
Ignored bad PDB record found on line 42625  
  
  
Duplicate atom serial number found: 7740  
Duplicate atom serial number found: 7741  
Duplicate atom serial number found: 7742  
Duplicate atom serial number found: 7743  
Duplicate atom serial number found: 7744  
3877 messages similar to the above omitted  
Ignored bad PDB record found on line 46509  
  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
4103 messages similar to the above omitted  
Ignored bad PDB record found on line 50619  
  
  
Duplicate atom serial number found: 4109  
Duplicate atom serial number found: 4110  
Duplicate atom serial number found: 4111  
Duplicate atom serial number found: 4112  
Duplicate atom serial number found: 4113  
3626 messages similar to the above omitted  
Ignored bad PDB record found on line 54252  
  
  
Duplicate atom serial number found: 7740  
Duplicate atom serial number found: 7741  
Duplicate atom serial number found: 7742  
Duplicate atom serial number found: 7743  
Duplicate atom serial number found: 7744  
3877 messages similar to the above omitted  
Ignored bad PDB record found on line 58136  
  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
4103 messages similar to the above omitted  
Ignored bad PDB record found on line 62246  
  
  
Duplicate atom serial number found: 4109  
Duplicate atom serial number found: 4110  
Duplicate atom serial number found: 4111  
Duplicate atom serial number found: 4112  
Duplicate atom serial number found: 4113  
3626 messages similar to the above omitted  
Ignored bad PDB record found on line 65879  
  
  
Duplicate atom serial number found: 7740  
Duplicate atom serial number found: 7741  
Duplicate atom serial number found: 7742  
Duplicate atom serial number found: 7743  
Duplicate atom serial number found: 7744  
3877 messages similar to the above omitted  
Ignored bad PDB record found on line 69763  
  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
4103 messages similar to the above omitted  
Ignored bad PDB record found on line 73873  
  
  
Duplicate atom serial number found: 4109  
Duplicate atom serial number found: 4110  
Duplicate atom serial number found: 4111  
Duplicate atom serial number found: 4112  
Duplicate atom serial number found: 4113  
3626 messages similar to the above omitted  
Ignored bad PDB record found on line 77506  
  
  
Duplicate atom serial number found: 7740  
Duplicate atom serial number found: 7741  
Duplicate atom serial number found: 7742  
Duplicate atom serial number found: 7743  
Duplicate atom serial number found: 7744  
3877 messages similar to the above omitted  
Ignored bad PDB record found on line 81390  
  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
4103 messages similar to the above omitted  
Ignored bad PDB record found on line 85500  
  
  
Duplicate atom serial number found: 4109  
Duplicate atom serial number found: 4110  
Duplicate atom serial number found: 4111  
Duplicate atom serial number found: 4112  
Duplicate atom serial number found: 4113  
3626 messages similar to the above omitted  
Ignored bad PDB record found on line 89133  
  
  
Duplicate atom serial number found: 7740  
Duplicate atom serial number found: 7741  
Duplicate atom serial number found: 7742  
Duplicate atom serial number found: 7743  
Duplicate atom serial number found: 7744  
3877 messages similar to the above omitted  
Ignored bad PDB record found on line 93017  
  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
4103 messages similar to the above omitted  
Ignored bad PDB record found on line 97127  
  
  
Duplicate atom serial number found: 4109  
Duplicate atom serial number found: 4110  
Duplicate atom serial number found: 4111  
Duplicate atom serial number found: 4112  
Duplicate atom serial number found: 4113  
3626 messages similar to the above omitted  
Ignored bad PDB record found on line 100760  
  
  
Duplicate atom serial number found: 7740  
Duplicate atom serial number found: 7741  
Duplicate atom serial number found: 7742  
Duplicate atom serial number found: 7743  
Duplicate atom serial number found: 7744  
3877 messages similar to the above omitted  
Ignored bad PDB record found on line 104644  
  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
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4103 messages similar to the above omitted  
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3626 messages similar to the above omitted  
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Duplicate atom serial number found: 4113  
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Chain information for apply_ncs.pdb #1  
---  
Chain | Description  
A AB AE BC BF CA CD D DB DE EC EF FA FD G GB GE HC HF IA ID J JB JE KC KF LA LD M MB ME NC NF OA OD P PB PE QC QF RA RD S SB SE TC TF UA UD VB VE W WC WF XA XD YB YE Z ZC | No description available  
AA AD B BB BE CC CF DA DD E EB EE FC FF GA GD H HB HE IC IF JA JD K KB KE LC LF MA MD N NB NE OC OF PA PD Q QB QE RC RF SA SD T TB TE UC UF VA VD WB WE X XC XF YA YD ZB ZE | No description available  
AC AF BA BD C CB CE DC DF EA ED F FB FE GC GF HA HD I IB IE JC JF KA KD L LB LE MC MF NA ND O OB OE PC PF QA QD R RB RE SC SF TA TD UB UE V VC VF WA WD XB XE Y YC YF ZA ZD | No description available  
  

> open /Users/rnkirchdoerf/Downloads/J145map.mrc

Opened J145map.mrc as #2, grid size 540,540,540, pixel 1.03, shown at level
0.189, step 4, values float32  

> hide #1 models

> volume #2 step 1

> show #1 models

> hide atoms

> style stick

Changed 697260 atom styles  

> hide #!2 models

> show cartoons

> select /P:82

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select add /R:192

36 atoms, 34 bonds, 2 residues, 1 model selected  

> select add /Q:83

52 atoms, 49 bonds, 3 residues, 1 model selected  

> select up

299 atoms, 300 bonds, 18 residues, 1 model selected  

> select up

11621 atoms, 11779 bonds, 749 residues, 1 model selected  

> ui tool show "Show Sequence Viewer"

> sequence chain /P

Alignment identifier is 1/P  

> ui tool show "Show Sequence Viewer"

> sequence chain /R

Alignment identifier is 1/R  

> ui tool show "Show Sequence Viewer"

> sequence chain /Q

Alignment identifier is 1/Q  

> select sequence vlvvpdtk

7860 atoms, 7860 bonds, 480 residues, 1 model selected  

> select up

42780 atoms, 43200 bonds, 2940 residues, 1 model selected  

> select up

246480 atoms, 250080 bonds, 15540 residues, 1 model selected  

> name prot1 selection

"selection": invalid atom specifier  

> name prot1 sel

> select

697260 atoms, 706740 bonds, 44940 residues, 3 models selected  

> select clear

> select prot1

Nothing selected  

> select sel

Nothing selected  

> select sequence vlvvpdtk

7860 atoms, 7860 bonds, 480 residues, 1 model selected  

> select clear

> select sequence vlvvpdtk

7860 atoms, 7860 bonds, 480 residues, 1 model selected  

> select up

42780 atoms, 43200 bonds, 2940 residues, 1 model selected  

> select up

246480 atoms, 250080 bonds, 15540 residues, 1 model selected  

> name prot1 sel

> select clear

> select prot1

Nothing selected  

> ui tool show "Color Actions"

> select sequence vlvvpdtk

7860 atoms, 7860 bonds, 480 residues, 1 model selected  

> select up

42780 atoms, 43200 bonds, 2940 residues, 1 model selected  

> select up

246480 atoms, 250080 bonds, 15540 residues, 1 model selected  

> color lightblue greyl

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> color light grey

> select sequence drlkqitign

10140 atoms, 10080 bonds, 600 residues, 1 model selected  

> select up

21600 atoms, 21540 bonds, 1380 residues, 1 model selected  

> select up

232920 atoms, 236160 bonds, 15300 residues, 1 model selected  

> color sel gray

> select sequence glptrmp

6660 atoms, 6720 bonds, 420 residues, 1 model selected  

> select up

38220 atoms, 38700 bonds, 2520 residues, 1 model selected  

> select up

217860 atoms, 220500 bonds, 14100 residues, 1 model selected  

> list sel

Unknown command: list sel  

> color sel dim grey

> select clear

> set bgColor white

> color zone #2 near #1 distance 5

> show #!2 models

> hide #1 models

> select sequence glptrm

5820 atoms, 5820 bonds, 360 residues, 1 model selected  

> select up

38220 atoms, 38700 bonds, 2520 residues, 1 model selected  

> select up

217860 atoms, 220500 bonds, 14100 residues, 1 model selected  

> color sel white

> color zone #2 near #1 distance 5

> color sel black

> color zone #2 near #1 distance 5

> color #2 #797979ff

> color #2 #5e5e5eff

> color sel ZRG1 MCV-S

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  

> color sel 5E5E5E

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  

> color sel iron

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  

> color #2 #5f5f5fff

> color #2 #606060ff

> color #2 #656565ff

> color #2 #6a6a6aff

> color #2 #6f6f6fff

> color #2 #737373ff

> color #2 #767676ff

> color #2 #787878ff

> color #2 #7c7c7cff

> color #2 #808080ff

> color #2 #868686ff

> color #2 #878787ff

> color #2 #888888ff

> color #2 #8b8b8bff

> color #2 #8c8c8cff

> color #2 #8e8e8eff

> color #2 #8f8f8fff

> color #2 #909090ff

> color #2 #919191ff

> color #2 #909090ff

> color #2 #8e8e8eff

> color #2 #8b8b8bff

> color #2 #868686ff

> color #2 #838383ff

> color #2 #808080ff

> color #2 #797979ff

> color #2 #767676ff

> color #2 #747474ff

> color #2 #737373ff

> color #2 #717171ff

> color #2 #707070ff

> color #2 #727272ff

> color #2 #787878ff

> color #2 #7c7c7cff

> color #2 #7e7e7eff

> color #2 #808080ff

> color #2 #878787ff

> color #2 #888888ff

> color #2 #898989ff

> color #2 #8b8b8bff

> color #2 #8c8c8cff

> color #2 #8d8d8dff

> color #2 #8f8f8fff

> color #2 #909090ff

> color #2 #919191ff

> color #2 #929292ff

> color #2 #939393ff

> color #2 #949494ff

> color #2 #959595ff

> color #2 #969696ff

> colordef

> color name

Missing or invalid "name" argument: Expected a text string  

> hide #!2 models

> show #1 models

> select clear

> select sequence glptrm

5820 atoms, 5820 bonds, 360 residues, 1 model selected  

> select up

38220 atoms, 38700 bonds, 2520 residues, 1 model selected  

> select up

217860 atoms, 220500 bonds, 14100 residues, 1 model selected  

> color sel #5e5e5eff

> color zone #2 near #1 distance 5

> hide #1 models

> show #!2 models

> lighting soft

> lighting full

> lighting soft

> hide #!2 models

> show #1 models

> color sel #a9a9a9ff

> color zone #2 near #1 distance 5

> show #!2 models

> hide #1 models

> show #1 models

> color sel #d6d6d6ff

> color zone #2 near #1 distance 5

> select vlvvpdtk

Expected an objects specifier or a keyword  

> select sequence vlvvpdtk

7860 atoms, 7860 bonds, 480 residues, 1 model selected  

> select up

42780 atoms, 43200 bonds, 2940 residues, 1 model selected  

> select up

246480 atoms, 250080 bonds, 15540 residues, 1 model selected  

> color sel white

> color zone #2 near #1 distance 5

> hide #1 models

> ui tool show "Side View"

> save /Users/rnkirchdoerf/Desktop/RVC41_1.png width 1200 height 1239
> supersample 3 transparentBackground true

> open 6ppo

6ppo title:  
Rhinovirus C15 complexed with domain I of receptor CDHR3 [more info...]  
  
Chain information for 6ppo #3  
---  
Chain | Description | UniProt  
A | Capsid protein VP1 | E5D8F2_9ENTO 1-279  
B | Capsid protein VP3 | E5D8F2_9ENTO 1-235  
C | Capsid protein VP2 | E5D8F2_9ENTO 1-265  
D | Capsid protein VP4 | E5D8F2_9ENTO 1-66  
U | Cadherin-related family member 3 | CDHR3_HUMAN 20-130  
  
Non-standard residues in 6ppo #3  
---  
CA — calcium ion  
  
6ppo mmCIF Assemblies  
---  
1| complete icosahedral assembly  
2| icosahedral asymmetric unit  
3| icosahedral pentamer  
4| icosahedral 23 hexamer  
5| icosahedral asymmetric unit, std point frame  
  

> matchmaker #3 to #1/R

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 apply_ncs.pdb, chain R (#1) with 6ppo, chain C (#3), sequence
alignment score = 1056.5  
RMSD between 178 pruned atom pairs is 0.735 angstroms; (across all 253 pairs:
3.476)  
  

> ~show

> ribbon

> select add #2

246480 atoms, 250080 bonds, 15540 residues, 4 models selected  

> select subtract #2

246480 atoms, 250080 bonds, 15540 residues, 1 model selected  

> show #1 models

> select clear

> view #1/R

> ~ribbon #3/U

> transparency 50

> matchmaker #3 to #1/Q

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 apply_ncs.pdb, chain Q (#1) with 6ppo, chain B (#3), sequence
alignment score = 965.5  
RMSD between 158 pruned atom pairs is 1.092 angstroms; (across all 235 pairs:
3.013)  
  

> color #1/Q sky blue

> hide #!2 models

> color #1/P sky blue

> color #3/A medium blue

> color #3/C forest green

> color #1/R medium sea green

> color #1/R lime green

> color #3/B firebrick

> color #1/Q salmon

> ~ribbon #1/Q:1-34

> ribbon #1/Q:1-34

> hide #!3 models

> show #!2 models

> show#1/P

Unknown command: show#1/P  

> show #1/P

> hide H

> ribspline cardinal

Unknown command: ribspline cardinal  

> cardinal

Unknown command: cardinal  

> ribspline

Unknown command: ribspline  

> lighting full

> save /Users/rnkirchdoerf/Desktop/RVC41_vp1.png width 1200 height 1239
> supersample 3 transparentBackground true

> hide #1 models

> hide #!2 models

> show #1 models

> show #!3 models

> hide

> view #3

> color #1,3 #ffffffff

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> select sequence vlvvpd

5729 atoms, 5729 bonds, 364 residues, 2 models selected  

> select up

42924 atoms, 43348 bonds, 2960 residues, 2 models selected  

> select up

248580 atoms, 252246 bonds, 15801 residues, 2 models selected  

> select down

42924 atoms, 43348 bonds, 2960 residues, 2 models selected  

> select down

5729 atoms, 5729 bonds, 364 residues, 2 models selected  

> select up

42924 atoms, 43348 bonds, 2960 residues, 2 models selected  

> select up

248580 atoms, 252246 bonds, 15801 residues, 2 models selected  

> color sel white

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> select sequence drlkqit

7781 atoms, 7720 bonds, 425 residues, 2 models selected  

> select up

21674 atoms, 21613 bonds, 1390 residues, 2 models selected  

> select up

234879 atoms, 238173 bonds, 15553 residues, 2 models selected  

> color sel #d6d6d6ff

> select glptrmp

Expected an objects specifier or a keyword  

> select sequence glptrmp

6660 atoms, 6720 bonds, 420 residues, 1 model selected  

> select up

38220 atoms, 38700 bonds, 2520 residues, 1 model selected  

> select up

217860 atoms, 220500 bonds, 14100 residues, 1 model selected  

> color sel dim grey

> select clear

> color #3/A firebrick

> color #3/A medium blue

> color #3/B firebrick

> color #3/B forest green

> color #3/B firebrick

> color #3/C forest green

> color #1/P sky blue

> color #1/R lime green

> color #1/Q salmon

> select #1/P,Q,R

11621 atoms, 11779 bonds, 749 residues, 1 model selected  

> select ~sel & ##selected

685639 atoms, 694961 bonds, 44191 residues, 1 model selected  

> hide sel

> ~ribbon sel

> view #3

> hide pseudobonds

> ui tool show "Side View"

> lighting soft

> lighting shadows true intensity 0.5

> lighting soft

> save /Users/rnkirchdoerf/Desktop/RVC41_C41_C15compare.png width 1200 height
> 1239 supersample 3 transparentBackground true


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

Log:
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/rnkirchdoerf/Downloads/apply_ncs.pdb

Summary of feedback from opening /Users/rnkirchdoerf/Downloads/apply_ncs.pdb  
---  
warnings | Ignored bad PDB record found on line 4111  
  
  
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Duplicate atom serial number found: 7740  
Duplicate atom serial number found: 7741  
Duplicate atom serial number found: 7742  
Duplicate atom serial number found: 7743  
Duplicate atom serial number found: 7744  
3877 messages similar to the above omitted  
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Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
4103 messages similar to the above omitted  
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Duplicate atom serial number found: 4109  
Duplicate atom serial number found: 4110  
Duplicate atom serial number found: 4111  
Duplicate atom serial number found: 4112  
Duplicate atom serial number found: 4113  
3626 messages similar to the above omitted  
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Duplicate atom serial number found: 7740  
Duplicate atom serial number found: 7741  
Duplicate atom serial number found: 7742  
Duplicate atom serial number found: 7743  
Duplicate atom serial number found: 7744  
3877 messages similar to the above omitted  
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Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
4103 messages similar to the above omitted  
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Duplicate atom serial number found: 4109  
Duplicate atom serial number found: 4110  
Duplicate atom serial number found: 4111  
Duplicate atom serial number found: 4112  
Duplicate atom serial number found: 4113  
3626 messages similar to the above omitted  
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Duplicate atom serial number found: 7740  
Duplicate atom serial number found: 7741  
Duplicate atom serial number found: 7742  
Duplicate atom serial number found: 7743  
Duplicate atom serial number found: 7744  
3877 messages similar to the above omitted  
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Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
4103 messages similar to the above omitted  
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Duplicate atom serial number found: 4109  
Duplicate atom serial number found: 4110  
Duplicate atom serial number found: 4111  
Duplicate atom serial number found: 4112  
Duplicate atom serial number found: 4113  
3626 messages similar to the above omitted  
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Duplicate atom serial number found: 7740  
Duplicate atom serial number found: 7741  
Duplicate atom serial number found: 7742  
Duplicate atom serial number found: 7743  
Duplicate atom serial number found: 7744  
3877 messages similar to the above omitted  
Ignored bad PDB record found on line 697621  
  
  
Ignored bad PDB record found on line 697622  
  
Chain information for apply_ncs.pdb #1  
---  
Chain | Description  
A AB AE BC BF CA CD D DB DE EC EF FA FD G GB GE HC HF IA ID J JB JE KC KF LA LD M MB ME NC NF OA OD P PB PE QC QF RA RD S SB SE TC TF UA UD VB VE W WC WF XA XD YB YE Z ZC | No description available  
AA AD B BB BE CC CF DA DD E EB EE FC FF GA GD H HB HE IC IF JA JD K KB KE LC LF MA MD N NB NE OC OF PA PD Q QB QE RC RF SA SD T TB TE UC UF VA VD WB WE X XC XF YA YD ZB ZE | No description available  
AC AF BA BD C CB CE DC DF EA ED F FB FE GC GF HA HD I IB IE JC JF KA KD L LB LE MC MF NA ND O OB OE PC PF QA QD R RB RE SC SF TA TD UB UE V VC VF WA WD XB XE Y YC YF ZA ZD | No description available  
  

> open /Users/rnkirchdoerf/Downloads/J145map.mrc

Opened J145map.mrc as #2, grid size 540,540,540, pixel 1.03, shown at level
0.189, step 4, values float32  




OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple

Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro18,1
      Model Number: Z14Z00105LL/A
      Chip: Unknown
      Total Number of Cores: 10 (8 performance and 2 efficiency)
      Memory: 32 GB
      System Firmware Version: 11881.121.1
      OS Loader Version: 11881.121.1

Software:

    System Software Overview:

      System Version: macOS 15.5 (24F74)
      Kernel Version: Darwin 24.5.0
      Time since boot: 15 days, 14 hours, 28 minutes

Graphics/Displays:

    Apple M1 Pro:

      Chipset Model: Apple M1 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 16
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        MZ279:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 75.00Hz
          Main Display: Yes
          Mirror: Off
          Online: Yes


Installed Packages:
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    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 2.4.1
    Babel: 2.15.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 1.2.1
    certifi: 2023.11.17
    cftime: 1.6.4
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.17
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.7
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.57.1
    ChimeraX-AtomicLibrary: 14.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.4.6
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.12.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.7
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-Clipper: 0.23.1
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.8
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.3
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.4
    ChimeraX-DiffPlot: 1.0
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.8
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.10
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.3
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.1
    ChimeraX-MedicalToolbar: 1.0.3
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.17
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.5
    ChimeraX-PDB: 2.7.5
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.1
    ChimeraX-PubChem: 2.2
    ChimeraX-QScore: 1.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.4.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.0.15
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.16.5
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.39.1
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.3
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.2.1
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.1
    decorator: 5.1.1
    docutils: 0.20.1
    executing: 2.0.1
    filelock: 3.13.4
    fonttools: 4.53.0
    funcparserlib: 2.0.0a0
    glfw: 2.7.0
    grako: 3.16.5
    h5py: 3.11.0
    html2text: 2024.2.26
    idna: 3.7
    ihm: 1.0
    imagecodecs: 2024.1.1
    imagesize: 1.4.1
    ipykernel: 6.29.2
    ipython: 8.21.0
    ipywidgets: 8.1.3
    jedi: 0.19.1
    jinja2: 3.1.4
    jupyter-client: 8.6.0
    jupyter-core: 5.7.2
    jupyterlab-widgets: 3.0.11
    kiwisolver: 1.4.5
    line-profiler: 4.1.2
    lxml: 5.2.1
    lz4: 4.3.3
    MarkupSafe: 2.1.5
    matplotlib: 3.8.4
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.0
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 23.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.3.0
    pip: 24.0
    pkginfo: 1.10.0
    platformdirs: 4.2.2
    prompt-toolkit: 3.0.47
    psutil: 5.9.8
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pygments: 2.17.2
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.1.2
    pyproject-hooks: 1.1.0
    PyQt6-commercial: 6.6.1
    PyQt6-Qt6: 6.6.3
    PyQt6-sip: 13.6.0
    PyQt6-WebEngine-commercial: 6.6.0
    PyQt6-WebEngine-Qt6: 6.6.3
    python-dateutil: 2.9.0.post0
    pytz: 2024.1
    pyzmq: 26.0.3
    qtconsole: 5.5.1
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.13.0
    setuptools: 69.5.1
    setuptools-scm: 8.0.4
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 7.2.6
    sphinx-autodoc-typehints: 2.0.1
    sphinxcontrib-applehelp: 1.0.8
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.6
    sphinxcontrib-htmlhelp: 2.0.5
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.7
    sphinxcontrib-serializinghtml: 1.1.10
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    tzdata: 2024.1
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    wcwidth: 0.2.13
    webcolors: 1.13
    wheel: 0.43.0
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    widgetsnbextension: 4.0.11