#14842 closed defect (can't reproduce)

Crash destroying tool

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

Description

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.4.dev202201260121 (2022-01-26 01:21:26 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault

Thread 0x00007000158f4000 (most recent call first):
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 316 in wait
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 574 in wait
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 1284 in run
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x000070000edbb000 (most recent call first):
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 316 in wait
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 574 in wait
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 1284 in run
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap

Current thread 0x00007ff84c345700 (most recent call first):
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 2303 in destroy
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 2173 in _destroy
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 806 in remove_tool
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 370 in remove_tool
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/tools.py", line 154 in delete
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 318 in event_loop
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py", line 867 in init
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py", line 1018 in 
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 197 in _run_module_as_main


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{
  "uptime" : 180000,
  "procRole" : "Foreground",
  "version" : 2,
  "userID" : 501,
  "deployVersion" : 210,
  "modelCode" : "MacBookPro14,1",
  "coalitionID" : 5347,
  "osVersion" : {
    "train" : "macOS 13.6",
    "build" : "22G120",
    "releaseType" : "User"
  },
  "captureTime" : "2024-03-28 12:30:29.5130 +0100",
  "incident" : "C5E84F6B-1E7C-458B-B9EC-E8863A1815A6",
  "pid" : 13315,
  "cpuType" : "X86-64",
  "roots_installed" : 0,
  "bug_type" : "309",
  "procLaunch" : "2024-03-27 18:34:52.7382 +0100",
  "procStartAbsTime" : 158540235812001,
  "procExitAbsTime" : 189709397482787,
  "procName" : "ChimeraX",
  "procPath" : "\/Applications\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX",
  "bundleInfo" : {"CFBundleShortVersionString":"1.4.0","CFBundleVersion":"1.4.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
  "storeInfo" : {"deviceIdentifierForVendor":"5C4D779D-F431-5F57-A1E6-F49C07708AC6","thirdParty":true},
  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "D220E473-3245-8690-4DCE-7F21D34439D7",
  "codeSigningID" : "edu.ucsf.cgl.ChimeraX",
  "codeSigningTeamID" : "LWV8X224YF",
  "codeSigningFlags" : 570490881,
  "codeSigningValidationCategory" : 6,
  "codeSigningTrustLevel" : 0,
  "wakeTime" : 6184,
  "sleepWakeUUID" : "4C8497E3-2E68-42D7-ACE2-E2796A8DB84B",
  "sip" : "disabled",
  "vmRegionInfo" : "0x237359a3c1a8 is not in any region.  Bytes after previous region: 38972086604201  Bytes before following region: 66574784151128\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      VM_ALLOCATE                 173d24000-17442f000    [ 7212K] rw-\/rwx SM=PRV  \n--->  GAP OF 0x5ffe8bbd1000 BYTES\n      MALLOC_NANO              600000000000-600008000000 [128.0M] rw-\/rwx SM=PRV  ",
  "exception" : {"codes":"0x0000000000000001, 0x0000237359a3c1a8","rawCodes":[1,38978332115368],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000237359a3c1a8"},
  "termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":13315},
  "vmregioninfo" : "0x237359a3c1a8 is not in any region.  Bytes after previous region: 38972086604201  Bytes before following region: 66574784151128\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      VM_ALLOCATE                 173d24000-17442f000    [ 7212K] rw-\/rwx SM=PRV  \n--->  GAP OF 0x5ffe8bbd1000 BYTES\n      MALLOC_NANO              600000000000-600008000000 [128.0M] rw-\/rwx SM=PRV  ",
  "extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
  "faultingThread" : 0,
  "threads" : 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    "arch" : "x86_64",
    "base" : 140703276015616,
    "size" : 40944,
    "uuid" : "f1798256-c6b5-335c-bbb5-7978acf41deb",
    "path" : "\/usr\/lib\/system\/libsystem_platform.dylib",
    "name" : "libsystem_platform.dylib"
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    "source" : "A",
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    "uuid" : "00000000-0000-0000-0000-000000000000"
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===== Log before crash start =====
UCSF ChimeraX version: 1.4.dev202201260121 (2022-01-26)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/petya/Desktop/BcsSS-Gb.cxs format session

opened ChimeraX session  

> select #2/B:200

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

> select up

40 atoms, 41 bonds, 6 residues, 1 model selected  

> select #3/A:196

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

> select add #2/B:199

10 atoms, 8 bonds, 2 residues, 2 models selected  

> select up

352 atoms, 362 bonds, 54 residues, 2 models selected  

> color sel purple

> select clear

Drag select of 17 residues  
Drag select of 38 residues  

> select clear

> cartoon style width 2 thickness 0.6

> lighting soft

> graphics silhouettes false

> graphics silhouettes true

> transparency #3 0 target c

> transparency #2 0 target c

> lighting soft

> ui tool show "Side View"

> lighting full

> lighting soft

> save BcsGfFLmodel.tiff format tiff width 5000 transparentBackground true

> select clear

> select #3/A:157

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

> select up

312 atoms, 321 bonds, 48 residues, 1 model selected  

> molmap #2 3.5

Opened 6pcz.pdb map 3.5 as #4, grid size 60,74,114, pixel 1.17, shown at level
0.105, step 1, values float32  

> hide #!4 models

> select clear

> hide #3 models

Drag select of 5 residues  

> select clear

> select #2/B:532

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

> select up

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

> select #2/B:530

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

> select #2/B:532

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

> select add #2/B:530

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

> select add #2/B:531

22 atoms, 19 bonds, 3 residues, 1 model selected  

> select add #2/B:533

30 atoms, 26 bonds, 4 residues, 1 model selected  

> select up

91 atoms, 92 bonds, 13 residues, 1 model selected  

> select #2/B:523

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select #2/B:532

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

> select add #2/B:537

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

> select add #2/B:548

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

> select add #2/B:554

41 atoms, 39 bonds, 4 residues, 1 model selected  

> select up

145 atoms, 147 bonds, 17 residues, 1 model selected  

> select add #2/B:542

154 atoms, 155 bonds, 18 residues, 1 model selected  

> select up

162 atoms, 165 bonds, 19 residues, 1 model selected  

> select add #2/B:559

171 atoms, 173 bonds, 20 residues, 1 model selected  

> select up

190 atoms, 195 bonds, 22 residues, 1 model selected  

> select add #2/B:550

198 atoms, 202 bonds, 23 residues, 1 model selected  

> select up

214 atoms, 220 bonds, 26 residues, 1 model selected  

> select add #2/B:534

220 atoms, 225 bonds, 27 residues, 1 model selected  

> select up

236 atoms, 243 bonds, 29 residues, 1 model selected  

> select add #2/B:530

243 atoms, 249 bonds, 30 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel azure

> color sel lavender

> color sel light cyan

> color sel light steel blue

> color sel thistle

> color sel lavender blush

> color sel pale turquoise

> color sel linen

> color sel wheat

> select clear

> select #2/B:278@CB

1 atom, 1 residue, 1 model selected  

> select clear

> select #2/B:215

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

> select clear

> save BcsGzoomtiff format tiff width 5000 transparentBackground true

> show #3 models

> save BcsGfFLmodel.-btiff format tiff width 5000 transparentBackground true

> save BcsGfFLmodel-b.tiff format tiff width 5000 transparentBackground true

> open /Users/petya/Downloads/5fgn-2.pdb

5fgn-2.pdb title:  
Integral membrane protein lipooligosaccharide phosphoethanolamine transferase
A (EPTA) from neisseria meningitidis [more info...]  
  
Chain information for 5fgn-2.pdb #5  
---  
Chain | Description | UniProt  
A | EPTA | E3D1H8_NEIM7  
  
Non-standard residues in 5fgn-2.pdb #5  
---  
BGL — 2-O-octyl-β-D-glucopyranose (2-O-octyl-β-D-glucose; 2-O-octyl-D-glucose;
2-O-octyl-glucose)  
LMT — dodecyl-β-D-maltoside  
ZN — zinc ion  
  

> matchmaker #5 to #4

No 'to' model specified  

> show #!4 models

> hide #3 models

> show #3 models

> hide #!4 models

> matchmaker #5 to #3

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 AF-P37659-F1-model_v4.pdb, chain A (#3) with 5fgn-2.pdb, chain A
(#5), sequence alignment score = 282.6  
RMSD between 61 pruned atom pairs is 1.011 angstroms; (across all 449 pairs:
17.418)  
  

> hide #!2 models

> hide #!1 models

> hide #!5 models

> ui tool show "Show Sequence Viewer"

QMainWindowLayout::tabPosition called with out-of-bounds value '0'  

> sequence chain #3/A

Alignment identifier is 3/A  

> select #3/A:155

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

> select #3/A:157-158

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

> select #3/A:157-559

3095 atoms, 3178 bonds, 403 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> matchmaker #5 to #3

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 AF-P37659-F1-model_v4.pdb, chain A (#3) with 5fgn-2.pdb, chain A
(#5), sequence alignment score = 69.5  
RMSD between 11 pruned atom pairs is 1.079 angstroms; (across all 143 pairs:
13.439)  
  

> show #!5 models

> hide #3 models

> select #5/A:465@CG

1 atom, 1 residue, 1 model selected  

> select up

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

> select add #5/A:91@CD

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

> select up

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

> select add #5/A:702@O

20 atoms, 18 bonds, 3 residues, 1 model selected  

> select up

22 atoms, 19 bonds, 4 residues, 1 model selected  

> select up

28 atoms, 25 bonds, 4 residues, 1 model selected  

> select add #5/A:281

33 atoms, 29 bonds, 5 residues, 1 model selected  

> select add #5/A:110@CB

34 atoms, 29 bonds, 6 residues, 1 model selected  

> select up

40 atoms, 35 bonds, 6 residues, 1 model selected  

> select add #5/A:99@CZ

41 atoms, 35 bonds, 7 residues, 1 model selected  

> select up

51 atoms, 46 bonds, 7 residues, 1 model selected  

> select add #5/A:328@CG

52 atoms, 46 bonds, 8 residues, 1 model selected  

> select up

60 atoms, 54 bonds, 8 residues, 1 model selected  

> select add #5/A:601@C7'

61 atoms, 54 bonds, 9 residues, 1 model selected  

> select up

108 atoms, 102 bonds, 9 residues, 1 model selected  

> select up

110 atoms, 103 bonds, 10 residues, 1 model selected  

> select up

116 atoms, 109 bonds, 10 residues, 1 model selected  

> select add #5/A:89

122 atoms, 114 bonds, 11 residues, 1 model selected  

> select add #5/A:188@OG1

123 atoms, 114 bonds, 12 residues, 1 model selected  

> select up

129 atoms, 120 bonds, 12 residues, 1 model selected  

> select add #5/A:57@CG

130 atoms, 120 bonds, 13 residues, 1 model selected  

> select up

137 atoms, 127 bonds, 13 residues, 1 model selected  

> select up

139 atoms, 128 bonds, 14 residues, 1 model selected  

> select up

141 atoms, 129 bonds, 15 residues, 1 model selected  

> select add #5/A:114@CB

142 atoms, 129 bonds, 16 residues, 1 model selected  

> select up

161 atoms, 148 bonds, 16 residues, 1 model selected  

> hide sel atoms

> select up

163 atoms, 149 bonds, 17 residues, 1 model selected  

> select up

167 atoms, 153 bonds, 17 residues, 1 model selected  

> hide sel atoms

> select add #5/A:194@CB

168 atoms, 153 bonds, 18 residues, 1 model selected  

> select up

173 atoms, 159 bonds, 18 residues, 1 model selected  

> select up

175 atoms, 160 bonds, 19 residues, 1 model selected  

> select up

181 atoms, 166 bonds, 19 residues, 1 model selected  

> select up

183 atoms, 167 bonds, 20 residues, 1 model selected  

> select up

191 atoms, 177 bonds, 20 residues, 1 model selected  

> hide sel atoms

Drag select of 11 residues  

> save /Users/petya/Desktop/LptA.cxs

> select clear

> select #5/A:211

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

> ui tool show "Show Sequence Viewer"

> sequence chain #5/A

Alignment identifier is 5/A  

> select #5/A:8

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

> select #5/A:8-211

1624 atoms, 1671 bonds, 204 residues, 1 model selected  

> color sel dark gray

> select #5/A:212-213

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

> select #5/A:212-543

2629 atoms, 2689 bonds, 332 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel #87cdebff

Drag select of 10 residues  

> select clear

> select #5/A:280@OG1

1 atom, 1 residue, 1 model selected  

> select add #5/A:453@NE2

2 atoms, 2 residues, 1 model selected  

> select add #5/A:240@CD

3 atoms, 3 residues, 1 model selected  

> select add #5/A:452@CG

4 atoms, 4 residues, 1 model selected  

> select up

34 atoms, 32 bonds, 4 residues, 1 model selected  

> color sel #ff2f92ff

> color sel #ff40ffff

> ui tool show "Color Actions"

> color sel plum

> color sel violet

> color sel byhetero

> style sel ball

Changed 34 atom styles  

> select #5/A:603@ZN

1 atom, 1 residue, 1 model selected  

> color sel #531b93ff

> size ligand atomRadius +.5

Changed 83 atom radii  

> size Zn atomRadius +.5

Changed 3 atom radii  

> select #5/A:212

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

> select up

93 atoms, 94 bonds, 12 residues, 1 model selected  

> select add #5/A:223

102 atoms, 102 bonds, 13 residues, 1 model selected  

> select up

109 atoms, 110 bonds, 14 residues, 1 model selected  

> select add #5/A:227

114 atoms, 114 bonds, 15 residues, 1 model selected  

> select up

158 atoms, 160 bonds, 21 residues, 1 model selected  

> color sel purple

> select #5/A:602@C5

1 atom, 1 residue, 1 model selected  

> select up

35 atoms, 36 bonds, 1 residue, 1 model selected  

> style sel ball

Changed 35 atom styles  

> ui tool show "Color Actions"

> color sel khaki

> color sel byhetero

> select clear

Drag select of 1 residues  

> select up

93 atoms, 94 bonds, 12 residues, 1 model selected  

> select clear

> save NmEptA-tiff format tiff width 5000 transparentBackground true

> save /Users/petya/Desktop/NmEptA-b.cxs

> open /Users/petya/Desktop/BcsSSb.cxs format session

Opened volumesum-RQABsharp-293-235.mrc as #4, grid size 410,410,410, pixel
1.05, shown at level 0.542, step 1, values float32  
opened ChimeraX session  

> select #3/A:1-2

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

> select #3/A:1-172

1397 atoms, 1439 bonds, 172 residues, 1 model selected  

> select clear

Drag select of BcsBcrown-part1.pdb_A SES surface, 444766 of 530850 triangles,
BcsBcrown-part1.pdb_B SES surface, 421459 of 522354 triangles, BcsBcrown-
part1.pdb_C SES surface, 501394 of 520266 triangles, BcsBcrown-part1.pdb_E SES
surface, 492419 of 527288 triangles, BcsB-part2.pdb_A SES surface, 521898 of
532766 triangles, BcsRQAB-part3.pdb_B SES surface, 518457 of 615264 triangles,
4247 residues, 8 pseudobonds  

> select clear

> select #1/B:593@OG1

1 atom, 1 residue, 1 model selected  

> select clear

> volume #4 level 0.04984

> volume #4 level 0.04204

> volume #4 level 0.07325

> volume #4 level 0.1201

> ui tool show "Side View"

> volume #4 level 0.1123

> save BcsSS_ecoli_inMap.tiff format tiff width 5000 transparentBackground
> true

> save /Users/petya/Desktop/BcsSS_inmap.cxs

> select clear

Drag select of BcsBcrown-part1.pdb_A SES surface, BcsBcrown-part1.pdb_B SES
surface, BcsBcrown-part1.pdb_C SES surface, BcsBcrown-part1.pdb_E SES surface,
BcsB-part2.pdb_A SES surface, BcsRQAB-part3.pdb_B SES surface, 572116 of
615264 triangles, 4485 residues, 9 pseudobonds, 4 volumesum-
RQABsharp-293-235.mrc  

> select clear

Drag select of BcsBcrown-part1.pdb_A SES surface, 265208 of 530850 triangles,
BcsBcrown-part1.pdb_B SES surface, 240196 of 522354 triangles, BcsBcrown-
part1.pdb_C SES surface, 325035 of 520266 triangles, BcsBcrown-part1.pdb_E SES
surface, 280634 of 527288 triangles, BcsB-part2.pdb_A SES surface, 353024 of
532766 triangles, BcsRQAB-part3.pdb_B SES surface, 341588 of 615264 triangles,
2905 residues, 3 pseudobonds  

> select up

28656 atoms, 29269 bonds, 3 pseudobonds, 3694 residues, 10 models selected  

> select up

34722 atoms, 35530 bonds, 3 pseudobonds, 4465 residues, 10 models selected  

> hide sel surfaces

> show sel surfaces

> hide sel surfaces

> select clear

Drag select of 2 residues  

> select up

151 atoms, 155 bonds, 20 residues, 2 models selected  

> select up

4996 atoms, 5111 bonds, 643 residues, 2 models selected  

> show sel surfaces

> hide sel surfaces

> select clear

Drag select of 2 residues  

> select up

534 atoms, 548 bonds, 68 residues, 2 models selected  

> select up

4486 atoms, 4591 bonds, 576 residues, 2 models selected  

> hide sel cartoons

Drag select of 3694 residues, 7 pseudobonds  

> select up

29337 atoms, 30003 bonds, 7 pseudobonds, 3780 residues, 11 models selected  

> select up

30236 atoms, 30939 bonds, 7 pseudobonds, 3889 residues, 11 models selected  

> show sel surfaces

> select clear

> save BcsSS_ecoli_inMap.tiff format tiff width 5000 transparentBackground
> true

> hide #!3 models

> show #!3 models

> hide #!3 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> show #!3 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!3 models

> show #!3 models

> hide #!2 models

> hide #!1 models

> show #!1 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> hide #!3 models

> hide #!4 models

> hide #6 models

> select #1

24330 atoms, 24893 bonds, 9 pseudobonds, 3132 residues, 2 models selected  

> show sel surfaces

> show sel atoms

> ~select #1

5 models selected  

> select clear

> hide #!1 surfaces

> select clear

> select #1/D:561@O

1 atom, 1 residue, 1 model selected  

> select up

9 atoms, 8 bonds, 1 residue, 2 models selected  

> select up

75 atoms, 76 bonds, 10 residues, 2 models selected  

> select up

4486 atoms, 4591 bonds, 576 residues, 2 models selected  

> select up

24330 atoms, 24893 bonds, 3132 residues, 2 models selected  

> select down

4486 atoms, 4591 bonds, 576 residues, 6 models selected  

> delete atoms (#!1 & sel)

> delete bonds (#!1 & sel)

> show #!2 models

> select #1

19844 atoms, 20302 bonds, 6 pseudobonds, 2556 residues, 2 models selected  

> hide sel atoms

> show sel surfaces

> show #!3 models

> select clear

Drag select of BcsBcrown-part1.pdb_A SES surface, 13326 of 530850 triangles,
BcsBcrown-part1.pdb_B SES surface, 669 of 522354 triangles, BcsBcrown-
part1.pdb_C SES surface, 54074 of 520266 triangles, BcsBcrown-part1.pdb_E SES
surface, 1303 of 527288 triangles, BcsB-part2.pdb_A SES surface, 484 of 532766
triangles, 98 residues  

> select clear

Drag select of BcsBcrown-part1.pdb_A SES surface, 266572 of 530850 triangles,
BcsBcrown-part1.pdb_B SES surface, 257388 of 522354 triangles, BcsBcrown-
part1.pdb_C SES surface, 323893 of 520266 triangles, BcsBcrown-part1.pdb_E SES
surface, 301631 of 527288 triangles, BcsB-part2.pdb_A SES surface, 364252 of
532766 triangles, BcsRQAB-part3.pdb_B SES surface, 298073 of 615264 triangles,
2497 residues, 2 pseudobonds  

> select up

24635 atoms, 25150 bonds, 2 pseudobonds, 3182 residues, 10 models selected  

> select up

30236 atoms, 30939 bonds, 2 pseudobonds, 3889 residues, 10 models selected  

> hide sel surfaces

> select clear

> select #3/B:735

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

> select up

97 atoms, 102 bonds, 10 residues, 2 models selected  

> select up

5396 atoms, 5526 bonds, 690 residues, 2 models selected  

> select down

97 atoms, 102 bonds, 10 residues, 2 models selected  

> select clear

> select #3/B:746

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

> select add #3/B:733

19 atoms, 18 bonds, 2 residues, 2 models selected  

> select add #3/B:757

27 atoms, 25 bonds, 3 residues, 2 models selected  

> select up

351 atoms, 362 bonds, 41 residues, 2 models selected  

> color (#!3 & sel) medium blue

> select clear

> ui tool show "Show Sequence Viewer"

> sequence chain #3/B #7/A #7/B #7/C #7/D #7/E #7/F #7/G #7/H

Alignment identifier is 1  

> select #3/B:523 #7/A-H:523

108 atoms, 108 bonds, 9 residues, 2 models selected  

> select #3/B:523-525 #7/A-H:523-525

306 atoms, 324 bonds, 27 residues, 2 models selected  

> select #3/B:523 #7/A-H:523

108 atoms, 108 bonds, 9 residues, 2 models selected  

> select #3/B:523-729 #7/A-H:523-729

14130 atoms, 14409 bonds, 1863 residues, 2 models selected  

> select #3/B:523-729 #7/A-H:523-729

14130 atoms, 14409 bonds, 1863 residues, 2 models selected  

> select #3/B:523-731 #7/A-H:523-731

14265 atoms, 14553 bonds, 1881 residues, 2 models selected  

> ui tool show "Color Actions"

> color sel lavender

> color sel thistle

> select clear

> select #3/B:210 #7/A-H:210

81 atoms, 72 bonds, 9 residues, 2 models selected  

> select #3/B:210-362 #7/A-H:210-362

10899 atoms, 11214 bonds, 1377 residues, 2 models selected  

> color (#!3 & sel) cornflower blue

> select clear

> ui tool show "Show Sequence Viewer"

> sequence chain #1/A #2/A

Alignment identifier is 1  

> select #1/A:210 #2/A:210

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

> select #1/A:210-362 #2/A:210-362

2422 atoms, 2492 bonds, 306 residues, 2 models selected  
1 [ID: 1] region 2 chains [144-296] RMSD: 100.849  
  

> color (#!1-2 & sel) cornflower blue

> select clear

> cartoon style width 2 thickness 0.6

> select #1/A:523 #2/A:523

24 atoms, 24 bonds, 2 residues, 2 models selected  

> select #1/A:523-730 #2/A:523-730

3156 atoms, 3218 bonds, 416 residues, 2 models selected  
1 [ID: 1] region 2 chains [436-643] RMSD: 94.128  
  

> ui tool show "Color Actions"

> color sel thistle

Drag select of 24 residues  

> select clear

> ui tool show "Show Sequence Viewer"

> sequence chain #1/B #1/C

Alignment identifier is 1  

> select #1/B-C:523

24 atoms, 24 bonds, 2 residues, 1 model selected  

> select #1/B-C:523-728

3120 atoms, 3180 bonds, 412 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel thistle

> select clear

> select #1/B-C:210

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

> select #1/B-C:210-362

2422 atoms, 2492 bonds, 306 residues, 1 model selected  

> color (#!1 & sel) cornflower blue

> select clear

> select #1/E:653

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

> ui tool show "Show Sequence Viewer"

> sequence chain #1/E

Alignment identifier is 1/E  

> select #1/E:523

12 atoms, 12 bonds, 1 residue, 1 model selected  

> select #1/E:523-728

1560 atoms, 1590 bonds, 206 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel thistle

> select clear

> select #1/E:210

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

> select #1/E:210-362

1211 atoms, 1246 bonds, 153 residues, 1 model selected  

> color (#!1 & sel) cornflower blue

> select clear

Drag select of 3798 residues, 7 pseudobonds  

> select up

29739 atoms, 25313 bonds, 7 pseudobonds, 3830 residues, 11 models selected  

> select up

30236 atoms, 25828 bonds, 7 pseudobonds, 3889 residues, 11 models selected  

> show sel surfaces

> select clear

> hide #!1-3 surfaces

> select add #3/B:764

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

> select add #3/B:736

19 atoms, 17 bonds, 2 residues, 2 models selected  

> select add #3/B:745

27 atoms, 24 bonds, 3 residues, 2 models selected  

> select add #3/B:775

35 atoms, 31 bonds, 4 residues, 2 models selected  

> select up

393 atoms, 405 bonds, 46 residues, 2 models selected  

> ui tool show "Color Actions"

> color (#!3 & sel) #005493ff

> color (#!3 & sel) #531b93ff

> select clear

Drag select of 2760 residues, 2 pseudobonds  

> select up

25833 atoms, 26390 bonds, 2 pseudobonds, 3331 residues, 10 models selected  

> select up

30236 atoms, 30939 bonds, 2 pseudobonds, 3889 residues, 10 models selected  

> select clear

Drag select of 3833 residues, 7 pseudobonds  

> select up

30198 atoms, 25790 bonds, 7 pseudobonds, 3886 residues, 12 models selected  

> select clear

> save /Users/petya/Desktop/BcsSS_Bdomains.cxs

Drag select of 2833 residues, 2 pseudobonds  

> select up

26299 atoms, 26873 bonds, 2 pseudobonds, 3391 residues, 10 models selected  

> select up

30236 atoms, 30939 bonds, 2 pseudobonds, 3889 residues, 10 models selected  

> show sel surfaces

> select clear

> ui tool show "Volume Viewer"

> volume #4 level 0.1357

> save BcsSS_ecoli_inMap-Bdomains.tiff format tiff width 5000
> transparentBackground true

> save BcsSS_ecoli_NOMAP-Bdomains.tiff format tiff width 5000
> transparentBackground true

> cartoon style width 2 thickness 0.7

> save BcsSS_ecoli_NOMAP-Bdomains.tiff format tiff width 5000
> transparentBackground true

> save BcsSS_ecoli_inMap-Bdomains.tiff format tiff width 5000
> transparentBackground true

> select clear

> ui tool show "Side View"

> save BcsB-crown-topview.tiff format tiff width 5000 transparentBackground
> true

> save /Users/petya/Desktop/BcsSS_Bdomains-b.cxs

Drag select of BcsBcrown-part1.pdb_A SES surface, 162219 of 530850 triangles,
BcsBcrown-part1.pdb_B SES surface, 268640 of 522354 triangles, BcsBcrown-
part1.pdb_C SES surface, 148197 of 520266 triangles, BcsBcrown-part1.pdb_E SES
surface, 451081 of 527288 triangles, BcsB-part2.pdb_A SES surface, 259687 of
532766 triangles, BcsRQAB-part3.pdb_B SES surface, 387251 of 615264 triangles,
2085 residues, 3 pseudobonds  

> select up

19402 atoms, 19824 bonds, 3 pseudobonds, 2498 residues, 10 models selected  

> select up

30236 atoms, 30939 bonds, 3 pseudobonds, 3889 residues, 10 models selected  

> hide sel surfaces

> select clear

> select #1/B:654

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

> select add #1/A:344

14 atoms, 12 bonds, 2 residues, 2 models selected  

> select up

80 atoms, 78 bonds, 11 residues, 3 models selected  

> select up

9940 atoms, 10170 bonds, 1280 residues, 3 models selected  

> view sel

> select clear

> ui tool show "Side View"

> select #1/B:618

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

> select add #1/B:619

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

> select add #1/B:620

24 atoms, 21 bonds, 3 residues, 2 models selected  

> select add #1/B:621

31 atoms, 27 bonds, 4 residues, 2 models selected  

> select add #1/B:623

36 atoms, 31 bonds, 5 residues, 2 models selected  

> select up

94 atoms, 93 bonds, 12 residues, 2 models selected  

> select add #1/B:627

108 atoms, 108 bonds, 13 residues, 2 models selected  

> select up

153 atoms, 155 bonds, 19 residues, 2 models selected  

> select add #1/B:650

162 atoms, 163 bonds, 20 residues, 2 models selected  

> select up

213 atoms, 214 bonds, 27 residues, 2 models selected  

> select add #1/B:646

221 atoms, 221 bonds, 28 residues, 2 models selected  

> select up

247 atoms, 247 bonds, 31 residues, 2 models selected  

> select add #1/B:648

252 atoms, 251 bonds, 32 residues, 2 models selected  

> select add #1/B:643

260 atoms, 258 bonds, 33 residues, 2 models selected  

> select up

346 atoms, 352 bonds, 44 residues, 2 models selected  

> color (#!1 & sel) #d783ffff

> select add #1/B:657

352 atoms, 357 bonds, 45 residues, 2 models selected  

> color (#!1 & sel) #7a81ffff

> color (#!1 & sel) #ff85ffff

> select add #1/A:341

356 atoms, 360 bonds, 46 residues, 2 models selected  

> select add #1/A:351

363 atoms, 367 bonds, 47 residues, 3 models selected  

> select add #1/A:350

372 atoms, 375 bonds, 48 residues, 3 models selected  

> select add #1/A:349

379 atoms, 381 bonds, 49 residues, 3 models selected  

> select clear

> select #1/A:352

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

> select add #1/A:351

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

> select add #1/A:350

24 atoms, 22 bonds, 3 residues, 2 models selected  

> select add #1/A:349

31 atoms, 28 bonds, 4 residues, 2 models selected  

> select add #1/A:348

40 atoms, 36 bonds, 5 residues, 2 models selected  

> select add #1/A:347

48 atoms, 43 bonds, 6 residues, 2 models selected  

> select add #1/A:346

55 atoms, 49 bonds, 7 residues, 2 models selected  

> select add #1/A:344

62 atoms, 55 bonds, 8 residues, 2 models selected  

> select up

236 atoms, 243 bonds, 29 residues, 2 models selected  

> select add #1/A:342

245 atoms, 251 bonds, 30 residues, 2 models selected  

> color (#!1 & sel) #00fdffff

> select down

245 atoms, 251 bonds, 30 residues, 2 models selected  

> color (#!1 & sel) cornflower blue

> select clear

> select #1/A:351

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

> select add #1/A:350

16 atoms, 15 bonds, 2 residues, 2 models selected  

> select add #1/A:349

23 atoms, 21 bonds, 3 residues, 2 models selected  

> select add #1/A:348

32 atoms, 29 bonds, 4 residues, 2 models selected  

> select add #1/A:347

40 atoms, 36 bonds, 5 residues, 2 models selected  

> select add #1/A:346

47 atoms, 42 bonds, 6 residues, 2 models selected  

> select add #1/A:345

54 atoms, 48 bonds, 7 residues, 2 models selected  

> select add #1/A:344

61 atoms, 54 bonds, 8 residues, 2 models selected  

> select add #1/A:343

67 atoms, 59 bonds, 9 residues, 2 models selected  

> color (#!1 & sel) #76d6ffff

> color (#!1 & sel) #00fdffff

> select clear

> graphics silhouettes true

> lighting soft

> lighting full

> select #1/E:619

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

> select up

23 atoms, 22 bonds, 3 residues, 2 models selected  

> select up

4960 atoms, 5074 bonds, 639 residues, 2 models selected  

> select up

19844 atoms, 20302 bonds, 2556 residues, 2 models selected  

> select down

4960 atoms, 5074 bonds, 639 residues, 5 models selected  

> hide sel cartoons

> select clear

> select #1/C:330

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

> select up

95 atoms, 94 bonds, 13 residues, 2 models selected  

> select up

4944 atoms, 5058 bonds, 637 residues, 2 models selected  

> select up

19844 atoms, 20302 bonds, 2556 residues, 2 models selected  

> select down

4944 atoms, 5058 bonds, 637 residues, 5 models selected  

> hide sel cartoons

> lighting full

> lighting shadows false

> lighting shadows true

> lighting full

> select add #1/B:557

4953 atoms, 5066 bonds, 638 residues, 2 models selected  

> select up

5002 atoms, 5117 bonds, 645 residues, 3 models selected  

> select up

9888 atoms, 10116 bonds, 1274 residues, 3 models selected  

> select add #1/A:344

9895 atoms, 10122 bonds, 1275 residues, 3 models selected  

> select up

9908 atoms, 10135 bonds, 1277 residues, 4 models selected  

> select up

14884 atoms, 15228 bonds, 1917 residues, 4 models selected  

> show sel surfaces

> transparency (#!1 & sel) 80

> select clear

Drag select of BcsBcrown-part1.pdb_B SES surface, 1770 of 522354 triangles,
cap far, 162 of 9327 triangles, 4 residues  

> select up

119 atoms, 118 bonds, 15 residues, 3 models selected  

> select up

4944 atoms, 5058 bonds, 637 residues, 3 models selected  

> select down

119 atoms, 118 bonds, 15 residues, 3 models selected  

> select down

31 atoms, 4 residues, 3 models selected  

> select down

31 atoms, 4 residues, 3 models selected  

> select down

31 atoms, 4 residues, 3 models selected  

> select down

31 atoms, 4 residues, 3 models selected  

> select down

31 atoms, 4 residues, 3 models selected  

> select clear

Drag select of BcsBcrown-part1.pdb_C SES surface, 3704 of 520266 triangles,
cap far, 123 of 15847 triangles  

> select up

14900 atoms, 6 pseudobonds, 1919 residues, 7 models selected  

> select down

1 model selected  

> select down

1 model selected  

> select clear

Drag select of BcsBcrown-part1.pdb_C SES surface, 2417 of 520266 triangles,
cap far, 137 of 15847 triangles  

> hide #!1-3 surfaces

> lighting soft

> ui tool show "Side View"

> select clear

Drag select of 1 residues  

> select up

109 atoms, 112 bonds, 13 residues, 2 models selected  

> select up

4996 atoms, 5111 bonds, 643 residues, 2 models selected  

> hide sel cartoons

> ui tool show "Side View"

> lighting full

> select add #1/B:244

5005 atoms, 5119 bonds, 644 residues, 3 models selected  

> select up

5121 atoms, 5238 bonds, 660 residues, 4 models selected  

> select up

9940 atoms, 10169 bonds, 1280 residues, 4 models selected  

> select subtract #1/B:626

9934 atoms, 10162 bonds, 1279 residues, 4 models selected  

> select up

9940 atoms, 10169 bonds, 1280 residues, 4 models selected  

> select up

24840 atoms, 25413 bonds, 3199 residues, 4 models selected  

> show sel surfaces

> hide sel surfaces

> select clear

> select #1/B:613

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

> select add #1/B:657

14 atoms, 12 bonds, 2 residues, 2 models selected  

> ui tool show "Show Sequence Viewer"

> sequence chain #1/B #1/C

Alignment identifier is 1  

> ui tool show "Show Sequence Viewer"

> sequence chain #1/A #2/A

Alignment identifier is 1  

> ui tool show "Show Sequence Viewer"

> sequence chain #1/B #1/C

Alignment identifier is 1  

> select #1/B:620

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

> select #1/B:613

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

> select add #1/B:657

14 atoms, 12 bonds, 2 residues, 2 models selected  

> select #1/B-C:614

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

> select #1/B-C:614-658

700 atoms, 712 bonds, 90 residues, 1 model selected  

> select #1/B-C:614

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

> select #1/B-C:614-657

688 atoms, 700 bonds, 88 residues, 1 model selected  

> select #1/B-C:613-614

32 atoms, 30 bonds, 4 residues, 1 model selected  

> select #1/B-C:613-657

704 atoms, 716 bonds, 90 residues, 1 model selected  

> ui tool show "Color Actions"

> color (#!1 & sel) #ffd479ff

> select clear

> select #1/A:344

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

> select add #1/A:343

13 atoms, 11 bonds, 2 residues, 2 models selected  

> select add #1/A:345

20 atoms, 17 bonds, 3 residues, 2 models selected  

> select add #1/A:346

27 atoms, 23 bonds, 4 residues, 2 models selected  

> select add #1/A:347

35 atoms, 30 bonds, 5 residues, 2 models selected  

> select add #1/A:348

44 atoms, 38 bonds, 6 residues, 2 models selected  

> select add #1/A:350

53 atoms, 46 bonds, 7 residues, 2 models selected  

> select add #1/A:351

60 atoms, 53 bonds, 8 residues, 2 models selected  

> select add #1/A:349

67 atoms, 59 bonds, 9 residues, 2 models selected  

> ui tool show "Color Actions"

> color sel aquamarine

> color sel sky blue

> color sel light sky blue

> color sel light pink

> color sel medium spring green

> color sel dark turquoise

> color sel turquoise

> color sel lawn green

> color sel chartreuse

> color sel green

> color sel lime

> color sel medium sea green

> color sel yellow green

> color sel light salmon

> color sel lawn green

> color sel spring green

> select clear

> select add #1/B:620

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

> select add #1/B:627

22 atoms, 22 bonds, 2 residues, 2 models selected  

> select add #1/B:654

29 atoms, 28 bonds, 3 residues, 2 models selected  

> select add #1/A:344

36 atoms, 34 bonds, 4 residues, 2 models selected  

> select add #1/A:302

45 atoms, 42 bonds, 5 residues, 3 models selected  

> select add #1/A:315

53 atoms, 49 bonds, 6 residues, 3 models selected  

> select add #1/A:278

61 atoms, 56 bonds, 7 residues, 3 models selected  

> select add #1/A:235

72 atoms, 67 bonds, 8 residues, 3 models selected  

> select add #1/A:268

80 atoms, 74 bonds, 9 residues, 3 models selected  

> view sel

> select clear

> ui tool show "Side View"

> select clear

> save BcsB-bComplContacts.tiff format tiff width 5000 transparentBackground
> true

> save /Users/petya/Desktop/BcsB_contacts.cxs

> view

> open /Users/petya/Desktop/BcsSS_Bdomains.cxs

Opened volumesum-RQABsharp-293-235.mrc as #4, grid size 410,410,410, pixel
1.05, shown at level 0.112, step 1, values float32  
opened ChimeraX session  

> cartoon style width 2 thickness 0.7

> graphics silhouettes true

Drag select of 4 volumesum-RQABsharp-293-235.mrc  

> transparency #4.1 60

> select clear

Drag select of 3120 residues, 3 pseudobonds  

> select up

27812 atoms, 28429 bonds, 3 pseudobonds, 3585 residues, 10 models selected  

> select up

30236 atoms, 30939 bonds, 3 pseudobonds, 3889 residues, 10 models selected  

> show sel surfaces

> select clear

Drag select of 4 volumesum-RQABsharp-293-235.mrc  

> transparency #4.1 70

> select clear

> save BcsSS_ecoli_inMap-Bdomains-b.tiff format tiff width 5000
> transparentBackground true

> save BcsSS_ecoli_NOMAP-Bdomains-b.tiff format tiff width 5000
> transparentBackground true

> ui tool show "Side View"

> save BcsSS_ecoli-TOPview-Bdomains-b.tiff format tiff width 5000
> transparentBackground true

> open /Users/petya/Downloads/BcsB-Rhodo_PP-mono.pdb

Chain information for BcsB-Rhodo_PP-mono.pdb #5  
---  
Chain | Description  
B | No description available  
  

> hide #!2 models

> hide #!3 models

> hide #!1 models

> show #!2 models

> matchmaker #5 to #2

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 BcsB-part2.pdb, chain A (#2) with BcsB-Rhodo_PP-mono.pdb, chain B
(#5), sequence alignment score = 318.5  
RMSD between 41 pruned atom pairs is 1.387 angstroms; (across all 523 pairs:
17.814)  
  

> select #2

4996 atoms, 5111 bonds, 1 pseudobond, 643 residues, 3 models selected  

> hide sel surfaces

> select clear

> select #2/A:343

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

> select #2/A:344

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

> select add #2/A:343

13 atoms, 11 bonds, 2 residues, 2 models selected  

> select add #2/A:345

20 atoms, 17 bonds, 3 residues, 2 models selected  

> select add #2/A:347

28 atoms, 24 bonds, 4 residues, 2 models selected  

> select add #2/A:346

35 atoms, 30 bonds, 5 residues, 2 models selected  

> select add #2/A:348

44 atoms, 38 bonds, 6 residues, 2 models selected  

> select add #2/A:349

51 atoms, 44 bonds, 7 residues, 2 models selected  

> select add #2/A:350

60 atoms, 52 bonds, 8 residues, 2 models selected  

> select add #2/A:351

67 atoms, 59 bonds, 9 residues, 2 models selected  

> select add #2/A:352

75 atoms, 66 bonds, 10 residues, 2 models selected  

> ui tool show "Color Actions"

> color sel spring green

> color sel medium spring green

> select #2/A:615

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

> select clear

> select #2/A:620

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

> select add #2/A:627

22 atoms, 22 bonds, 2 residues, 2 models selected  

> select add #2/A:653

28 atoms, 27 bonds, 3 residues, 2 models selected  

> select up

142 atoms, 142 bonds, 18 residues, 2 models selected  

> select add #2/A:623

147 atoms, 146 bonds, 19 residues, 2 models selected  

> select up

163 atoms, 164 bonds, 21 residues, 2 models selected  

> select add #2/A:657

169 atoms, 169 bonds, 22 residues, 2 models selected  

> select add #2/A:646

177 atoms, 176 bonds, 23 residues, 2 models selected  

> select up

325 atoms, 331 bonds, 43 residues, 2 models selected  

> select add #2/A:618

333 atoms, 338 bonds, 44 residues, 2 models selected  

> select add #2/A:617

341 atoms, 345 bonds, 45 residues, 2 models selected  

> select add #2/A:615

350 atoms, 353 bonds, 46 residues, 2 models selected  

> select #2/A:667

11 atoms, 11 bonds, 1 residue, 1 model selected  

> select add #2/A:620

19 atoms, 18 bonds, 2 residues, 2 models selected  

> select add #2/A:627

33 atoms, 33 bonds, 3 residues, 2 models selected  

> select add #2/A:653

39 atoms, 38 bonds, 4 residues, 2 models selected  

> select add #2/A:623

44 atoms, 42 bonds, 5 residues, 2 models selected  

> select add #2/A:632

52 atoms, 49 bonds, 6 residues, 2 models selected  

> select up

351 atoms, 357 bonds, 46 residues, 2 models selected  

> select clear

> select add #2/A:620

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

> select add #2/A:627

22 atoms, 22 bonds, 2 residues, 2 models selected  

> select add #2/A:655

30 atoms, 29 bonds, 3 residues, 2 models selected  

> select add #2/A:623

35 atoms, 33 bonds, 4 residues, 2 models selected  

> select add #2/A:648

40 atoms, 37 bonds, 5 residues, 2 models selected  

> select up

296 atoms, 302 bonds, 38 residues, 2 models selected  

> select add #2/A:618

304 atoms, 309 bonds, 39 residues, 2 models selected  

> select add #2/A:617

312 atoms, 316 bonds, 40 residues, 2 models selected  

> color (#!2 & sel) #fffc79ff

> color (#!2 & sel) #ffd479ff

> select clear

> cartoon style width 2 thickness 0.7

> ui tool show "Show Sequence Viewer"

> sequence chain #5/B

Alignment identifier is 5/B  

> select clear

> select #5/B:189

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

> select #5/B:187-189

18 atoms, 17 bonds, 3 residues, 1 model selected  

> select #5/B:54-189

1040 atoms, 1061 bonds, 136 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel medium purple

> color sel medium slate blue

> color sel slate blue

> color sel medium slate blue

> color sel #8367deff

> select clear

> select #5/B:451

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

> select add #5/B:310

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

> select #5/B:310-311

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

> select #5/B:310-451

1082 atoms, 1109 bonds, 142 residues, 1 model selected  

> select clear

> select #5/B:310

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

> select #5/B:310-451

1082 atoms, 1109 bonds, 142 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel #7259c2ff

> select clear

> select #5/B:189

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

> select #2/A:209

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

> select add #2/A:208

15 atoms, 13 bonds, 2 residues, 2 models selected  

> select add #2/A:207

23 atoms, 20 bonds, 3 residues, 2 models selected  

> ui tool show "Show Sequence Viewer"

> sequence chain #5/B

Alignment identifier is 5/B  

> select #5/B:676-677

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

> select #5/B:498-677

1240 atoms, 1271 bonds, 1 pseudobond, 168 residues, 2 models selected  

> select clear

> select #5/B:189

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

> select #5/B:54-55

21 atoms, 23 bonds, 2 residues, 1 model selected  

> select #5/B:54-189

1040 atoms, 1061 bonds, 136 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel #a496f8ff

> color sel #7259c2ff

> select clear

> hide #!2 models

> select #5/B:309

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

> select add #5/B:190

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

> select #5/B:190

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select #5/B:190-309

873 atoms, 895 bonds, 120 residues, 1 model selected  

> show #!2 models

> hide #!2 models

> color sel cornflower blue

> select clear

> select #5/B:452

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

> select #5/B:453

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

> select #5/B:453-677

1575 atoms, 1615 bonds, 1 pseudobond, 213 residues, 2 models selected  

> ui tool show "Color Actions"

> color sel thistle


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

Log:
UCSF ChimeraX version: 1.4.dev202201260121 (2022-01-26)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.1 INTEL-20.6.4
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 640
OpenGL vendor: Intel Inc.

Locale: UTF-8
Qt version: PyQt5 5.15.2, Qt 5.15.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro14,1
      Processor Name: Dual-Core Intel Core i7
      Processor Speed: 2.5 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: 16 GB
      System Firmware Version: 515.0.0.0.0
      OS Loader Version: 577.140.2~15
      SMC Version (system): 2.43f11

Software:

    System Software Overview:

      System Version: macOS 13.6 (22G120)
      Kernel Version: Darwin 22.6.0
      Time since boot: 7 days, 10 hours, 25 minutes

Graphics/Displays:

    Intel Iris Plus Graphics 640:

      Chipset Model: Intel Iris Plus Graphics 640
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x5926
      Revision ID: 0x0006
      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: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.2
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 3.0.0
    certifi: 2021.5.30
    cftime: 1.5.2
    charset-normalizer: 2.0.10
    ChimeraX-AddCharge: 1.2.2
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.33.1
    ChimeraX-AtomicLibrary: 5.0
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.1
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.6.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.2
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.1
    ChimeraX-CommandLine: 1.2
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.4.dev202201260121
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    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
    ChimeraX-Label: 1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.6
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.5
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.5.1
    ChimeraX-ModelPanel: 1.3.1
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.8
    ChimeraX-PDB: 2.6.5
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.6
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.7.4
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.0.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.16
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0.1
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    cxservices: 1.1
    cycler: 0.11.0
    Cython: 0.29.26
    debugpy: 1.5.1
    decorator: 5.1.1
    docutils: 0.17.1
    entrypoints: 0.3
    filelock: 3.4.2
    fonttools: 4.29.0
    funcparserlib: 1.0.0a0
    grako: 3.16.5
    h5py: 3.6.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.26
    imagecodecs: 2021.11.20
    imagesize: 1.3.0
    ipykernel: 6.6.1
    ipython: 7.31.1
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.0.3
    jupyter-client: 7.1.0
    jupyter-core: 4.9.1
    kiwisolver: 1.3.2
    line-profiler: 3.4.0
    lxml: 4.7.1
    lz4: 3.1.10
    MarkupSafe: 2.0.1
    matplotlib: 3.5.1
    matplotlib-inline: 0.1.3
    msgpack: 1.0.3
    nest-asyncio: 1.5.4
    netCDF4: 1.5.8
    networkx: 2.6.3
    numexpr: 2.8.1
    numpy: 1.22.1
    openvr: 1.16.802
    packaging: 21.0
    ParmEd: 3.4.3
    parso: 0.8.3
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.0.0
    pip: 21.3.1
    pkginfo: 1.8.2
    prompt-toolkit: 3.0.24
    psutil: 5.9.0
    ptyprocess: 0.7.0
    pycollada: 0.7.2
    pydicom: 2.2.2
    Pygments: 2.11.2
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.7
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.2
    pytz: 2021.3
    pyzmq: 22.3.0
    qtconsole: 5.2.2
    QtPy: 2.0.0
    RandomWords: 0.3.0
    requests: 2.27.1
    scipy: 1.7.3
    setuptools: 59.8.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.3.2
    sphinx-autodoc-typehints: 1.15.2
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-community: 1.0.0
    tables: 3.7.0
    tifffile: 2021.11.2
    tinyarray: 1.2.4
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.8
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.1
    wheel-filename: 1.3.0

Change History (2)

comment:1 by Eric Pettersen, 19 months ago

Component: UnassignedWindow Toolkit
Owner: set to Eric Pettersen
Platform: all
Project: ChimeraX
Status: newaccepted
Summary: ChimeraX bug report submissionCrash destroying tool

comment:2 by Eric Pettersen, 19 months ago

Resolution: can't reproduce
Status: acceptedclosed
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