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Opened 21 months ago
Closed 21 months ago
#14842 closed defect (can't reproduce)
Crash destroying tool
| Reported by: | 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
{"app_name":"ChimeraX","timestamp":"2024-03-28 12:30:35.00 +0100","app_version":"1.4.0","slice_uuid":"9596eff5-d2be-396c-9c4e-6177235c3dae","build_version":"1.4.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 13.6 (22G120)","roots_installed":0,"name":"ChimeraX","incident_id":"C5E84F6B-1E7C-458B-B9EC-E8863A1815A6"}
{
"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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},
"deploymentId" : 240000394
},
{
"rolloutId" : "6391cacc75b0720ff1f8c695",
"factorPackIds" : {
"COREOS_ICD" : "63957f508061fa721c8edc4a"
},
"deploymentId" : 240000007
}
],
"experiments" : [
{
"treatmentId" : "5d51a80d-93ec-47e1-9027-675002e78e4a",
"experimentId" : "6384d56b96e8d228551ec182",
"deploymentId" : 400000030
},
{
"treatmentId" : "7906dd23-001e-4717-afdb-ab178331d1ba",
"experimentId" : "65e637a6afcca6238e6618d0",
"deploymentId" : 400000001
}
]
}
}
===== 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 , 21 months ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash destroying tool |
comment:2 by , 21 months ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
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