![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 3 years ago
Closed 3 years ago
#8813 closed defect (can't reproduce)
Crash using color chooser
| Reported by: | Owned by: | pett | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Platform | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| 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 (2022-06-03 23:39:42 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Aborted
Thread 0x00007000129e2000 (most recent call first):
File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 316 in wait
File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 574 in wait
File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 1297 in run
File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Current thread 0x000000010f06d600 (most recent call first):
File "/Applications/ChimeraX-1.4.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-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py", line 870 in init
File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py", line 1021 in
File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
File "/Applications/ChimeraX-1.4.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" : 390000,
"procLaunch" : "2023-04-09 15:23:17.6688 +0100",
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro16,1",
"procStartAbsTime" : 334211558876956,
"coalitionID" : 23181,
"osVersion" : {
"train" : "macOS 12.6",
"build" : "21G115",
"releaseType" : "User"
},
"captureTime" : "2023-04-10 22:18:10.2938 +0100",
"incident" : "6BAA80C5-F08A-41D5-AE49-8765D72407B4",
"bug_type" : "309",
"pid" : 72991,
"procExitAbsTime" : 397752750548564,
"cpuType" : "X86-64",
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.4.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.4.0","CFBundleVersion":"1.4.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"7841F1B0-6FDF-574F-9FE7-1B6C001C285D","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "8406F0E9-B2E9-806C-4DD5-C5AF70116039",
"wakeTime" : 3102,
"bridgeVersion" : {"build":"19P6067","train":"6.6"},
"sleepWakeUUID" : "4E026731-E9F2-4E73-AB91-3EE7F06DDC6E",
"sip" : "enabled",
"isCorpse" : 1,
"exception" : {"codes":"0x0000000000000000, 0x0000000000000000","rawCodes":[0,0],"type":"EXC_CRASH","signal":"SIGABRT"},
"ktriageinfo" : "VM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\n",
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"faultingThread" : 0,
"threads" : 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===== Log before crash start =====
UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/benjin/Desktop/1. Write up/0. Bioinformatics/0. Structure-based
> homology search/Multimeric/AF_MspA.pdb"
AF_MspA.pdb title:
Alphafold monomer V2.0 prediction for porin MSPA (A0QR29) [more info...]
Chain information for AF_MspA.pdb #1
---
Chain | Description | UniProt
A | porin MSPA | MSPA_MYCS2
> ui tool show "Show Sequence Viewer"
> sequence chain /A
Alignment identifier is 1/A
> select /A:65
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /A:65-79
126 atoms, 130 bonds, 15 residues, 1 model selected
> select /A:138-139
11 atoms, 11 bonds, 2 residues, 1 model selected
> select /A:138-148
71 atoms, 71 bonds, 11 residues, 1 model selected
> select /A:138-139
11 atoms, 11 bonds, 2 residues, 1 model selected
> select /A:138-147
63 atoms, 63 bonds, 10 residues, 1 model selected
> select /A:140
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:140-149
64 atoms, 63 bonds, 10 residues, 1 model selected
> select /A:148
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:140-148
60 atoms, 59 bonds, 9 residues, 1 model selected
> select
> /A:29-36,42-48,51-55,65-78,86-96,99-108,139-148,152-163,166-171,174-178,186-195,200-204
785 atoms, 790 bonds, 103 residues, 1 model selected
> select /A:148
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:139-148
64 atoms, 63 bonds, 10 residues, 1 model selected
> open "/Users/benjin/Desktop/1. Write up/0. Bioinformatics/0. Structure-based
> homology search/Multimeric/AF_MdtP.pdb"
AF_MdtP.pdb title:
Alphafold monomer V2.0 prediction for multidrug resistance outer membrane
protein MDTP (P32714) [more info...]
Chain information for AF_MdtP.pdb #2
---
Chain | Description | UniProt
A | multidrug resistance outer membrane protein MDTP | MDTP_ECOLI
> select #1/A:78
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/A:65-78
122 atoms, 126 bonds, 14 residues, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain #2/A
Alignment identifier is 2/A
> select #2/A:328-329
17 atoms, 17 bonds, 2 residues, 1 model selected
> select #2/A:328-339
95 atoms, 97 bonds, 12 residues, 1 model selected
> log metadata #1
Metadata for AF_MspA.pdb #1
---
Title | Alphafold monomer V2.0 prediction for porin MSPA (A0QR29)
Source (natural) | Mycolicibacterium smegmatis (strain ATCC 700084 / MC(2)155)
> log chains #1
Chain information for AF_MspA.pdb #1
---
Chain | Description | UniProt
A | porin MSPA | MSPA_MYCS2
> select #1/A:86-87
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #1/A:86-96
82 atoms, 82 bonds, 11 residues, 1 model selected
> close
> open "/Users/benjin/Desktop/1. Write up/0. Bioinformatics/0. Structure-based
> homology search/Multimeric/AF_TolC.pdb"
AF_TolC.pdb title:
Alphafold monomer V2.0 prediction for outer membrane protein tolc (P02930)
[more info...]
Chain information for AF_TolC.pdb #1
---
Chain | Description | UniProt
A | outer membrane protein tolc | TOLC_ECOLI
> open "/Users/benjin/Desktop/1. Write up/0. Bioinformatics/0. Structure-based
> homology search/Multimeric/AF_HofQ.pdb"
AF_HofQ.pdb title:
Alphafold monomer V2.0 prediction for DNA utilization protein hofq (P34749)
[more info...]
Chain information for AF_HofQ.pdb #2
---
Chain | Description | UniProt
A | DNA utilization protein hofq | HOFQ_ECOLI
Drag select of 18 residues
> select clear
> ui tool show "Show Sequence Viewer"
> sequence chain #1/A
Alignment identifier is 1/A
> select #1/A:269
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/A:269-284
113 atoms, 113 bonds, 16 residues, 1 model selected
> select #1/A:289
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/A:288-289
18 atoms, 17 bonds, 2 residues, 1 model selected
> select #1/A:284
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/A:269-284
113 atoms, 113 bonds, 16 residues, 1 model selected
> select #1/A:299
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/A:299-311
94 atoms, 94 bonds, 13 residues, 1 model selected
> select #1/A:270
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:270-285
110 atoms, 110 bonds, 16 residues, 1 model selected
> select #1/A:83
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:83-98
117 atoms, 117 bonds, 16 residues, 1 model selected
> select #1/A:74
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:63-74
91 atoms, 92 bonds, 12 residues, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain #2/A
Alignment identifier is 2/A
> select #2/A:315
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #2/A:315-327
110 atoms, 111 bonds, 13 residues, 1 model selected
> select #2/A:180
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/A:180-183
33 atoms, 32 bonds, 4 residues, 1 model selected
> select #2/A:261
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #2/A:254-261
64 atoms, 63 bonds, 8 residues, 1 model selected
> select #2/A:262
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2/A:262-263
13 atoms, 13 bonds, 2 residues, 1 model selected
> select #2/A:242
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #2/A:242-250
71 atoms, 70 bonds, 9 residues, 1 model selected
> select #2/A:239
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:230-239
78 atoms, 79 bonds, 10 residues, 1 model selected
> close #1
> open "/Users/benjin/Desktop/1. Write up/0. Bioinformatics/0. Structure-based
> homology search/Multimeric/AF_MdtP.pdb"
AF_MdtP.pdb title:
Alphafold monomer V2.0 prediction for multidrug resistance outer membrane
protein MDTP (P32714) [more info...]
Chain information for AF_MdtP.pdb #1
---
Chain | Description | UniProt
A | multidrug resistance outer membrane protein MDTP | MDTP_ECOLI
> ui tool show "Show Sequence Viewer"
> sequence chain #1/A
Alignment identifier is 1/A
> select #1/A:107
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A:107-119
100 atoms, 99 bonds, 13 residues, 1 model selected
> select #1/A:141
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #1/A:141-155
115 atoms, 117 bonds, 15 residues, 1 model selected
> select #1/A:328
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/A:328-339
95 atoms, 97 bonds, 12 residues, 1 model selected
> select #1/A:359
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:351-359
77 atoms, 79 bonds, 9 residues, 1 model selected
> close #2
> close
> open "/Users/benjin/Desktop/1. Write up/0. Bioinformatics/0. Structure-based
> homology search/Multimeric/AF_MspA.pdb"
AF_MspA.pdb title:
Alphafold monomer V2.0 prediction for porin MSPA (A0QR29) [more info...]
Chain information for AF_MspA.pdb #1
---
Chain | Description | UniProt
A | porin MSPA | MSPA_MYCS2
> ui tool show "Show Sequence Viewer"
> sequence chain /A
Alignment identifier is 1/A
> select /A:65-66
20 atoms, 19 bonds, 2 residues, 1 model selected
> select /A:65-78
122 atoms, 126 bonds, 14 residues, 1 model selected
> select /A:42
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:42-46
38 atoms, 37 bonds, 5 residues, 1 model selected
> select /A:86-87
13 atoms, 12 bonds, 2 residues, 1 model selected
> select /A:86-96
82 atoms, 82 bonds, 11 residues, 1 model selected
> select /A:99
14 atoms, 15 bonds, 1 residue, 1 model selected
> select /A:99-108
76 atoms, 78 bonds, 10 residues, 1 model selected
> select /A:139-140
11 atoms, 10 bonds, 2 residues, 1 model selected
> select /A:139-148
64 atoms, 63 bonds, 10 residues, 1 model selected
> open "/Users/benjin/Desktop/1. Write up/0. Bioinformatics/0. Structure-based
> homology search/Multimeric/AF_GspD.pdb"
AF_GspD.pdb title:
Alphafold monomer V2.0 prediction for curli production assembly/transport
component CSGG (P0AEA2) [more info...]
Chain information for AF_GspD.pdb #2
---
Chain | Description | UniProt
A | curli production assembly/transport component CSGG | CSGG_ECOLI
> close #1
> open /Users/benjin/Downloads/pdb3m2l.ent
pdb3m2l.ent title:
Crystal structure of the M113F mutant of α-hemolysin [more info...]
Chain information for pdb3m2l.ent #1
---
Chain | Description | UniProt
A B C D E F G | α-hemolysin | HLA_STAAU
> show cartoons
> hide cartoons
> hide atoms
> show cartoons
> ui tool show "Show Sequence Viewer"
> sequence chain #1/A #1/B #1/C #1/D #1/E #1/F #1/G
Alignment identifier is 1
> select #1/A-G:132-133
84 atoms, 77 bonds, 14 residues, 1 model selected
> select #1/A-G:132-152
1057 atoms, 1071 bonds, 147 residues, 1 model selected
> select #1/A-G:109
49 atoms, 42 bonds, 7 residues, 1 model selected
> select #1/A-G:109-127
1038 atoms, 1059 bonds, 133 residues, 1 model selected
> close #1
> mlp
Map values for surface "AF_GspD.pdb_A SES surface": minimum -25.74, mean
-4.26, maximum 23.78
To also show corresponding color key, enter the above mlp command and add key
true
> transparency 80
> transparency 50
> ui tool show "Show Sequence Viewer"
> sequence chain /A
Alignment identifier is 2/A
> select /A:161-162
12 atoms, 11 bonds, 2 residues, 1 model selected
> select /A:161-180
156 atoms, 156 bonds, 20 residues, 1 model selected
> select /A:180
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:169-180
94 atoms, 93 bonds, 12 residues, 1 model selected
> select /A:161
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:161-169
70 atoms, 70 bonds, 9 residues, 1 model selected
> select /A:136
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:136-146
83 atoms, 83 bonds, 11 residues, 1 model selected
> select /A:186
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:161
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:161-169
70 atoms, 70 bonds, 9 residues, 1 model selected
> select /A:136
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:136-146
83 atoms, 83 bonds, 11 residues, 1 model selected
> select /A:186
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:186-191
43 atoms, 42 bonds, 6 residues, 1 model selected
> select /A:192-193
13 atoms, 12 bonds, 2 residues, 1 model selected
> select /A:192-199
63 atoms, 63 bonds, 8 residues, 1 model selected
> select /A:201
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:201-210
81 atoms, 82 bonds, 10 residues, 1 model selected
> open "/Users/benjin/Desktop/1. Write up/0. Bioinformatics/0. Structure-based
> homology search/Multimeric/AF_CusC.pdb"
AF_CusC.pdb title:
Alphafold monomer V2.0 prediction for cation efflux system protein cusc
(P77211) [more info...]
Chain information for AF_CusC.pdb #1
---
Chain | Description | UniProt
A | cation efflux system protein cusc | CUSC_ECOLI
> close #2
> ui tool show "Show Sequence Viewer"
> sequence chain /A
Alignment identifier is 1/A
> select /A:101
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:101-111
78 atoms, 79 bonds, 11 residues, 1 model selected
> select /A:121
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:121-134
109 atoms, 110 bonds, 14 residues, 1 model selected
> select /A:318
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /A:307-318
77 atoms, 76 bonds, 12 residues, 1 model selected
> select /A:330-331
12 atoms, 11 bonds, 2 residues, 1 model selected
> select /A:330-340
94 atoms, 97 bonds, 11 residues, 1 model selected
> open "/Users/benjin/Desktop/1. Write up/0. Bioinformatics/0. Structure-based
> homology search/Multimeric/AF_MdtP.pdb"
AF_MdtP.pdb title:
Alphafold monomer V2.0 prediction for multidrug resistance outer membrane
protein MDTP (P32714) [more info...]
Chain information for AF_MdtP.pdb #2
---
Chain | Description | UniProt
A | multidrug resistance outer membrane protein MDTP | MDTP_ECOLI
> log metadata #2
Metadata for AF_MdtP.pdb #2
---
Title | Alphafold monomer V2.0 prediction for multidrug resistance outer
membrane protein MDTP (P32714)
Source (natural) | Escherichia coli (strain K12)
> log chains #2
Chain information for AF_MdtP.pdb #2
---
Chain | Description | UniProt
A | multidrug resistance outer membrane protein MDTP | MDTP_ECOLI
> open /Users/benjin/Downloads/AF-Q51487-F1-model_v4.pdb
AF-Q51487-F1-model_v4.pdb title:
Alphafold monomer V2.0 prediction for outer membrane protein OPRM (Q51487)
[more info...]
Chain information for AF-Q51487-F1-model_v4.pdb #3
---
Chain | Description | UniProt
A | outer membrane protein OPRM | OPRM_PSEAE
> open /Users/benjin/Downloads/AF-Q51487-F1-model_v4.pdb
AF-Q51487-F1-model_v4.pdb title:
Alphafold monomer V2.0 prediction for outer membrane protein OPRM (Q51487)
[more info...]
Chain information for AF-Q51487-F1-model_v4.pdb #4
---
Chain | Description | UniProt
A | outer membrane protein OPRM | OPRM_PSEAE
> ui tool show "Show Sequence Viewer"
> sequence chain #3/A #4/A
Alignment identifier is 1
> select #3/A:105-106 #4/A:105-106
24 atoms, 22 bonds, 4 residues, 2 models selected
> select #3/A:105-116 #4/A:105-116
174 atoms, 172 bonds, 24 residues, 2 models selected
Outer Membrane Protein OPRM [ID: 1] region 2 chains [105-116] RMSD: 0.000
> close #1
> close #2
> close #4
> select /A:327
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /A:316-327
78 atoms, 77 bonds, 12 residues, 1 model selected
> select /A:348
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:339-348
81 atoms, 84 bonds, 10 residues, 1 model selected
> select /A:127
5 atoms, 4 bonds, 1 residue, 1 model selected
> select /A:127-143
126 atoms, 128 bonds, 17 residues, 1 model selected
> select /A:116
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:105-116
87 atoms, 86 bonds, 12 residues, 1 model selected
> open /Users/benjin/Downloads/pdb3d5k.ent
pdb3d5k.ent title:
Crystal structure of the OPRM channel In A non-symmetrical space group [more
info...]
Chain information for pdb3d5k.ent #1
---
Chain | Description | UniProt
A B C | OPRM | OPRM_PSEAE
Non-standard residues in pdb3d5k.ent #1
---
CL — chloride ion
NA — sodium ion
> close #3
> ui tool show "Show Sequence Viewer"
> sequence chain /A /B /C
Alignment identifier is 1
> select /A-C:110-111
39 atoms, 36 bonds, 6 residues, 1 model selected
> select /A-C:110-126
378 atoms, 384 bonds, 51 residues, 1 model selected
> select /A-C:88
24 atoms, 21 bonds, 3 residues, 1 model selected
> select /A-C:88-99
261 atoms, 258 bonds, 36 residues, 1 model selected
> select /A-C:299
18 atoms, 15 bonds, 3 residues, 1 model selected
> select /A-C:299-310
234 atoms, 231 bonds, 36 residues, 1 model selected
> select /A-C:336
21 atoms, 18 bonds, 3 residues, 1 model selected
> select /A-C:322-336
366 atoms, 381 bonds, 45 residues, 1 model selected
> open /Users/benjin/Downloads/AF-I6X9D2-F1-model_v4.pdb
AF-I6X9D2-F1-model_v4.pdb title:
Alphafold monomer V2.0 prediction for mce-family related protein (I6X9D2)
[more info...]
Chain information for AF-I6X9D2-F1-model_v4.pdb #2
---
Chain | Description | UniProt
A | mce-family related protein | I6X9D2_MYCTU
> close #1
> ui tool show "Show Sequence Viewer"
> sequence chain /A
Alignment identifier is 2/A
> select /A:59
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:54-59
46 atoms, 45 bonds, 6 residues, 1 model selected
> open /Users/benjin/Downloads/AF-Q6MX49-F1-model_v4.pdb
AF-Q6MX49-F1-model_v4.pdb title:
Alphafold monomer V2.0 prediction for ppe family protein PPE5 (Q6MX49) [more
info...]
Chain information for AF-Q6MX49-F1-model_v4.pdb #1
---
Chain | Description | UniProt
A | ppe family protein PPE5 | Q6MX49_MYCTU
> select add #2
649 atoms, 665 bonds, 84 residues, 1 model selected
> select add #1
15905 atoms, 16224 bonds, 2288 residues, 2 models selected
> mlp sel
Map values for surface "AF-Q6MX49-F1-model_v4.pdb_A SES surface": minimum
-28.28, mean -2.941, maximum 25.4
Map values for surface "AF-I6X9D2-F1-model_v4.pdb_A SES surface": minimum
-24.87, mean -2.315, maximum 22.55
To also show corresponding color key, enter the above mlp command and add key
true
> undo
> redo
> undo
> close #2
> open "/Users/benjin/Desktop/Multimeric candiates/AF-I6X8E6-F1-model_v4
> (1).pdb"
AF-I6X8E6-F1-model_v4 (1).pdb title:
Alphafold monomer V2.0 prediction for uncharacterized protein (I6X8E6) [more
info...]
Chain information for AF-I6X8E6-F1-model_v4 (1).pdb #2
---
Chain | Description | UniProt
A | uncharacterized protein | I6X8E6_MYCTU
> close #1
> select clear
> mlp
Map values for surface "AF-I6X8E6-F1-model_v4 (1).pdb_A SES surface": minimum
-23.36, mean -2.949, maximum 23.22
To also show corresponding color key, enter the above mlp command and add key
true
> mlp
Map values for surface "AF-I6X8E6-F1-model_v4 (1).pdb_A SES surface": minimum
-23.36, mean -2.949, maximum 23.22
To also show corresponding color key, enter the above mlp command and add key
true
> undo
> redo
> hide surfaces
Drag select of 14 residues
> select clear
> select add #2
832 atoms, 868 bonds, 112 residues, 1 model selected
> color byattribute pLddt
No known/registered numeric attribute pLddt
> close #2
> ui tool show AlphaFold
Fetching I6X8E6 UniProt info from https://www.uniprot.org/uniprot/I6X8E6.xml
> alphafold match I6X8E6
Fetching AlphaFold database settings from
https://www.rbvi.ucsf.edu/chimerax/data/status/alphafold_database.json
Fetching compressed AlphaFold I6X8E6 from
https://alphafold.ebi.ac.uk/files/AF-I6X8E6-F1-model_v2.cif
1 AlphaFold model found using UniProt identifier: I6X8E6 (UniProt I6X8E6)
Opened 1 AlphaFold model
> alphafold pae #1 uniprotId I6X8E6
Fetching compressed AlphaFold PAE I6X8E6 from
https://alphafold.ebi.ac.uk/files/AF-I6X8E6-F1-predicted_aligned_error_v2.json
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> ui tool show "Show Sequence Viewer"
> sequence chain /A
Alignment identifier is 1/A
> select /A:86
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /A:64-86
205 atoms, 217 bonds, 23 residues, 1 model selected
> select /A:64-86
205 atoms, 217 bonds, 23 residues, 1 model selected
> select /A:46
4 atoms, 3 bonds, 1 residue, 1 model selected
> select /A:46-86
344 atoms, 361 bonds, 41 residues, 1 model selected
> select /A:112
8 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:1-112
832 atoms, 868 bonds, 112 residues, 1 model selected
> select /A:112
8 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:1-112
832 atoms, 868 bonds, 112 residues, 1 model selected
> mlp sel
Map values for surface "AlphaFold I6X8E6_A SES surface": minimum -23.36, mean
-2.949, maximum 23.22
To also show corresponding color key, enter the above mlp command and add key
true
> transparency (#!1 & sel) 50
> undo
> redo
> undo
> redo
> hide sel surfaces
> select /A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:1-112
832 atoms, 868 bonds, 112 residues, 1 model selected
> hide sel surfaces
> select subtract #1
1 model selected
> alphafold pae #1 uniprotId I6X8E6
> open "/Users/benjin/Desktop/Monomeric candidates/AF-I6X7P2-F1-model_v4.pdb"
AF-I6X7P2-F1-model_v4.pdb title:
Alphafold monomer V2.0 prediction for uncharacterized protein (I6X7P2) [more
info...]
Chain information for AF-I6X7P2-F1-model_v4.pdb #2
---
Chain | Description | UniProt
A | uncharacterized protein | I6X7P2_MYCTU
> close #1
> mlp
Map values for surface "AF-I6X7P2-F1-model_v4.pdb_A SES surface": minimum
-27.75, mean -4.872, maximum 22.4
To also show corresponding color key, enter the above mlp command and add key
true
> open /Users/benjin/Downloads/AF-I6XHD1-F1-model_v4.pdb
AF-I6XHD1-F1-model_v4.pdb title:
Alphafold monomer V2.0 prediction for uncharacterized protein (I6XHD1) [more
info...]
Chain information for AF-I6XHD1-F1-model_v4.pdb #1
---
Chain | Description | UniProt
A | uncharacterized protein | I6XHD1_MYCTU
> close #1
> close #2
> open /Users/benjin/Downloads/AF-I6XHD1-F1-model_v4.pdb
AF-I6XHD1-F1-model_v4.pdb title:
Alphafold monomer V2.0 prediction for uncharacterized protein (I6XHD1) [more
info...]
Chain information for AF-I6XHD1-F1-model_v4.pdb #1
---
Chain | Description | UniProt
A | uncharacterized protein | I6XHD1_MYCTU
> mlp
Map values for surface "AF-I6XHD1-F1-model_v4.pdb_A SES surface": minimum
-26.88, mean -5.195, maximum 21.67
To also show corresponding color key, enter the above mlp command and add key
true
> coulombic
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for AF-I6XHD1-F1-model_v4.pdb_A SES surface #1.1: minimum,
-14.29, mean -1.41, maximum 9.56
To also show corresponding color key, enter the above coulombic command and
add key true
> mlp
Map values for surface "AF-I6XHD1-F1-model_v4.pdb_A SES surface": minimum
-26.88, mean -5.195, maximum 21.67
To also show corresponding color key, enter the above mlp command and add key
true
> close #1
> open /Users/benjin/Desktop/Structure/PDB/pdb1uun.ent format pdb
No such file/path: /Users/benjin/Desktop/Structure/PDB/pdb1uun.ent
> open "/Users/benjin/Desktop/1. Write up/0. Bioinformatics/0. Structure-based
> homology search/Monomeric /12_AF_Tsx.pdb"
12_AF_Tsx.pdb title:
Alphafold monomer V2.0 prediction for nucleoside-specific channel- forming
protein TSX (P0A927) [more info...]
Chain information for 12_AF_Tsx.pdb #1
---
Chain | Description | UniProt
A | nucleoside-specific channel-forming protein TSX | TSX_ECOLI
> mlp
Map values for surface "12_AF_Tsx.pdb_A SES surface": minimum -29.57, mean
-2.558, maximum 24.84
To also show corresponding color key, enter the above mlp command and add key
true
> open "/Users/benjin/Desktop/1. Write up/0. Bioinformatics/0. Structure-based
> homology search/Monomeric /8_AF_YfaZ.pdb"
8_AF_YfaZ.pdb title:
Alphafold monomer V2.0 prediction for outer membrane protein yfaz (P76471)
[more info...]
Chain information for 8_AF_YfaZ.pdb #2
---
Chain | Description | UniProt
A | outer membrane protein yfaz | YFAZ_ECOLI
> close #1
> coulombic
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for 8_AF_YfaZ.pdb_A SES surface #2.1: minimum, -20.75, mean
-2.68, maximum 13.99
To also show corresponding color key, enter the above coulombic command and
add key true
> mlp
Map values for surface "8_AF_YfaZ.pdb_A SES surface": minimum -27.7, mean
-4.367, maximum 23.12
To also show corresponding color key, enter the above mlp command and add key
true
> close #2
> open /Users/benjin/Downloads/AF-I6XHD1-F1-model_v4.pdb
AF-I6XHD1-F1-model_v4.pdb title:
Alphafold monomer V2.0 prediction for uncharacterized protein (I6XHD1) [more
info...]
Chain information for AF-I6XHD1-F1-model_v4.pdb #1
---
Chain | Description | UniProt
A | uncharacterized protein | I6XHD1_MYCTU
> mlp
Map values for surface "AF-I6XHD1-F1-model_v4.pdb_A SES surface": minimum
-26.88, mean -5.195, maximum 21.67
To also show corresponding color key, enter the above mlp command and add key
true
> open "/Users/benjin/Desktop/Monomeric candidates/AF-I6X7P2-F1-model_v4.pdb"
AF-I6X7P2-F1-model_v4.pdb title:
Alphafold monomer V2.0 prediction for uncharacterized protein (I6X7P2) [more
info...]
Chain information for AF-I6X7P2-F1-model_v4.pdb #2
---
Chain | Description | UniProt
A | uncharacterized protein | I6X7P2_MYCTU
> close #1
> mlp
Map values for surface "AF-I6X7P2-F1-model_v4.pdb_A SES surface": minimum
-27.75, mean -4.872, maximum 22.4
To also show corresponding color key, enter the above mlp command and add key
true
> open "/Users/benjin/Desktop/Monomeric candidates/AF-I6X7P2-F1-model_v4.pdb"
AF-I6X7P2-F1-model_v4.pdb title:
Alphafold monomer V2.0 prediction for uncharacterized protein (I6X7P2) [more
info...]
Chain information for AF-I6X7P2-F1-model_v4.pdb #1
---
Chain | Description | UniProt
A | uncharacterized protein | I6X7P2_MYCTU
> select add #2
1313 atoms, 1345 bonds, 176 residues, 1 model selected
> close #2
> mlp
Map values for surface "AF-I6X7P2-F1-model_v4.pdb_A SES surface": minimum
-27.75, mean -4.872, maximum 22.4
To also show corresponding color key, enter the above mlp command and add key
true
> open /Users/benjin/Downloads/AF-O06555-F1-model_v4.pdb
AF-O06555-F1-model_v4.pdb title:
Alphafold monomer V2.0 prediction for conserved ala-, pro-rich protein
(O06555) [more info...]
Chain information for AF-O06555-F1-model_v4.pdb #2
---
Chain | Description | UniProt
A | conserved ala-, pro-rich protein | O06555_MYCTU
> close #1
> mlp
Map values for surface "AF-O06555-F1-model_v4.pdb_A SES surface": minimum
-26.21, mean -4.743, maximum 24.43
To also show corresponding color key, enter the above mlp command and add key
true
> open /Users/benjin/Downloads/AF-O05592-F1-model_v4.pdb
AF-O05592-F1-model_v4.pdb title:
Alphafold monomer V2.0 prediction for uncharacterized protein (O05592) [more
info...]
Chain information for AF-O05592-F1-model_v4.pdb #1
---
Chain | Description | UniProt
A | uncharacterized protein | O05592_MYCTU
> close #2
> mlp
Map values for surface "AF-O05592-F1-model_v4.pdb_A SES surface": minimum
-30.36, mean -6.171, maximum 24.45
To also show corresponding color key, enter the above mlp command and add key
true
> open /Users/benjin/Downloads/AF-O69715-F1-model_v4.pdb
AF-O69715-F1-model_v4.pdb title:
Alphafold monomer V2.0 prediction for uncharacterized protein (O69715) [more
info...]
Chain information for AF-O69715-F1-model_v4.pdb #2
---
Chain | Description | UniProt
A | uncharacterized protein | O69715_MYCTU
> close #2
> close #1
> open /Users/benjin/Downloads/AF-O69715-F1-model_v4.pdb
AF-O69715-F1-model_v4.pdb title:
Alphafold monomer V2.0 prediction for uncharacterized protein (O69715) [more
info...]
Chain information for AF-O69715-F1-model_v4.pdb #1
---
Chain | Description | UniProt
A | uncharacterized protein | O69715_MYCTU
> mlp
Map values for surface "AF-O69715-F1-model_v4.pdb_A SES surface": minimum
-24.49, mean -5.122, maximum 21.92
To also show corresponding color key, enter the above mlp command and add key
true
> open /Users/benjin/Downloads/AF-O53527-F1-model_v4.pdb
AF-O53527-F1-model_v4.pdb title:
Alphafold monomer V2.0 prediction for uncharacterized protein (O53527) [more
info...]
Chain information for AF-O53527-F1-model_v4.pdb #2
---
Chain | Description | UniProt
A | uncharacterized protein | O53527_MYCTU
> select add #1
898 atoms, 917 bonds, 119 residues, 1 model selected
> select subtract #1
1 model selected
> hide #2 models
> close #2
> undo
> close #1
> open /Users/benjin/Downloads/AF-O53527-F1-model_v4.pdb
AF-O53527-F1-model_v4.pdb title:
Alphafold monomer V2.0 prediction for uncharacterized protein (O53527) [more
info...]
Chain information for AF-O53527-F1-model_v4.pdb #1
---
Chain | Description | UniProt
A | uncharacterized protein | O53527_MYCTU
> mlp
Map values for surface "AF-O53527-F1-model_v4.pdb_A SES surface": minimum
-26.94, mean -4.219, maximum 23.46
To also show corresponding color key, enter the above mlp command and add key
true
> close #1
> open /Users/benjin/Downloads/AF-Q6MX48-F1-model_v4.pdb
AF-Q6MX48-F1-model_v4.pdb title:
Alphafold monomer V2.0 prediction for ppe family protein PPE6 (Q6MX48) [more
info...]
Chain information for AF-Q6MX48-F1-model_v4.pdb #1
---
Chain | Description | UniProt
A | ppe family protein PPE6 | Q6MX48_MYCTU
> mlp
Map values for surface "AF-Q6MX48-F1-model_v4.pdb_A SES surface": minimum
-28.82, mean -3.232, maximum 23.35
To also show corresponding color key, enter the above mlp command and add key
true
> hide surfaces
> ui tool show "Show Sequence Viewer"
> sequence chain /A
Alignment identifier is 1/A
> select /A:503-504
13 atoms, 12 bonds, 2 residues, 1 model selected
> select /A:503-510
61 atoms, 61 bonds, 8 residues, 1 model selected
> select /A:565
4 atoms, 3 bonds, 1 residue, 1 model selected
> select /A:565-566
9 atoms, 8 bonds, 2 residues, 1 model selected
> select /A:701
4 atoms, 3 bonds, 1 residue, 1 model selected
> select /A:701-702
15 atoms, 15 bonds, 2 residues, 1 model selected
> select /A:416-417
13 atoms, 12 bonds, 2 residues, 1 model selected
> select /A:416-510
696 atoms, 713 bonds, 95 residues, 1 model selected
> select add #1
6993 atoms, 7158 bonds, 963 residues, 2 models selected
> select subtract #1
1 model selected
> save /Users/benjin/Desktop/image1.png supersample 3
> open /Users/benjin/Desktop/AF-Q6MX49-PPE5.pdb
AF-Q6MX49-PPE5.pdb title:
Alphafold monomer V2.0 prediction for ppe family protein PPE5 (Q6MX49) [more
info...]
Chain information for AF-Q6MX49-PPE5.pdb #2
---
Chain | Description | UniProt
A | ppe family protein PPE5 | Q6MX49_MYCTU
> close #2
> close #1
> open /Users/benjin/Downloads/AF-Q6MX48-F1-model_v4.pdb
AF-Q6MX48-F1-model_v4.pdb title:
Alphafold monomer V2.0 prediction for ppe family protein PPE6 (Q6MX48) [more
info...]
Chain information for AF-Q6MX48-F1-model_v4.pdb #1
---
Chain | Description | UniProt
A | ppe family protein PPE6 | Q6MX48_MYCTU
> close
> open /Users/benjin/Desktop/AF-Q6MX48-F1-model_v4.pdb
AF-Q6MX48-F1-model_v4.pdb title:
Alphafold monomer V2.0 prediction for ppe family protein PPE6 (Q6MX48) [more
info...]
Chain information for AF-Q6MX48-F1-model_v4.pdb #1
---
Chain | Description | UniProt
A | ppe family protein PPE6 | Q6MX48_MYCTU
> close
> open /Users/benjin/Desktop/AF-Q6MX48-PPE6.pdb
AF-Q6MX48-PPE6.pdb title:
Alphafold monomer V2.0 prediction for ppe family protein PPE6 (Q6MX48) [more
info...]
Chain information for AF-Q6MX48-PPE6.pdb #1
---
Chain | Description | UniProt
A | ppe family protein PPE6 | Q6MX48_MYCTU
> close
> open /Users/benjin/Desktop/AF-Q6MX49-PPE5.pdb
AF-Q6MX49-PPE5.pdb title:
Alphafold monomer V2.0 prediction for ppe family protein PPE5 (Q6MX49) [more
info...]
Chain information for AF-Q6MX49-PPE5.pdb #1
---
Chain | Description | UniProt
A | ppe family protein PPE5 | Q6MX49_MYCTU
> mlp
Map values for surface "AF-Q6MX49-PPE5.pdb_A SES surface": minimum -28.28,
mean -2.941, maximum 25.4
To also show corresponding color key, enter the above mlp command and add key
true
> undo
Undo failed, probably because structures have been modified.
> close #1
> open /Users/benjin/Desktop/AF-Q6MX48-PPE6.pdb
AF-Q6MX48-PPE6.pdb title:
Alphafold monomer V2.0 prediction for ppe family protein PPE6 (Q6MX48) [more
info...]
Chain information for AF-Q6MX48-PPE6.pdb #1
---
Chain | Description | UniProt
A | ppe family protein PPE6 | Q6MX48_MYCTU
> open /Users/benjin/Desktop/AF-Q6MX49-PPE5.pdb
AF-Q6MX49-PPE5.pdb title:
Alphafold monomer V2.0 prediction for ppe family protein PPE5 (Q6MX49) [more
info...]
Chain information for AF-Q6MX49-PPE5.pdb #2
---
Chain | Description | UniProt
A | ppe family protein PPE5 | Q6MX49_MYCTU
> close #1
> open /Users/benjin/Desktop/AF-Q6MX49-PPE5.pdb
AF-Q6MX49-PPE5.pdb title:
Alphafold monomer V2.0 prediction for ppe family protein PPE5 (Q6MX49) [more
info...]
Chain information for AF-Q6MX49-PPE5.pdb #1
---
Chain | Description | UniProt
A | ppe family protein PPE5 | Q6MX49_MYCTU
Fetching Q6MX49 UniProt info from https://www.uniprot.org/uniprot/Q6MX49.xml
> alphafold match Q6MX49
Fetching compressed AlphaFold Q6MX49 from
https://alphafold.ebi.ac.uk/files/AF-Q6MX49-F1-model_v2.cif
1 AlphaFold model found using UniProt identifier: Q6MX49 (UniProt Q6MX49)
Opened 1 AlphaFold model
> close #1
> hide #2 models
> preset "overall look" "publication 2 (depth-cued)"
Using preset: Overall Look / Publication 2 (Depth-Cued)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes f
lighting depthCue t
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
Must choose path to predicted aligned file
File "Q6MX49" does not exist.
> alphafold pae #3 uniprotId Q6MX49
Fetching compressed AlphaFold PAE Q6MX49 from
https://alphafold.ebi.ac.uk/files/AF-Q6MX49-F1-predicted_aligned_error_v2.json
> color bfactor #3 palette alphafold
15256 atoms, 2204 residues, atom bfactor range 20.9 to 92.5
> alphafold pae #3 colorDomains true
> color bfactor #3 palette alphafold
15256 atoms, 2204 residues, atom bfactor range 20.9 to 92.5
> alphafold pae #3 uniprotId Q6MX49
> undo
> alphafold pae #3 uniprotId Q6MX49
> alphafold pae #3 colorDomains true
> color bfactor #3 palette alphafold
15256 atoms, 2204 residues, atom bfactor range 20.9 to 92.5
> alphafold pae #3 colorDomains true
> color bfactor #3 palette alphafold
15256 atoms, 2204 residues, atom bfactor range 20.9 to 92.5
> alphafold pae #3 uniprotId Q6MX49
> color bfactor #3 palette alphafold
15256 atoms, 2204 residues, atom bfactor range 20.9 to 92.5
> save /Users/benjin/Desktop/image1.png supersample 3
> open /Users/benjin/Downloads/uniprot-
> compressed_true_download_true_fields_accession_2Creviewed_2C-2023.04.10-09.06.15.31.xlsx/[Content_Types].xml
Opened [Content_Types].xml
> open /Users/benjin/Downloads/uniprot-
> compressed_true_download_true_fields_accession_2Creviewed_2C-2023.04.10-09.06.15.31.xlsx/xl/worksheets/sheet1.xml
Opened sheet1.xml
> mlp #3
Map values for surface "AlphaFold Q6MX49_A SES surface": minimum -28.28, mean
-2.941, maximum 25.4
To also show corresponding color key, enter the above mlp command and add key
true
> close #2
> close
> open /Users/benjin/Desktop/AF-Q6MX48-PPE6.pdb
AF-Q6MX48-PPE6.pdb title:
Alphafold monomer V2.0 prediction for ppe family protein PPE6 (Q6MX48) [more
info...]
Chain information for AF-Q6MX48-PPE6.pdb #1
---
Chain | Description | UniProt
A | ppe family protein PPE6 | Q6MX48_MYCTU
> alphafold pae #1 uniprotId Q6MX48
Fetching compressed AlphaFold PAE Q6MX48 from
https://alphafold.ebi.ac.uk/files/AF-Q6MX48-F1-predicted_aligned_error_v2.json
> alphafold pae #1 colorDomains true
> color bfactor #1 palette alphafold
6993 atoms, 963 residues, atom bfactor range 22.1 to 98.5
> save /Users/benjin/Desktop/image1.png supersample 3
> help help:user/tools/alphafold.html#pae
> alphafold pae #1 uniprotId Q6MX48
> ui tool show "Show Sequence Viewer"
> sequence chain /A
Alignment identifier is 1/A
> select /A:205
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:205-207
16 atoms, 15 bonds, 3 residues, 1 model selected
> select /A:205
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:205-440
1673 atoms, 1709 bonds, 236 residues, 1 model selected
> select /A:205
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:205-255
352 atoms, 357 bonds, 51 residues, 1 model selected
> select /A:416
5 atoms, 4 bonds, 1 residue, 1 model selected
> select /A:416-511
703 atoms, 721 bonds, 96 residues, 1 model selected
> select /A:417-418
16 atoms, 15 bonds, 2 residues, 1 model selected
> select /A:417-449
247 atoms, 252 bonds, 33 residues, 1 model selected
> select /A:416
5 atoms, 4 bonds, 1 residue, 1 model selected
> select /A:416-454
290 atoms, 296 bonds, 39 residues, 1 model selected
> select /A:416
5 atoms, 4 bonds, 1 residue, 1 model selected
> select /A:416-511
703 atoms, 721 bonds, 96 residues, 1 model selected
> alphafold pae #1 uniprotId Q6MX48
> color bfactor #1 palette alphafold
6993 atoms, 963 residues, atom bfactor range 22.1 to 98.5
> help help:user/tools/alphafold.html#pae
> Extended β-strands
Unknown command: Extended β-strands
> (416-511)
Unknown command: (416-511)
> color bfactor palette alphafold
6993 atoms, 963 residues, atom bfactor range 22.1 to 98.5
> key red:low orange: yellow: cornflowerblue: blue:high
> select clear
> open "/Users/benjin/Desktop/Part III Project/Presentation/20230113
> Biochemistry Symposium/MmpL5_coiled conservation_AlphaFold.pdb"
MmpL5_coiled conservation_AlphaFold.pdb title:
Alphafold monomer V2.0 prediction for siderophore exporter MMPL5 (P9WJV1)
[more info...]
Chain information for MmpL5_coiled conservation_AlphaFold.pdb #3
---
Chain | Description | UniProt
A | siderophore exporter MMPL5 | MMPL5_MYCTU
> close #1
> hide #3 models
> close
> open "/Users/benjin/Desktop/Part III Project/0. Bioinformatics seq /MmpL Mtb
> analysis_Adam/AF_MmpL5_conserved between paralogues.pdb"
AF_MmpL5_conserved between paralogues.pdb title:
Alphafold monomer V2.0 prediction for siderophore exporter MMPL5 (P9WJV1)
[more info...]
Chain information for AF_MmpL5_conserved between paralogues.pdb #1
---
Chain | Description | UniProt
A | siderophore exporter MMPL5 | MMPL5_MYCTU
> open "/Users/benjin/Desktop/Part III Project/0. Bioinformatics seq /MmpL Mtb
> analysis_Adam/Mtb MmpL5 coiled coil aligned paralogue.cxs"
opened ChimeraX session
> open "/Users/benjin/Desktop/1. Write up/TrimericS5L5 2.pdb"
Summary of feedback from opening /Users/benjin/Desktop/1. Write
up/TrimericS5L5 2.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ILE B 2
ARG B 7 1 6
Start residue of secondary structure not found: HELIX 2 2 TRP B 9 THR B 30 1
22
Start residue of secondary structure not found: HELIX 3 3 PHE C 23 THR C 30 1
8
Start residue of secondary structure not found: HELIX 4 4 ALA C 32 THR C 49 1
18
Start residue of secondary structure not found: HELIX 5 5 LEU C 53 ILE C 59 1
7
46 messages similar to the above omitted
Chain information for TrimericS5L5 2.pdb
---
Chain | Description
3.1/B 3.2/B 3.3/B | No description available
3.4/B 3.4/C 3.4/D | No description available
3.1/C 3.2/C 3.3/C | No description available
3.4/E 3.4/F 3.4/G | No description available
Associated TrimericS5L5 2.pdb (3.1) chain C to MmpL5 with 0 mismatches
Associated TrimericS5L5 2.pdb (3.2) chain C to MmpL5 with 0 mismatches
Associated TrimericS5L5 2.pdb (3.3) chain C to MmpL5 with 0 mismatches
Associated TrimericS5L5 2.pdb (3.4) chain B to MmpL5 with 0 mismatches
Associated TrimericS5L5 2.pdb (3.4) chain C to MmpL5 with 0 mismatches
Associated TrimericS5L5 2.pdb (3.4) chain D to MmpL5 with 0 mismatches
> close #1-2
> ui tool show "AlphaFold Error Plot"
> help help:user/tools/alphafold.html#pae
> color bfactor palette alphafold
31974 atoms, 4170 residues, atom bfactor range 24.5 to 98.8
> hide surfaces
> select add #3
31974 atoms, 32598 bonds, 4170 residues, 5 models selected
> hide sel surfaces
> show sel surfaces
> hide sel surfaces
> undo
> hide #!3.1 models
> show #!3.1 models
> hide #!3.1 models
> show #!3.1 models
> hide #!3.3 models
> show #!3.3 models
> hide #!3.4 models
> show #!3.4 models
> hide #!3.4 models
> show #!3.4 models
> hide #!3.4 models
> show #!3.4 models
> hide #!3.4 models
> color bfactor palette alphafold
31974 atoms, 4170 residues, 12 surfaces, atom bfactor range 24.5 to 98.8
> save /Users/benjin/Desktop/image1.png supersample 3
> save /Users/benjin/Desktop/image2.png supersample 3
> save /Users/benjin/Desktop/image3.png supersample 3
> hide #!3.1 models
> show #!3.1 models
> hide #!3.2 models
> show #!3.2 models
> hide #!3.2 models
> show #!3.2 models
> show #!3.4 models
> hide #!3.4 models
> hide #!3 models
> show #!3 models
> show #!3.4 models
> hide #!3.4 models
> ui tool show "Color Actions"
> color bychain
> undo
> save /Users/benjin/Desktop/image1.png supersample 3
> ui tool show "Color Actions"
> color bypolymer
> color bychain
> color bypolymer
> color bychain
> color #3.1 #ff40ff transparency 0
> color #3.1 #ff2600 transparency 0
> color #3.1 #fffb00 transparency 0
> color #3.1 #c13a5b transparency 0
> color #3.1 #4498d8 transparency 0
> color #3.2 #4498d8 transparency 0
> color #3.3 #4498d8 transparency 0
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 ATI-4.8.101
OpenGL renderer: AMD Radeon Pro 5500M OpenGL Engine
OpenGL vendor: ATI Technologies Inc.
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro16,1
Processor Name: 8-Core Intel Core i9
Processor Speed: 2.3 GHz
Number of Processors: 1
Total Number of Cores: 8
L2 Cache (per Core): 256 KB
L3 Cache: 16 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
System Firmware Version: 1731.140.2.0.0 (iBridge: 19.16.16067.0.0,0)
OS Loader Version: 540.120.3~22
Software:
System Software Overview:
System Version: macOS 12.6 (21G115)
Kernel Version: Darwin 21.6.0
Time since boot: 17 days 9:34
Graphics/Displays:
Intel UHD Graphics 630:
Chipset Model: Intel UHD Graphics 630
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x3e9b
Revision ID: 0x0002
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Family: Supported, Metal GPUFamily macOS 2
AMD Radeon Pro 5500M:
Chipset Model: AMD Radeon Pro 5500M
Type: GPU
Bus: PCIe
PCIe Lane Width: x16
VRAM (Total): 4 GB
Vendor: AMD (0x1002)
Device ID: 0x7340
Revision ID: 0x0040
ROM Revision: 113-D3220E-190
VBIOS Version: 113-D32206U1-020
Option ROM Version: 113-D32206U1-020
EFI Driver Version: 01.A1.190
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Family: Supported, Metal GPUFamily macOS 2
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 3072 x 1920 Retina
Framebuffer Depth: 24-Bit Color (ARGB8888)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.3
Babel: 2.10.1
backcall: 0.2.0
blockdiag: 3.0.0
certifi: 2021.10.8
cftime: 1.6.0
charset-normalizer: 2.0.12
ChimeraX-AddCharge: 1.2.3
ChimeraX-AddH: 2.1.3
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2.1
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.4.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.39.1
ChimeraX-AtomicLibrary: 7.0
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.1
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.1
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.7
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: 2.2.4
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.1
ChimeraX-CommandLine: 1.2.3
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.4
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: 1.1
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: 1.2
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: 1.1.1
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: 2.7
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.5.5
ChimeraX-ModelPanel: 1.3.2
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: 1.9
ChimeraX-PDB: 2.6.6
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: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.6
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: 1.8
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: 1.1.1
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.18.3
ChimeraX-uniprot: 2.2
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.1.2
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: 1.1.0
ChimeraX-Zone: 1.0
colorama: 0.4.4
cxservices: 1.2
cycler: 0.11.0
Cython: 0.29.26
debugpy: 1.6.0
decorator: 5.1.1
docutils: 0.17.1
entrypoints: 0.4
filelock: 3.4.2
fonttools: 4.33.3
funcparserlib: 1.0.0
grako: 3.16.5
h5py: 3.7.0
html2text: 2020.1.16
idna: 3.3
ihm: 0.27
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: 4.10.0
kiwisolver: 1.4.2
line-profiler: 3.4.0
lxml: 4.7.1
lz4: 3.1.10
MarkupSafe: 2.1.1
matplotlib: 3.5.1
matplotlib-inline: 0.1.3
msgpack: 1.0.3
nest-asyncio: 1.5.5
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: 9.0.1
pip: 21.3.1
pkginfo: 1.8.2
prompt-toolkit: 3.0.29
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: 3.0.9
PyQt6-commercial: 6.3.0
PyQt6-Qt6: 6.3.0
PyQt6-sip: 13.3.1
PyQt6-WebEngine-commercial: 6.3.0
PyQt6-WebEngine-Qt6: 6.3.0
python-dateutil: 2.8.2
pytz: 2022.1
pyzmq: 23.1.0
qtconsole: 5.3.0
QtPy: 2.1.0
RandomWords: 0.3.0
requests: 2.27.1
scipy: 1.7.3
setuptools: 59.8.0
sfftk-rw: 0.7.2
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: 1.26.9
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.37.1
wheel-filename: 1.3.0
Change History (2)
comment:1 by , 3 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Platform |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash using color chooser |
comment:2 by , 3 years ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
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