![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 2 years ago
Closed 2 years ago
#9167 closed defect (nonchimerax)
Graphics crash, macOS 13.1, Intel Iris Plus Graphics
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Graphics | 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: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Aborted
Current thread 0x00007ff850a1c8c0 (most recent call first):
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/opengl.py", line 235 in swap_buffers
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/opengl.py", line 497 in swap_buffers
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/view.py", line 191 in draw
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/updateloop.py", line 73 in draw_new_frame
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/updateloop.py", line 139 in _redraw_timer_callback
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 275 in event_loop
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 892 in init
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 1043 in
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
File "/Applications/ChimeraX-1.6.1.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" : 430000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 502,
"deployVersion" : 210,
"modelCode" : "MacBookPro16,2",
"coalitionID" : 49947,
"osVersion" : {
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"build" : "22C65",
"releaseType" : "User"
},
"captureTime" : "2023-06-12 11:37:32.8286 +0100",
"incident" : "6D532D15-F7C1-4B55-88E3-1E73DB855610",
"pid" : 54158,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2023-06-11 08:32:36.4720 +0100",
"procStartAbsTime" : 418900424556681,
"procExitAbsTime" : 437967692813321,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.6.1.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.6.1","CFBundleVersion":"1.6.1.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"67FBC5BD-9817-5885-9FE5-8E2771D6B9F4","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "F46F41C5-FF6C-941F-A528-C0FEEB51179E",
"throttleTimeout" : 2147483647,
"wakeTime" : 88,
"bridgeVersion" : {"build":"20P2059","train":"7.1"},
"sleepWakeUUID" : "66870800-E43D-40D8-B246-0036D302C996",
"sip" : "enabled",
"exception" : {"codes":"0x0000000000000000, 0x0000000000000000","rawCodes":[0,0],"type":"EXC_CRASH","signal":"SIGABRT"},
"ktriageinfo" : "VM - Waiting on busy page was interrupted\nVM - Waiting on busy page was interrupted\nVM - Fault was interrupted\n",
"asi" : {"libsystem_c.dylib":["abort() called"]},
"asiSignatures" : ["Graphics hardware encountered an error and was reset: 0x00000011\n"],
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"faultingThread" : 0,
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===== Log before crash start =====
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/bo1il/Downloads/PafA-like_Bacteroides/final.casp.pdb
Chain information for final.casp.pdb #1
---
Chain | Description
? | No description available
> open /Users/bo1il/Downloads/PafA-like_Bacteroides/c5tj3A_.1.pdb
Chain information for c5tj3A_.1.pdb #2
---
Chain | Description
? | No description available
> toolshed show
> select #1/?#2/?
7994 atoms, 8186 bonds, 1000 residues, 2 models selected
> ui tool show Matchmaker
> matchmaker #2 to #1
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 final.casp.pdb, chain (blank) (#1) with c5tj3A_.1.pdb, chain
(blank) (#2), sequence alignment score = 2597.5
RMSD between 500 pruned atom pairs is 0.000 angstroms; (across all 500 pairs:
0.000)
> ui tool show "Show Sequence Viewer"
> sequence chain #1/? #2/?
Alignment identifier is 1
> hide #1 models
> show #1 models
> hide #1 models
> select
> #1/*:28-34,62-64,98-101,106-109,149-152,169-174,179-181,276-282,326-331,376-380,383-386,415-420,448-452,478-482,488-490
> #2/*:28-34,62-64,98-101,106-109,149-152,169-174,179-181,276-282,326-331,376-380,383-386,415-420,448-452,478-482,488-490
1192 atoms, 1194 bonds, 144 residues, 2 models selected
> select
> #1/*:39-42,46-48,54-60,76-85,89-92,135-143,156-163,192-200,202-206,217-219,250-266,284-292,297-320,340-345,355-370,388-394,398-411,431-439,496-507
> #2/*:39-42,46-48,54-60,76-85,89-92,135-143,156-163,192-200,202-206,217-219,250-266,284-292,297-320,340-345,355-370,388-394,398-411,431-439,496-507
2818 atoms, 2820 bonds, 352 residues, 2 models selected
> select
> #1/*:28-34,62-64,98-101,106-109,149-152,169-174,179-181,276-282,326-331,376-380,383-386,415-420,448-452,478-482,488-490
> #2/*:28-34,62-64,98-101,106-109,149-152,169-174,179-181,276-282,326-331,376-380,383-386,415-420,448-452,478-482,488-490
1192 atoms, 1194 bonds, 144 residues, 2 models selected
> open
> /Users/u1471847/Documents/SARISA/Flavo_ExoP/Comparative_genomics/PafA_Prevotella_KCOM1933.pdb
Chain information for PafA_Prevotella_KCOM1933.pdb #3
---
Chain | Description
? | No description available
> hide #2 models
> hide #3 models
> show #3 models
> show #2 models
> show #1 models
> hide #1 models
> select
> #1/*:39-42,46-48,54-60,76-85,89-92,135-143,156-163,192-200,202-206,217-219,250-266,284-292,297-320,340-345,355-370,388-394,398-411,431-439,496-507
> #2/*:39-42,46-48,54-60,76-85,89-92,135-143,156-163,192-200,202-206,217-219,250-266,284-292,297-320,340-345,355-370,388-394,398-411,431-439,496-507
2818 atoms, 2820 bonds, 352 residues, 2 models selected
> ui tool show "Modeller Comparative"
> modeller comparative 1:1 numModels 5 fast false multichain true hetPreserve
> false hydrogens false waterPreserve false
No Modeller license key provided. Get a license key by registering at the
Modeller web site.
> ui tool show "Show Sequence Viewer"
> sequence chain #3/?
Alignment identifier is 3/
> select
> #3/*:37-40,44-46,52-58,74-83,87-90,119-122,134-142,155-162,191-199,202-208,213-228,246-254,259-282,302-307,320-325,349-355,359-372,394-401,424-427,437-440,462-473
1394 atoms, 1399 bonds, 175 residues, 1 model selected
> select #1/*:33 #2/*:33
14 atoms, 12 bonds, 2 residues, 2 models selected
> select #1/*:33-113 #2/*:33-113
1314 atoms, 1340 bonds, 162 residues, 2 models selected
1 [ID: 1] region 2 chains [12-92] RMSD: 0.001
> select add #3
5042 atoms, 5158 bonds, 631 residues, 3 models selected
> select subtract #3
1314 atoms, 1340 bonds, 162 residues, 2 models selected
> select add #2
4654 atoms, 4763 bonds, 581 residues, 2 models selected
> select subtract #2
657 atoms, 670 bonds, 81 residues, 1 model selected
> select add #1
3997 atoms, 4093 bonds, 500 residues, 1 model selected
> select subtract #1
Nothing selected
> select add #1
3997 atoms, 4093 bonds, 500 residues, 1 model selected
> select subtract #1
Nothing selected
> select add #2
3997 atoms, 4093 bonds, 500 residues, 1 model selected
> select subtract #2
Nothing selected
> select add #3
3728 atoms, 3818 bonds, 469 residues, 1 model selected
> select subtract #3
Nothing selected
> open
> /Users/u1471847/Documents/SARISA/Flavo_ExoP/Comparative_genomics/PafA_0023.py
Traceback (most recent call last):
File
"/Users/u1471847/Documents/SARISA/Flavo_ExoP/Comparative_genomics/PafA_0023.py",
line 3, in
import cPickle, base64
ModuleNotFoundError: No module named 'cPickle'
Failed opening file
/Users/u1471847/Documents/SARISA/Flavo_ExoP/Comparative_genomics/PafA_0023.py:
Error opening python file
/Users/u1471847/Documents/SARISA/Flavo_ExoP/Comparative_genomics/PafA_0023.py
> open
> /Users/u1471847/Documents/SARISA/Flavo_ExoP/Comparative_genomics/PafA_0023.py
Traceback (most recent call last):
File
"/Users/u1471847/Documents/SARISA/Flavo_ExoP/Comparative_genomics/PafA_0023.py",
line 3, in
import cPickle, base64
ModuleNotFoundError: No module named 'cPickle'
Failed opening file
/Users/u1471847/Documents/SARISA/Flavo_ExoP/Comparative_genomics/PafA_0023.py:
Error opening python file
/Users/u1471847/Documents/SARISA/Flavo_ExoP/Comparative_genomics/PafA_0023.py
> open
> /Users/u1471847/Documents/SARISA/Flavo_ExoP/Comparative_genomics/PafA_mucilagnibacter.pdb
Chain information for PafA_mucilagnibacter.pdb #4
---
Chain | Description
? | No description available
> hide #4 models
> show #4 models
> select
> #1/*:39-42,46-48,54-60,76-85,89-92,135-143,156-163,192-200,202-206,217-219,250-266,284-292,297-320,340-345,355-370,388-394,398-411,431-439,496-507
> #2/*:39-42,46-48,54-60,76-85,89-92,135-143,156-163,192-200,202-206,217-219,250-266,284-292,297-320,340-345,355-370,388-394,398-411,431-439,496-507
2818 atoms, 2820 bonds, 352 residues, 2 models selected
> select #1/*:239 #2/*:239
18 atoms, 16 bonds, 2 residues, 2 models selected
> select #1/*:239-241 #2/*:239-241
50 atoms, 48 bonds, 6 residues, 2 models selected
1 [ID: 1] region 2 chains [218-220] RMSD: 0.000
> select #3/*:154
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/*:154-156
28 atoms, 27 bonds, 3 residues, 1 model selected
> select #3/*:156
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #3/*:154-156
28 atoms, 27 bonds, 3 residues, 1 model selected
> select #3/*:154
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/*:154
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide #3 models
> hide #4 models
> select
> #3/*:37-40,44-46,52-58,74-83,87-90,119-122,134-142,155-162,191-199,202-208,213-228,246-254,259-282,302-307,320-325,349-355,359-372,394-401,424-427,437-440,462-473
1394 atoms, 1399 bonds, 175 residues, 1 model selected
> hide #2 models
> show #3 models
> select #3/*:156
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #3/*:154-156
28 atoms, 27 bonds, 3 residues, 1 model selected
> show sel atoms
> select #3/*:155
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/*:155
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3/*:154
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/*:154
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/*:239 #2/*:239
18 atoms, 16 bonds, 2 residues, 2 models selected
> select #1/*:239-241 #2/*:239-241
50 atoms, 48 bonds, 6 residues, 2 models selected
1 [ID: 1] region 2 chains [218-220] RMSD: 0.000
> show #2 models
> select #1/*:239 #2/*:239
18 atoms, 16 bonds, 2 residues, 2 models selected
> select #1/*:239-241 #2/*:239-241
50 atoms, 48 bonds, 6 residues, 2 models selected
1 [ID: 1] region 2 chains [218-220] RMSD: 0.000
> select #1/*:241 #2/*:241
16 atoms, 14 bonds, 2 residues, 2 models selected
> select #1/*:239-241 #2/*:239-241
50 atoms, 48 bonds, 6 residues, 2 models selected
1 [ID: 1] region 2 chains [218-220] RMSD: 0.000
> select
> #1/*:39-42,46-48,54-60,76-85,89-92,135-143,156-163,192-200,202-206,217-219,250-266,284-292,297-320,340-345,355-370,388-394,398-411,431-439,496-507
> #2/*:39-42,46-48,54-60,76-85,89-92,135-143,156-163,192-200,202-206,217-219,250-266,284-292,297-320,340-345,355-370,388-394,398-411,431-439,496-507
2818 atoms, 2820 bonds, 352 residues, 2 models selected
> select #1/*:308 #2/*:308
22 atoms, 20 bonds, 2 residues, 2 models selected
> select #1/*:306-308 #2/*:306-308
54 atoms, 52 bonds, 6 residues, 2 models selected
1 [ID: 1] region 2 chains [285-287] RMSD: 0.001
> select
> #1/*:39-42,46-48,54-60,76-85,89-92,135-143,156-163,192-200,202-206,217-219,250-266,284-292,297-320,340-345,355-370,388-394,398-411,431-439,496-507
> #2/*:39-42,46-48,54-60,76-85,89-92,135-143,156-163,192-200,202-206,217-219,250-266,284-292,297-320,340-345,355-370,388-394,398-411,431-439,496-507
2818 atoms, 2820 bonds, 352 residues, 2 models selected
> select #1/*:203-204 #2/*:203-204
38 atoms, 38 bonds, 4 residues, 2 models selected
> select #1/*:203-205 #2/*:203-205
60 atoms, 60 bonds, 6 residues, 2 models selected
1 [ID: 1] region 2 chains [182-184] RMSD: 0.000
> select #1/*:143 #2/*:143
14 atoms, 12 bonds, 2 residues, 2 models selected
> select #1/*:143-162 #2/*:143-162
294 atoms, 298 bonds, 40 residues, 2 models selected
1 [ID: 1] region 2 chains [122-141] RMSD: 0.001
> select #1/*:156 #2/*:156
22 atoms, 20 bonds, 2 residues, 2 models selected
> select #1/*:154-156 #2/*:154-156
58 atoms, 60 bonds, 6 residues, 2 models selected
1 [ID: 1] region 2 chains [133-135] RMSD: 0.001
> select
> #1/*:39-42,46-48,54-60,76-85,89-92,135-143,156-163,192-200,202-206,217-219,250-266,284-292,297-320,340-345,355-370,388-394,398-411,431-439,496-507
> #2/*:39-42,46-48,54-60,76-85,89-92,135-143,156-163,192-200,202-206,217-219,250-266,284-292,297-320,340-345,355-370,388-394,398-411,431-439,496-507
2818 atoms, 2820 bonds, 352 residues, 2 models selected
> select #1/*:155 #2/*:155
22 atoms, 22 bonds, 2 residues, 2 models selected
> select #1/*:155 #2/*:155
22 atoms, 22 bonds, 2 residues, 2 models selected
1 [ID: 1] region 2 chains [134] RMSD: 0.001
> select #1/*:157 #2/*:157
16 atoms, 14 bonds, 2 residues, 2 models selected
> select #1/*:155-157 #2/*:155-157
60 atoms, 60 bonds, 6 residues, 2 models selected
1 [ID: 1] region 2 chains [134-136] RMSD: 0.001
> show sel & #2 atoms
> select #1/*:156 #2/*:156
22 atoms, 20 bonds, 2 residues, 2 models selected
> select #1/*:156 #2/*:156
22 atoms, 20 bonds, 2 residues, 2 models selected
1 [ID: 1] region 2 chains [135] RMSD: 0.001
> hide sel & #2 atoms
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #4 models
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
> select #1/*:157 #2/*:157
16 atoms, 14 bonds, 2 residues, 2 models selected
> select #1/*:155-157 #2/*:155-157
60 atoms, 60 bonds, 6 residues, 2 models selected
1 [ID: 1] region 2 chains [134-136] RMSD: 0.001
> style sel & #2 ball
Changed 30 atom styles
> select #3/*:154
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/*:154-156
28 atoms, 27 bonds, 3 residues, 1 model selected
> style sel ball
Changed 28 atom styles
> select #1/*:156 #2/*:156
22 atoms, 20 bonds, 2 residues, 2 models selected
> select #1/*:156 #2/*:156
22 atoms, 20 bonds, 2 residues, 2 models selected
1 [ID: 1] region 2 chains [135] RMSD: 0.001
> style sel & #2 sphere
Changed 11 atom styles
> show sel & #2 atoms
> style sel & #2 ball
Changed 11 atom styles
> select #3/*:155
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/*:155
8 atoms, 7 bonds, 1 residue, 1 model selected
> style sel ball
Changed 8 atom styles
> show sel atoms
> show sel cartoons
> hide sel cartoons
> show sel cartoons
> hide sel cartoons
> show sel atoms
> hide sel atoms
> show sel atoms
> hide sel cartoons
> show sel cartoons
> hide sel cartoons
> show sel cartoons
> hide sel cartoons
> select
> #3/*:37-40,44-46,52-58,74-83,87-90,119-122,134-142,155-162,191-199,202-208,213-228,246-254,259-282,302-307,320-325,349-355,359-372,394-401,424-427,437-440,462-473
1394 atoms, 1399 bonds, 175 residues, 1 model selected
> hide #4 models
> show #4 models
> hide #4 models
> select #1/*:316 #2/*:316
16 atoms, 14 bonds, 2 residues, 2 models selected
> select #1/*:316-318 #2/*:316-318
50 atoms, 48 bonds, 6 residues, 2 models selected
1 [ID: 1] region 2 chains [295-297] RMSD: 0.000
> lighting simple
> lighting soft
> lighting full
> lighting soft
> set bgColor black
> set bgColor white
> color bfactor sel & #2
25 atoms, 3 residues, atom bfactor range 0 to 0
> color bfactor sel & #2
25 atoms, 3 residues, atom bfactor range 0 to 0
> view sel
> select #3/*:154
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/*:154-156
28 atoms, 27 bonds, 3 residues, 1 model selected
> view sel
> hide sel cartoons
> show sel cartoons
> hide sel cartoons
> show sel cartoons
> ui tool show "Show Sequence Viewer"
> sequence chain #4/?
Alignment identifier is 4/
> select #4/*:171
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #4/*:171-173
28 atoms, 27 bonds, 3 residues, 1 model selected
> style #2-3 ball
Changed 7725 atom styles
> style #2-3 ball
Changed 7725 atom styles
> show #4 models
> style sel ball
Changed 28 atom styles
> style sel ball
Changed 28 atom styles
> style sel ball
Changed 28 atom styles
> show sel atoms
> hide sel atoms
> show sel atoms
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> select #4/*:171
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #4/*:171
9 atoms, 8 bonds, 1 residue, 1 model selected
> open /Users/bo1il/Downloads/5tj3.pdb
5tj3.pdb title:
Crystal structure of wild type alkaline phosphatase pafa to 1.7A resolution
[more info...]
Chain information for 5tj3.pdb #5
---
Chain | Description | UniProt
A | AP PAFA | ALPH_ELIME 21-546
Non-standard residues in 5tj3.pdb #5
---
ZN — zinc ion
> style sel stick
Changed 9 atom styles
> style sel stick
Changed 9 atom styles
> select #4/*:171
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #4/*:171-173
28 atoms, 27 bonds, 3 residues, 1 model selected
> style sel stick
Changed 28 atom styles
> select #3/*:156
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #3/*:154-156
28 atoms, 27 bonds, 3 residues, 1 model selected
> style sel stick
Changed 28 atom styles
> select
> #3/*:26-32,60-62,96-99,104-107,148-151,168-173,178-180,238-244,288-293,313-315,337-341,344-347,376-381,410-414,418-420,444-448,454-456
639 atoms, 648 bonds, 78 residues, 1 model selected
> select #1/*:155 #2/*:155
22 atoms, 22 bonds, 2 residues, 2 models selected
> select #1/*:155-157 #2/*:155-157
60 atoms, 60 bonds, 6 residues, 2 models selected
1 [ID: 1] region 2 chains [134-136] RMSD: 0.001
> style sel & #2 stick
Changed 30 atom styles
> select #3/*:72
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3/*:72
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3/*:80
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #3/*:78-80
22 atoms, 22 bonds, 3 residues, 1 model selected
> select #3/*:79-80
12 atoms, 11 bonds, 2 residues, 1 model selected
> select #3/*:79-80
12 atoms, 11 bonds, 2 residues, 1 model selected
> select #3/*:83
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3/*:83
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3/*:74
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3/*:74
7 atoms, 6 bonds, 1 residue, 1 model selected
> style sel stick
Changed 7 atom styles
> show sel atoms
> hide #4 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> ui tool show "Show Sequence Viewer"
> sequence chain #5/A
Alignment identifier is 5/A
> select #5/A:162
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/A:162-164
28 atoms, 27 bonds, 3 residues, 1 model selected
> style sel stick
Changed 28 atom styles
> show sel atoms
> hide #2 models
> show #2 models
> hide #!5 models
> show #!5 models
> ui mousemode right select
> ui mousemode right swapaa
> select #5/A:162
9 atoms, 8 bonds, 1 residue, 1 model selected
> ui mousemode right swapaa
> select
> #5/A:43-52,56-64,78-89,91-96,126-131,141-150,162-171,198-214,223-227,253-286,302-312,315-340,358-365,376-389,405-413,415-429,450-459,490-494,518-528
1781 atoms, 1797 bonds, 228 residues, 1 model selected
> select
> #1/*:39-42,46-48,54-60,76-85,89-92,135-143,156-163,192-200,202-206,217-219,250-266,284-292,297-320,340-345,355-370,388-394,398-411,431-439,496-507
> #2/*:39-42,46-48,54-60,76-85,89-92,135-143,156-163,192-200,202-206,217-219,250-266,284-292,297-320,340-345,355-370,388-394,398-411,431-439,496-507
2818 atoms, 2820 bonds, 352 residues, 2 models selected
> select #1/*:155 #2/*:155
22 atoms, 22 bonds, 2 residues, 2 models selected
> select #1/*:155-157 #2/*:155-157
60 atoms, 60 bonds, 6 residues, 2 models selected
1 [ID: 1] region 2 chains [134-136] RMSD: 0.001
> ui mousemode right distance
> nucleotides sel & #2 tube/slab shape box
> nucleotides sel & #2 atoms
> style nucleic & sel & #2 stick
Changed 0 atom styles
> style sel & #2 ball
Changed 30 atom styles
> nucleotides sel & #2 atoms
> style nucleic & sel & #2 stick
Changed 0 atom styles
> nucleotides sel & #2 ladder
> nucleotides sel & #2 atoms
> style nucleic & sel & #2 stick
Changed 0 atom styles
> style sel & #2 sphere
Changed 30 atom styles
> style sel & #2 sphere
Changed 30 atom styles
> style sel & #2 ball
Changed 30 atom styles
> color bfactor sel & #2
30 atoms, 3 residues, atom bfactor range 0 to 0
> color bfactor sel & #2
30 atoms, 3 residues, atom bfactor range 0 to 0
> style sel & #2 ball
Changed 30 atom styles
> style sel & #2 ball
Changed 30 atom styles
> color sel & #2 bynucleotide
> color bfactor sel & #2
30 atoms, 3 residues, atom bfactor range 0 to 0
> mlp sel & #2
Map values for surface "c5tj3A_.1.pdb_ SES surface": minimum -27.73, mean
-3.887, maximum 28.44
To also show corresponding color key, enter the above mlp command and add key
true
> coulombic sel & #!2
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for c5tj3A_.1.pdb_ SES surface #2.1: minimum, -19.49, mean
-1.08, maximum 15.28
To also show corresponding color key, enter the above coulombic command and
add key true
> coulombic sel & #!2
Coulombic values for c5tj3A_.1.pdb_ SES surface #2.1: minimum, -19.49, mean
-1.08, maximum 15.28
To also show corresponding color key, enter the above coulombic command and
add key true
> coulombic sel & #!2
Coulombic values for c5tj3A_.1.pdb_ SES surface #2.1: minimum, -19.49, mean
-1.08, maximum 15.28
To also show corresponding color key, enter the above coulombic command and
add key true
> select
> #5/A:43-52,56-64,78-89,91-96,126-131,141-150,162-171,198-214,223-227,253-286,302-312,315-340,358-365,376-389,405-413,415-429,450-459,490-494,518-528
1781 atoms, 1797 bonds, 228 residues, 1 model selected
> select #5/A:162
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/A:162-164
28 atoms, 27 bonds, 3 residues, 1 model selected
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Assigning partial charges to residue TPO (net charge -2) with am1-bcc method
Running ANTECHAMBER command:
/Applications/ChimeraX-1.6.1.app/Contents/bin/amber20/bin/antechamber -ek
qm_theory='AM1', -i
/var/folders/0q/884v7wdx6xbfdqmy0_x_z1w00000gp/T/tmp9572p_y7/ante.in.mol2 -fi
mol2 -o
/var/folders/0q/884v7wdx6xbfdqmy0_x_z1w00000gp/T/tmp9572p_y7/ante.out.mol2 -fo
mol2 -c bcc -nc -2 -j 5 -s 2 -dr n
(TPO) ``
(TPO) `Welcome to antechamber 20.0: molecular input file processor.`
(TPO) ``
(TPO) `Info: Finished reading file
(/var/folders/0q/884v7wdx6xbfdqmy0_x_z1w00000gp/T/tmp9572p_y7/ante.in.mol2);
atoms read (29), bonds read (28).`
(TPO) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(TPO) `Running:
/Applications/ChimeraX-1.6.1.app/Contents/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`
(TPO) ``
(TPO) ``
(TPO) `Running:
/Applications/ChimeraX-1.6.1.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`
(TPO) `Info: Total number of electrons: 134; net charge: -2`
(TPO) ``
(TPO) `Running: /Applications/ChimeraX-1.6.1.app/Contents/bin/amber20/bin/sqm
-O -i sqm.in -o sqm.out`
(TPO) ``
(TPO) `Running:
/Applications/ChimeraX-1.6.1.app/Contents/bin/amber20/bin/am1bcc -i
ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p
/Applications/ChimeraX-1.6.1.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT
-s 2 -j 1`
(TPO) ``
(TPO) `Running:
/Applications/ChimeraX-1.6.1.app/Contents/bin/amber20/bin/atomtype -f ac -p
bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`
(TPO) ``
Charges for residue TPO determined
Coulombic values for 5tj3.pdb_A SES surface #5.3: minimum, -21.27, mean -2.57,
maximum 14.32
To also show corresponding color key, enter the above coulombic command and
add key true
> color sel byhetero
> hide sel surfaces
> show sel surfaces
> hide sel surfaces
> show sel surfaces
> hide sel surfaces
> select #1/*:155-156 #2/*:155-156
44 atoms, 44 bonds, 4 residues, 2 models selected
> select #1/*:155-157 #2/*:155-157
60 atoms, 60 bonds, 6 residues, 2 models selected
1 [ID: 1] region 2 chains [134-136] RMSD: 0.001
> hide sel & #!2 surfaces
> style sel & #!2 stick
Changed 30 atom styles
> style sel & #!2 sphere
Changed 30 atom styles
> style sel & #!2 ball
Changed 30 atom styles
> style sel & #!2 stick
Changed 30 atom styles
> nucleotides sel & #!2 atoms
> style nucleic & sel & #!2 stick
Changed 0 atom styles
> nucleotides sel & #!2 atoms
> style nucleic & sel & #!2 stick
Changed 0 atom styles
> nucleotides sel & #!2 tube/slab shape box
> hide sel & #!2 atoms
> show sel & #!2 atoms
> color sel & #!2 bynucleotide
> color sel & #!2 bychain
> color sel & #!2 byhetero
> color sel & #!2 bychain
> select #1/*:35 #2/*:35
16 atoms, 14 bonds, 2 residues, 2 models selected
> select #1/*:35-36 #2/*:35-36
34 atoms, 32 bonds, 4 residues, 2 models selected
1 [ID: 1] region 2 chains [14-15] RMSD: 0.000
> select #5/A:38-39
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #5/A:38-39
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #5/A:38
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/*:35-36 #2/*:35-36
34 atoms, 32 bonds, 4 residues, 2 models selected
> select #1/*:35-36 #2/*:35-36
34 atoms, 32 bonds, 4 residues, 2 models selected
1 [ID: 1] region 2 chains [14-15] RMSD: 0.000
> select #1/*:34-35 #2/*:34-35
32 atoms, 30 bonds, 4 residues, 2 models selected
> select #1/*:34-75 #2/*:34-75
716 atoms, 728 bonds, 84 residues, 2 models selected
1 [ID: 1] region 2 chains [13-54] RMSD: 0.001
> select #1/*:35 #2/*:35
16 atoms, 14 bonds, 2 residues, 2 models selected
> select #1/*:35 #2/*:35
16 atoms, 14 bonds, 2 residues, 2 models selected
1 [ID: 1] region 2 chains [14] RMSD: 0.000
> style sel & #!2 stick
Changed 8 atom styles
> style sel & #!2 stick
Changed 8 atom styles
> show sel & #!2 atoms
> select #1/*:315 #2/*:315
16 atoms, 14 bonds, 2 residues, 2 models selected
> select #1/*:315 #2/*:315
16 atoms, 14 bonds, 2 residues, 2 models selected
1 [ID: 1] region 2 chains [294] RMSD: 0.001
> select #1/*:307 #2/*:307
16 atoms, 14 bonds, 2 residues, 2 models selected
> select #1/*:307 #2/*:307
16 atoms, 14 bonds, 2 residues, 2 models selected
1 [ID: 1] region 2 chains [286] RMSD: 0.001
> select #5/A:353
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #5/A:352-353
18 atoms, 18 bonds, 2 residues, 1 model selected
> select #1/*:342 #2/*:342
16 atoms, 14 bonds, 2 residues, 2 models selected
> select #1/*:342-343 #2/*:342-343
32 atoms, 30 bonds, 4 residues, 2 models selected
1 [ID: 1] region 2 chains [321-322] RMSD: 0.000
> select #1/*:346 #2/*:346
24 atoms, 24 bonds, 2 residues, 2 models selected
> select #1/*:346-347 #2/*:346-347
46 atoms, 46 bonds, 4 residues, 2 models selected
1 [ID: 1] region 2 chains [325-326] RMSD: 0.001
> select #1/*:351 #2/*:351
8 atoms, 6 bonds, 2 residues, 2 models selected
> select #1/*:351-352 #2/*:351-352
26 atoms, 24 bonds, 4 residues, 2 models selected
1 [ID: 1] region 2 chains [330-331] RMSD: 0.000
> select #1/*:353-354 #2/*:353-354
42 atoms, 44 bonds, 4 residues, 2 models selected
> select #1/*:353-355 #2/*:353-355
58 atoms, 60 bonds, 6 residues, 2 models selected
1 [ID: 1] region 2 chains [332-334] RMSD: 0.000
> select #1/*:364 #2/*:364
16 atoms, 14 bonds, 2 residues, 2 models selected
> select #1/*:330-364 #2/*:330-364
524 atoms, 534 bonds, 70 residues, 2 models selected
1 [ID: 1] region 2 chains [309-343] RMSD: 0.000
> select
> #1/*:39-42,46-48,54-60,76-85,89-92,135-143,156-163,192-200,202-206,217-219,250-266,284-292,297-320,340-345,355-370,388-394,398-411,431-439,496-507
> #2/*:39-42,46-48,54-60,76-85,89-92,135-143,156-163,192-200,202-206,217-219,250-266,284-292,297-320,340-345,355-370,388-394,398-411,431-439,496-507
2818 atoms, 2820 bonds, 352 residues, 2 models selected
> select #1/*:362 #2/*:362
16 atoms, 14 bonds, 2 residues, 2 models selected
> select #1/*:358-362 #2/*:358-362
68 atoms, 66 bonds, 10 residues, 2 models selected
1 [ID: 1] region 2 chains [337-341] RMSD: 0.000
> select #1/*:372 #2/*:372
18 atoms, 16 bonds, 2 residues, 2 models selected
> select #1/*:367-372 #2/*:367-372
90 atoms, 90 bonds, 12 residues, 2 models selected
1 [ID: 1] region 2 chains [346-351] RMSD: 0.001
> select
> #1/*:39-42,46-48,54-60,76-85,89-92,135-143,156-163,192-200,202-206,217-219,250-266,284-292,297-320,340-345,355-370,388-394,398-411,431-439,496-507
> #2/*:39-42,46-48,54-60,76-85,89-92,135-143,156-163,192-200,202-206,217-219,250-266,284-292,297-320,340-345,355-370,388-394,398-411,431-439,496-507
2818 atoms, 2820 bonds, 352 residues, 2 models selected
> select #1/*:338-339 #2/*:338-339
30 atoms, 30 bonds, 4 residues, 2 models selected
> select #1/*:338-339 #2/*:338-339
30 atoms, 30 bonds, 4 residues, 2 models selected
1 [ID: 1] region 2 chains [317-318] RMSD: 0.001
> select #1/*:340-341 #2/*:340-341
18 atoms, 16 bonds, 4 residues, 2 models selected
> select #1/*:329-341 #2/*:329-341
174 atoms, 176 bonds, 26 residues, 2 models selected
1 [ID: 1] region 2 chains [308-320] RMSD: 0.000
> select #1/*:329-330 #2/*:329-330
28 atoms, 26 bonds, 4 residues, 2 models selected
> select #1/*:329-332 #2/*:329-332
50 atoms, 48 bonds, 8 residues, 2 models selected
1 [ID: 1] region 2 chains [308-311] RMSD: 0.000
> select #1/*:333-334 #2/*:333-334
22 atoms, 20 bonds, 4 residues, 2 models selected
> select #1/*:333-335 #2/*:333-335
46 atoms, 46 bonds, 6 residues, 2 models selected
1 [ID: 1] region 2 chains [312-314] RMSD: 0.001
> select #1/*:333 #2/*:333
14 atoms, 12 bonds, 2 residues, 2 models selected
> show sel & #!2 atoms
> style sel & #!2 stick
Changed 7 atom styles
> select #1/*:334 #2/*:334
8 atoms, 6 bonds, 2 residues, 2 models selected
> select #1/*:334 #2/*:334
8 atoms, 6 bonds, 2 residues, 2 models selected
1 [ID: 1] region 2 chains [313] RMSD: 0.001
> style sel & #!2 stick
Changed 4 atom styles
> show sel & #!2 atoms
> style sel & #!2 stick
Changed 4 atom styles
> style sel & #!2 stick
Changed 4 atom styles
> style sel & #!2 ball
Changed 4 atom styles
> style sel & #!2 ball
Changed 4 atom styles
> show sel & #!2 atoms
> hide sel & #!2 atoms
> show sel & #!2 atoms
> select #1/*:335 #2/*:335
24 atoms, 24 bonds, 2 residues, 2 models selected
> select #1/*:335 #2/*:335
24 atoms, 24 bonds, 2 residues, 2 models selected
1 [ID: 1] region 2 chains [314] RMSD: 0.000
> show sel & #!2 atoms
> style sel & #!2 stick
Changed 12 atom styles
> hide sel & #!2 atoms
> select #1/*:334 #2/*:334
8 atoms, 6 bonds, 2 residues, 2 models selected
> select #1/*:334 #2/*:334
8 atoms, 6 bonds, 2 residues, 2 models selected
1 [ID: 1] region 2 chains [313] RMSD: 0.001
> show sel & #!2 cartoons
> hide sel & #!2 cartoons
> show sel & #!2 cartoons
> hide sel & #!2 atoms
> show sel & #!2 atoms
> show sel & #!2 cartoons
> show sel & #!2 surfaces
> hide sel & #!2 surfaces
> show sel & #!2 atoms
> hide sel & #!2 atoms
> show sel & #!2 atoms
> show sel & #!2 cartoons
> hide sel & #!2 cartoons
> show sel & #!2 cartoons
> select
> #1/*:39-42,46-48,54-60,76-85,89-92,135-143,156-163,192-200,202-206,217-219,250-266,284-292,297-320,340-345,355-370,388-394,398-411,431-439,496-507
> #2/*:39-42,46-48,54-60,76-85,89-92,135-143,156-163,192-200,202-206,217-219,250-266,284-292,297-320,340-345,355-370,388-394,398-411,431-439,496-507
2818 atoms, 2820 bonds, 352 residues, 2 models selected
> select #1/*:35 #2/*:35
16 atoms, 14 bonds, 2 residues, 2 models selected
> select #1/*:35 #2/*:35
16 atoms, 14 bonds, 2 residues, 2 models selected
1 [ID: 1] region 2 chains [14] RMSD: 0.000
> select
> #1/*:28-34,62-64,98-101,106-109,149-152,169-174,179-181,276-282,326-331,376-380,383-386,415-420,448-452,478-482,488-490
> #2/*:28-34,62-64,98-101,106-109,149-152,169-174,179-181,276-282,326-331,376-380,383-386,415-420,448-452,478-482,488-490
1192 atoms, 1194 bonds, 144 residues, 2 models selected
> select #1/*:34 #2/*:34
16 atoms, 14 bonds, 2 residues, 2 models selected
> select #1/*:22-34 #2/*:22-34
192 atoms, 196 bonds, 26 residues, 2 models selected
1 [ID: 1] region 2 chains [1-13] RMSD: 0.000
> hide sel & #!2 cartoons
> hide sel & #!2 atoms
> hide sel & #!2 surfaces
> select #1/*:37 #2/*:37
16 atoms, 14 bonds, 2 residues, 2 models selected
> select #1/*:37-44 #2/*:37-44
136 atoms, 136 bonds, 16 residues, 2 models selected
1 [ID: 1] region 2 chains [16-23] RMSD: 0.001
> hide sel & #!2 cartoons
> show sel & #!2 cartoons
> hide sel & #!2 cartoons
> select #5/A:37
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #5/A:24-37
102 atoms, 103 bonds, 14 residues, 1 model selected
> hide sel cartoons
> select
> #5/A:43-52,56-64,78-89,91-96,126-131,141-150,162-171,198-214,223-227,253-286,302-312,315-340,358-365,376-389,405-413,415-429,450-459,490-494,518-528
1781 atoms, 1797 bonds, 228 residues, 1 model selected
> select #5/A:309
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #5/A:309
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/*:361 #2/*:361
16 atoms, 14 bonds, 2 residues, 2 models selected
> select #1/*:356-361 #2/*:356-361
90 atoms, 88 bonds, 12 residues, 2 models selected
1 [ID: 1] region 2 chains [335-340] RMSD: 0.000
> select #1/*:274-317 #2/*:274-317
706 atoms, 714 bonds, 88 residues, 2 models selected
> select #1/*:274-318 #2/*:274-318
724 atoms, 732 bonds, 90 residues, 2 models selected
1 [ID: 1] region 2 chains [253-297] RMSD: 0.000
> select #1/*:306-307 #2/*:306-307
32 atoms, 30 bonds, 4 residues, 2 models selected
> select #1/*:306-316 #2/*:306-316
172 atoms, 170 bonds, 22 residues, 2 models selected
1 [ID: 1] region 2 chains [285-295] RMSD: 0.000
> select #1/*:328-329 #2/*:328-329
28 atoms, 26 bonds, 4 residues, 2 models selected
> select #1/*:321-329 #2/*:321-329
130 atoms, 128 bonds, 18 residues, 2 models selected
1 [ID: 1] region 2 chains [300-308] RMSD: 0.000
> select #1/*:321 #2/*:321
14 atoms, 12 bonds, 2 residues, 2 models selected
> select #1/*:302-321 #2/*:302-321
330 atoms, 330 bonds, 40 residues, 2 models selected
1 [ID: 1] region 2 chains [281-300] RMSD: 0.000
> select #1/*:342 #2/*:342
16 atoms, 14 bonds, 2 residues, 2 models selected
> select #1/*:342-353 #2/*:342-353
188 atoms, 192 bonds, 24 residues, 2 models selected
1 [ID: 1] region 2 chains [321-332] RMSD: 0.000
> select #1/*:305 #2/*:305
22 atoms, 20 bonds, 2 residues, 2 models selected
> select #1/*:305-385 #2/*:305-385
1280 atoms, 1302 bonds, 162 residues, 2 models selected
1 [ID: 1] region 2 chains [284-364] RMSD: 0.000
> select #1/*:264 #2/*:264
16 atoms, 14 bonds, 2 residues, 2 models selected
> select #1/*:264-286 #2/*:264-286
352 atoms, 354 bonds, 46 residues, 2 models selected
1 [ID: 1] region 2 chains [243-265] RMSD: 0.001
> select #1/*:289 #2/*:289
20 atoms, 20 bonds, 2 residues, 2 models selected
> select #1/*:289 #2/*:289
20 atoms, 20 bonds, 2 residues, 2 models selected
1 [ID: 1] region 2 chains [268] RMSD: 0.001
> style sel & #!2 stick
Changed 10 atom styles
> show sel & #!2 atoms
> select #1/*:290 #2/*:290
22 atoms, 20 bonds, 2 residues, 2 models selected
> select #1/*:290 #2/*:290
22 atoms, 20 bonds, 2 residues, 2 models selected
1 [ID: 1] region 2 chains [269] RMSD: 0.000
> show sel & #!2 atoms
> style sel & #!2 stick
Changed 11 atom styles
> select #1/*:289 #2/*:289
20 atoms, 20 bonds, 2 residues, 2 models selected
> select #1/*:289 #2/*:289
20 atoms, 20 bonds, 2 residues, 2 models selected
1 [ID: 1] region 2 chains [268] RMSD: 0.001
> hide sel & #!2 atoms
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
Missing or invalid "chains" argument: only initial part "#1" of atom specifier
valid
Missing or invalid "chains" argument: only initial part "#1" of atom specifier
valid
Missing or invalid "chains" argument: only initial part "#1" of atom specifier
valid
Missing or invalid "chains" argument: only initial part "#1" of atom specifier
valid
Missing or invalid "chains" argument: only initial part "#1" of atom specifier
valid
Missing or invalid "chains" argument: only initial part "#1" of atom specifier
valid
> select #5/A:84-85
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #5/A:84
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #5/A:88
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #5/A:78-88
84 atoms, 85 bonds, 11 residues, 1 model selected
> select #5/A:79
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #5/A:79
11 atoms, 10 bonds, 1 residue, 1 model selected
> select
> #1/*:39-42,46-48,54-60,76-85,89-92,135-143,156-163,192-200,202-206,217-219,250-266,284-292,297-320,340-345,355-370,388-394,398-411,431-439,496-507
> #2/*:39-42,46-48,54-60,76-85,89-92,135-143,156-163,192-200,202-206,217-219,250-266,284-292,297-320,340-345,355-370,388-394,398-411,431-439,496-507
2818 atoms, 2820 bonds, 352 residues, 2 models selected
> select #1/*:85 #2/*:85
14 atoms, 12 bonds, 2 residues, 2 models selected
> select #1/*:78 #2/*:78
12 atoms, 10 bonds, 2 residues, 2 models selected
> select #1/*:78 #2/*:78
12 atoms, 10 bonds, 2 residues, 2 models selected
1 [ID: 1] region 2 chains [57] RMSD: 0.000
> select #1/*:76 #2/*:76
22 atoms, 20 bonds, 2 residues, 2 models selected
> select #1/*:74 #2/*:74
14 atoms, 12 bonds, 2 residues, 2 models selected
> select #1/*:74 #2/*:74
14 atoms, 12 bonds, 2 residues, 2 models selected
1 [ID: 1] region 2 chains [53] RMSD: 0.001
> select #1/*:75 #2/*:75
16 atoms, 14 bonds, 2 residues, 2 models selected
> select #1/*:75-76 #2/*:75-76
38 atoms, 36 bonds, 4 residues, 2 models selected
1 [ID: 1] region 2 chains [54-55] RMSD: 0.001
> select #1/*:76 #2/*:76
22 atoms, 20 bonds, 2 residues, 2 models selected
> select #1/*:76 #2/*:76
22 atoms, 20 bonds, 2 residues, 2 models selected
1 [ID: 1] region 2 chains [55] RMSD: 0.000
> style sel & #!2 stick
Changed 11 atom styles
> show sel & #!2 atoms
> view sel
> view
> view sel
> select #1/*:203-204 #2/*:203-204
38 atoms, 38 bonds, 4 residues, 2 models selected
> select #1/*:203-205 #2/*:203-205
60 atoms, 60 bonds, 6 residues, 2 models selected
1 [ID: 1] region 2 chains [182-184] RMSD: 0.000
> select #1/*:243 #2/*:243
22 atoms, 22 bonds, 2 residues, 2 models selected
> select #1/*:243-244 #2/*:243-244
44 atoms, 44 bonds, 4 residues, 2 models selected
1 [ID: 1] region 2 chains [222-223] RMSD: 0.000
> select #1/*:113-114 #2/*:113-114
28 atoms, 26 bonds, 4 residues, 2 models selected
> select #1/*:113-119 #2/*:113-119
100 atoms, 100 bonds, 14 residues, 2 models selected
1 [ID: 1] region 2 chains [92-98] RMSD: 0.001
> select
> #1/*:39-42,46-48,54-60,76-85,89-92,135-143,156-163,192-200,202-206,217-219,250-266,284-292,297-320,340-345,355-370,388-394,398-411,431-439,496-507
> #2/*:39-42,46-48,54-60,76-85,89-92,135-143,156-163,192-200,202-206,217-219,250-266,284-292,297-320,340-345,355-370,388-394,398-411,431-439,496-507
2818 atoms, 2820 bonds, 352 residues, 2 models selected
> select #1/*:126-157 #2/*:126-157
486 atoms, 494 bonds, 64 residues, 2 models selected
> select #1/*:126-156 #2/*:126-156
470 atoms, 478 bonds, 62 residues, 2 models selected
1 [ID: 1] region 2 chains [105-135] RMSD: 0.000
> select #1/*:154 #2/*:154
14 atoms, 14 bonds, 2 residues, 2 models selected
> select #1/*:154-157 #2/*:154-157
74 atoms, 76 bonds, 8 residues, 2 models selected
1 [ID: 1] region 2 chains [133-136] RMSD: 0.001
> select #1/*:157 #2/*:157
16 atoms, 14 bonds, 2 residues, 2 models selected
> select #1/*:155-157 #2/*:155-157
60 atoms, 60 bonds, 6 residues, 2 models selected
1 [ID: 1] region 2 chains [134-136] RMSD: 0.001
> rainbow sel & #!2
> color sel & #!2 byhetero
> color sel & #!2 bychain
> color sel & #!2 byhetero
> color sel & #!2 bychain
> color sel & #!2 bypolymer
> color sel & #!2 byhetero
> select #5/A:100
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/A:100
8 atoms, 7 bonds, 1 residue, 1 model selected
> style sel stick
Changed 8 atom styles
> show sel atoms
> select #1/*:72 #2/*:72
16 atoms, 14 bonds, 2 residues, 2 models selected
> select #1/*:72 #2/*:72
16 atoms, 14 bonds, 2 residues, 2 models selected
1 [ID: 1] region 2 chains [51] RMSD: 0.001
> select #1/*:66-67 #2/*:66-67
34 atoms, 32 bonds, 4 residues, 2 models selected
> select #1/*:66-73 #2/*:66-73
140 atoms, 142 bonds, 16 residues, 2 models selected
1 [ID: 1] region 2 chains [45-52] RMSD: 0.001
> select #1/*:92-93 #2/*:92-93
24 atoms, 22 bonds, 4 residues, 2 models selected
> select #1/*:91-93 #2/*:91-93
40 atoms, 38 bonds, 6 residues, 2 models selected
1 [ID: 1] region 2 chains [70-72] RMSD: 0.001
> select #1/*:98 #2/*:98
22 atoms, 20 bonds, 2 residues, 2 models selected
> select #1/*:98-101 #2/*:98-101
88 atoms, 92 bonds, 8 residues, 2 models selected
1 [ID: 1] region 2 chains [77-80] RMSD: 0.000
> select #1/*:102 #2/*:102
14 atoms, 14 bonds, 2 residues, 2 models selected
> select #1/*:102-112 #2/*:102-112
174 atoms, 176 bonds, 22 residues, 2 models selected
1 [ID: 1] region 2 chains [81-91] RMSD: 0.000
> select #1/*:48 #2/*:48
16 atoms, 14 bonds, 2 residues, 2 models selected
> select #1/*:48-54 #2/*:48-54
118 atoms, 120 bonds, 14 residues, 2 models selected
1 [ID: 1] region 2 chains [27-33] RMSD: 0.001
> select #1/*:84-85 #2/*:84-85
38 atoms, 38 bonds, 4 residues, 2 models selected
> select #1/*:62-85 #2/*:62-85
390 atoms, 396 bonds, 48 residues, 2 models selected
1 [ID: 1] region 2 chains [41-64] RMSD: 0.000
> select #1/*:110-111 #2/*:110-111
26 atoms, 24 bonds, 4 residues, 2 models selected
> select #1/*:110-121 #2/*:110-121
180 atoms, 182 bonds, 24 residues, 2 models selected
1 [ID: 1] region 2 chains [89-100] RMSD: 0.000
> select #1/*:96 #2/*:96
10 atoms, 8 bonds, 2 residues, 2 models selected
> select #1/*:96-97 #2/*:96-97
28 atoms, 26 bonds, 4 residues, 2 models selected
1 [ID: 1] region 2 chains [75-76] RMSD: 0.000
> select #1/*:97-98 #2/*:97-98
40 atoms, 38 bonds, 4 residues, 2 models selected
> select #1/*:97-98 #2/*:97-98
40 atoms, 38 bonds, 4 residues, 2 models selected
1 [ID: 1] region 2 chains [76-77] RMSD: 0.000
> select #1/*:97 #2/*:97
18 atoms, 16 bonds, 2 residues, 2 models selected
> select #1/*:97 #2/*:97
18 atoms, 16 bonds, 2 residues, 2 models selected
1 [ID: 1] region 2 chains [76] RMSD: 0.000
> style sel & #!2 stick
Changed 9 atom styles
> show sel & #!2 atoms
> rainbow sel & #!2
> color sel & #!2 bychain
> color sel & #!2 byhetero
> select
> #3/*:37-40,44-46,52-58,74-83,87-90,119-122,134-142,155-162,191-199,202-208,213-228,246-254,259-282,302-307,320-325,349-355,359-372,394-401,424-427,437-440,462-473
1394 atoms, 1399 bonds, 175 residues, 1 model selected
> select
> #1/*:28-34,62-64,98-101,106-109,149-152,169-174,179-181,276-282,326-331,376-380,383-386,415-420,448-452,478-482,488-490
> #2/*:28-34,62-64,98-101,106-109,149-152,169-174,179-181,276-282,326-331,376-380,383-386,415-420,448-452,478-482,488-490
1192 atoms, 1194 bonds, 144 residues, 2 models selected
> select
> #1/*:39-42,46-48,54-60,76-85,89-92,135-143,156-163,192-200,202-206,217-219,250-266,284-292,297-320,340-345,355-370,388-394,398-411,431-439,496-507
> #2/*:39-42,46-48,54-60,76-85,89-92,135-143,156-163,192-200,202-206,217-219,250-266,284-292,297-320,340-345,355-370,388-394,398-411,431-439,496-507
2818 atoms, 2820 bonds, 352 residues, 2 models selected
> select
> #1/*:28-34,62-64,98-101,106-109,149-152,169-174,179-181,276-282,326-331,376-380,383-386,415-420,448-452,478-482,488-490
> #2/*:28-34,62-64,98-101,106-109,149-152,169-174,179-181,276-282,326-331,376-380,383-386,415-420,448-452,478-482,488-490
1192 atoms, 1194 bonds, 144 residues, 2 models selected
> select
> #1/*:39-42,46-48,54-60,76-85,89-92,135-143,156-163,192-200,202-206,217-219,250-266,284-292,297-320,340-345,355-370,388-394,398-411,431-439,496-507
> #2/*:39-42,46-48,54-60,76-85,89-92,135-143,156-163,192-200,202-206,217-219,250-266,284-292,297-320,340-345,355-370,388-394,398-411,431-439,496-507
2818 atoms, 2820 bonds, 352 residues, 2 models selected
> select
> #1/*:28-34,62-64,98-101,106-109,149-152,169-174,179-181,276-282,326-331,376-380,383-386,415-420,448-452,478-482,488-490
> #2/*:28-34,62-64,98-101,106-109,149-152,169-174,179-181,276-282,326-331,376-380,383-386,415-420,448-452,478-482,488-490
1192 atoms, 1194 bonds, 144 residues, 2 models selected
> select
> #1/*:39-42,46-48,54-60,76-85,89-92,135-143,156-163,192-200,202-206,217-219,250-266,284-292,297-320,340-345,355-370,388-394,398-411,431-439,496-507
> #2/*:39-42,46-48,54-60,76-85,89-92,135-143,156-163,192-200,202-206,217-219,250-266,284-292,297-320,340-345,355-370,388-394,398-411,431-439,496-507
2818 atoms, 2820 bonds, 352 residues, 2 models selected
> select #1/*:22 #2/*:22
16 atoms, 14 bonds, 2 residues, 2 models selected
> select #1/* #2/*
7994 atoms, 8186 bonds, 1000 residues, 2 models selected
1 [ID: 1] region 2 chains [1-500] RMSD: 0.000
> hide sel & #!2 cartoons
> hide sel & #!2 atoms
> show sel & #!2 atoms
> hide sel & #!2 atoms
> show sel & #!2 cartoons
> select
> #5/A:43-52,56-64,78-89,91-96,126-131,141-150,162-171,198-214,223-227,253-286,302-312,315-340,358-365,376-389,405-413,415-429,450-459,490-494,518-528
1781 atoms, 1797 bonds, 228 residues, 1 model selected
> select #4/*:171-173
28 atoms, 27 bonds, 3 residues, 1 model selected
> select #4/*:172
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #4/*:172
8 atoms, 7 bonds, 1 residue, 1 model selected
> open /Users/bo1il/Downloads/pdb2rh6.ent
pdb2rh6.ent title:
Structure of xac NPP for evaluation of refinement methodology [more info...]
Chain information for pdb2rh6.ent #6
---
Chain | Description | UniProt
A B | phosphodiesterase-nucleotide pyrophosphatase | Q8PIS1_XANAC 40-432
Non-standard residues in pdb2rh6.ent #6
---
AMP — adenosine monophosphate
ZN — zinc ion
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> color #6 #7adb89ff
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> ui tool show "Show Sequence Viewer"
> sequence chain #6/A #6/B
Alignment identifier is 2
> select
> #6/A-B:57-63,66-76,89-100,102-107,125-135,139-147,162-166,179-197,207-217,220-244,246-248,271-275,297-306,318-325,347-354,369-373,396-406,419-423
2654 atoms, 2678 bonds, 342 residues, 1 model selected
> select #6/A-B:91
22 atoms, 22 bonds, 2 residues, 1 model selected
> select #6/A-B:90-91
36 atoms, 36 bonds, 4 residues, 1 model selected
> style sel stick
Changed 36 atom styles
> show sel atoms
> show sel cartoons
> hide sel cartoons
> show sel cartoons
> hide sel cartoons
> show sel cartoons
> color sel bychain
> hide #!5 models
> show #!5 models
> hide #!5 models
> hide #!2 models
> hide #!6 models
> show #!6 models
> select add #6
6624 atoms, 6129 bonds, 19 pseudobonds, 1440 residues, 2 models selected
> select subtract #6
Nothing selected
> show #!6 atoms
> hide #!6 models
> show #!6 models
> show #!5 models
> ui tool show Matchmaker
> matchmaker #3-4#!5-6 to #1
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 final.casp.pdb, chain (blank) (#1) with
PafA_Prevotella_KCOM1933.pdb, chain (blank) (#3), sequence alignment score =
850.4
RMSD between 381 pruned atom pairs is 0.221 angstroms; (across all 457 pairs:
2.586)
Matchmaker final.casp.pdb, chain (blank) (#1) with PafA_mucilagnibacter.pdb,
chain (blank) (#4), sequence alignment score = 1009.3
RMSD between 425 pruned atom pairs is 0.220 angstroms; (across all 495 pairs:
2.942)
Matchmaker final.casp.pdb, chain (blank) (#1) with 5tj3.pdb, chain A (#5),
sequence alignment score = 1086.3
RMSD between 442 pruned atom pairs is 0.213 angstroms; (across all 495 pairs:
1.602)
Matchmaker final.casp.pdb, chain (blank) (#1) with pdb2rh6.ent, chain A (#6),
sequence alignment score = 221.9
RMSD between 140 pruned atom pairs is 0.988 angstroms; (across all 348 pairs:
11.374)
> show #1 models
> ui tool show "Side View"
> lighting flat
> graphics silhouettes false
> lighting shadows true intensity 0.5
> graphics silhouettes true
> lighting soft
> lighting full
> lighting flat
> lighting simple
> graphics silhouettes false
> view
> select #6/A
3293 atoms, 3052 bonds, 10 pseudobonds, 712 residues, 2 models selected
> select #6/B
3331 atoms, 3077 bonds, 9 pseudobonds, 728 residues, 2 models selected
> hide sel cartoons
> hide sel surfaces
> hide sel atoms
> select #6/B
3331 atoms, 3077 bonds, 9 pseudobonds, 728 residues, 2 models selected
> select #6/A
3293 atoms, 3052 bonds, 10 pseudobonds, 712 residues, 2 models selected
> hide sel atoms
> select
> #5/A:43-52,56-64,78-89,91-96,126-131,141-150,162-171,198-214,223-227,253-286,302-312,315-340,358-365,376-389,405-413,415-429,450-459,490-494,518-528
1781 atoms, 1797 bonds, 228 residues, 1 model selected
> select
> #6/A-B:57-63,66-76,89-100,102-107,125-135,139-147,162-166,179-197,207-217,220-244,246-248,271-275,297-306,318-325,347-354,369-373,396-406,419-423
2654 atoms, 2678 bonds, 342 residues, 1 model selected
> select
> #5/A:43-52,56-64,78-89,91-96,126-131,141-150,162-171,198-214,223-227,253-286,302-312,315-340,358-365,376-389,405-413,415-429,450-459,490-494,518-528
1781 atoms, 1797 bonds, 228 residues, 1 model selected
> select #5/A:162
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/A:162
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/A:161
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/A:161-171
79 atoms, 79 bonds, 11 residues, 1 model selected
> select #6/A-B:125-126
30 atoms, 28 bonds, 4 residues, 1 model selected
> select #6/A-B:125-133
128 atoms, 126 bonds, 18 residues, 1 model selected
> select #6/A-B:139
14 atoms, 14 bonds, 2 residues, 1 model selected
> select #6/A-B:139-149
166 atoms, 170 bonds, 22 residues, 1 model selected
> select #6/A-B:134-162
450 atoms, 474 bonds, 58 residues, 1 model selected
> select #6/A-B:134-161
440 atoms, 464 bonds, 56 residues, 1 model selected
> select #6/A-B:82
16 atoms, 14 bonds, 2 residues, 1 model selected
> select #6/A-B:82-99
286 atoms, 298 bonds, 36 residues, 1 model selected
> select #6/A-B:91
22 atoms, 22 bonds, 2 residues, 1 model selected
> select #6/A-B:90-91
36 atoms, 36 bonds, 4 residues, 1 model selected
> style sel stick
Changed 36 atom styles
> show sel atoms
> select #6/A-B:111
16 atoms, 14 bonds, 2 residues, 1 model selected
> select #6/A-B:111
16 atoms, 14 bonds, 2 residues, 1 model selected
> style sel stick
Changed 16 atom styles
> show sel atoms
> hide sel atoms
> show sel atoms
> color sel byhetero
> select #6/A-B:90
14 atoms, 12 bonds, 2 residues, 1 model selected
> select #6/A-B:90-91
36 atoms, 36 bonds, 4 residues, 1 model selected
> style sel stick
Changed 36 atom styles
> style sel stick
Changed 36 atom styles
> select #1/* #2/*
7994 atoms, 8186 bonds, 1000 residues, 2 models selected
> select #1/*:69 #2/*:69
24 atoms, 24 bonds, 2 residues, 2 models selected
> select #1/*:69-71 #2/*:69-71
58 atoms, 60 bonds, 6 residues, 2 models selected
1 [ID: 1] region 2 chains [48-50] RMSD: 0.000
> select #1/*:74-75 #2/*:74-75
30 atoms, 28 bonds, 4 residues, 2 models selected
> select #1/*:74-75 #2/*:74-75
30 atoms, 28 bonds, 4 residues, 2 models selected
1 [ID: 1] region 2 chains [53-54] RMSD: 0.001
> select #1/*:106 #2/*:106
22 atoms, 20 bonds, 2 residues, 2 models selected
> select #1/*:106-109 #2/*:106-109
70 atoms, 70 bonds, 8 residues, 2 models selected
1 [ID: 1] region 2 chains [85-88] RMSD: 0.001
> select #1/*:66-67 #2/*:66-67
34 atoms, 32 bonds, 4 residues, 2 models selected
> select #1/*:66-75 #2/*:66-75
170 atoms, 172 bonds, 20 residues, 2 models selected
1 [ID: 1] region 2 chains [45-54] RMSD: 0.001
> select
> #1/*:39-42,46-48,54-60,76-85,89-92,135-143,156-163,192-200,202-206,217-219,250-266,284-292,297-320,340-345,355-370,388-394,398-411,431-439,496-507
> #2/*:39-42,46-48,54-60,76-85,89-92,135-143,156-163,192-200,202-206,217-219,250-266,284-292,297-320,340-345,355-370,388-394,398-411,431-439,496-507
2818 atoms, 2820 bonds, 352 residues, 2 models selected
> select #1/*:90-91 #2/*:90-91
28 atoms, 26 bonds, 4 residues, 2 models selected
> select #1/*:81-91 #2/*:81-91
152 atoms, 154 bonds, 22 residues, 2 models selected
1 [ID: 1] region 2 chains [60-70] RMSD: 0.000
> select #6/A-B:107
8 atoms, 6 bonds, 2 residues, 1 model selected
> select #6/A-B:102-107
100 atoms, 104 bonds, 12 residues, 1 model selected
> hide #1 models
> show #1 models
> hide #!5 models
> select #6/A-B:96-97
30 atoms, 28 bonds, 4 residues, 1 model selected
> select #6/A-B:96-102
104 atoms, 102 bonds, 14 residues, 1 model selected
> select #1/*:75-76 #2/*:75-76
38 atoms, 36 bonds, 4 residues, 2 models selected
> select #1/*:75-80 #2/*:75-80
86 atoms, 84 bonds, 12 residues, 2 models selected
1 [ID: 1] region 2 chains [54-59] RMSD: 0.000
> select #1/*:58-59 #2/*:58-59
38 atoms, 36 bonds, 4 residues, 2 models selected
> select #1/*:54-59 #2/*:54-59
116 atoms, 116 bonds, 12 residues, 2 models selected
1 [ID: 1] region 2 chains [33-38] RMSD: 0.000
> select #1/*:51 #2/*:51
18 atoms, 16 bonds, 2 residues, 2 models selected
> select #1/*:51-91 #2/*:51-91
658 atoms, 668 bonds, 82 residues, 2 models selected
1 [ID: 1] region 2 chains [30-70] RMSD: 0.001
> select #1/*:62-63 #2/*:62-63
32 atoms, 30 bonds, 4 residues, 2 models selected
> select #1/*:62-67 #2/*:62-67
110 atoms, 110 bonds, 12 residues, 2 models selected
1 [ID: 1] region 2 chains [41-46] RMSD: 0.001
> select #1/*:100 #2/*:100
22 atoms, 22 bonds, 2 residues, 2 models selected
> select #1/*:93-100 #2/*:93-100
140 atoms, 144 bonds, 16 residues, 2 models selected
1 [ID: 1] region 2 chains [72-79] RMSD: 0.000
> select #1/*:102 #2/*:102
14 atoms, 14 bonds, 2 residues, 2 models selected
> select #1/*:102-107 #2/*:102-107
98 atoms, 100 bonds, 12 residues, 2 models selected
1 [ID: 1] region 2 chains [81-86] RMSD: 0.000
> select #1/*:98-99 #2/*:98-99
50 atoms, 52 bonds, 4 residues, 2 models selected
> select #1/*:77-99 #2/*:77-99
334 atoms, 340 bonds, 46 residues, 2 models selected
1 [ID: 1] region 2 chains [56-78] RMSD: 0.000
> select #1/*:83-84 #2/*:83-84
40 atoms, 40 bonds, 4 residues, 2 models selected
> select #1/*:83-88 #2/*:83-88
90 atoms, 90 bonds, 12 residues, 2 models selected
1 [ID: 1] region 2 chains [62-67] RMSD: 0.000
> select #1/*:88 #2/*:88
14 atoms, 12 bonds, 2 residues, 2 models selected
> select #1/*:87-88 #2/*:87-88
28 atoms, 26 bonds, 4 residues, 2 models selected
1 [ID: 1] region 2 chains [66-67] RMSD: 0.000
> select #1/*:84 #2/*:84
24 atoms, 24 bonds, 2 residues, 2 models selected
> select #1/*:84-85 #2/*:84-85
38 atoms, 38 bonds, 4 residues, 2 models selected
1 [ID: 1] region 2 chains [63-64] RMSD: 0.000
> select #1/*:87-88 #2/*:87-88
28 atoms, 26 bonds, 4 residues, 2 models selected
> select #1/*:87-89 #2/*:87-89
42 atoms, 42 bonds, 6 residues, 2 models selected
1 [ID: 1] region 2 chains [66-68] RMSD: 0.001
> select #1/*:79 #2/*:79
10 atoms, 8 bonds, 2 residues, 2 models selected
> select #1/*:79-81 #2/*:79-81
36 atoms, 34 bonds, 6 residues, 2 models selected
1 [ID: 1] region 2 chains [58-60] RMSD: 0.000
> select #1/*:81 #2/*:81
10 atoms, 8 bonds, 2 residues, 2 models selected
> select #1/*:81-85 #2/*:81-85
74 atoms, 74 bonds, 10 residues, 2 models selected
1 [ID: 1] region 2 chains [60-64] RMSD: 0.000
> select #1/*:85 #2/*:85
14 atoms, 12 bonds, 2 residues, 2 models selected
> select #1/*:85-89 #2/*:85-89
64 atoms, 64 bonds, 10 residues, 2 models selected
1 [ID: 1] region 2 chains [64-68] RMSD: 0.000
> select #1/*:76-77 #2/*:76-77
32 atoms, 30 bonds, 4 residues, 2 models selected
> select #1/*:76-92 #2/*:76-92
238 atoms, 240 bonds, 34 residues, 2 models selected
1 [ID: 1] region 2 chains [55-71] RMSD: 0.000
> hide #!6 models
> select #1/*:93-94 #2/*:93-94
24 atoms, 22 bonds, 4 residues, 2 models selected
> select #1/*:84-94 #2/*:84-94
156 atoms, 158 bonds, 22 residues, 2 models selected
1 [ID: 1] region 2 chains [63-73] RMSD: 0.001
> select #1/*:76 #2/*:76
22 atoms, 20 bonds, 2 residues, 2 models selected
> select #1/*:76-81 #2/*:76-81
80 atoms, 78 bonds, 12 residues, 2 models selected
1 [ID: 1] region 2 chains [55-60] RMSD: 0.000
> select #1/*:74-75 #2/*:74-75
30 atoms, 28 bonds, 4 residues, 2 models selected
> select #1/*:74-83 #2/*:74-83
136 atoms, 134 bonds, 20 residues, 2 models selected
1 [ID: 1] region 2 chains [53-62] RMSD: 0.000
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!5 models
> hide #!5 models
> show #!5 models
> show #!6 models
> hide #!5 models
> select #6/A-B:90
14 atoms, 12 bonds, 2 residues, 1 model selected
> select #6/A-B:90
14 atoms, 12 bonds, 2 residues, 1 model selected
> select #5/A:63
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #5/A:63
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #5/A:79
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #5/A:79
11 atoms, 10 bonds, 1 residue, 1 model selected
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> select #1/*:85 #2/*:85
14 atoms, 12 bonds, 2 residues, 2 models selected
> select #1/*:85 #2/*:85
14 atoms, 12 bonds, 2 residues, 2 models selected
1 [ID: 1] region 2 chains [64] RMSD: 0.000
> hide #1 models
> show #1 models
> hide #!6 models
> show #!6 models
> select
> #5/A:43-52,56-64,78-89,91-96,126-131,141-150,162-171,198-214,223-227,253-286,302-312,315-340,358-365,376-389,405-413,415-429,450-459,490-494,518-528
1781 atoms, 1797 bonds, 228 residues, 1 model selected
> select #5/A:84
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #5/A:84-85
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #5/A:80
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #5/A:79-80
16 atoms, 15 bonds, 2 residues, 1 model selected
> hide #!6 models
> show #!6 models
> select #1/*:85 #2/*:85
14 atoms, 12 bonds, 2 residues, 2 models selected
> select #1/*:85-88 #2/*:85-88
50 atoms, 48 bonds, 8 residues, 2 models selected
1 [ID: 1] region 2 chains [64-67] RMSD: 0.000
> select #1/*:81 #2/*:81
10 atoms, 8 bonds, 2 residues, 2 models selected
> select #1/*:81-82 #2/*:81-82
20 atoms, 18 bonds, 4 residues, 2 models selected
1 [ID: 1] region 2 chains [60-61] RMSD: 0.000
> select
> #1/*:39-42,46-48,54-60,76-85,89-92,135-143,156-163,192-200,202-206,217-219,250-266,284-292,297-320,340-345,355-370,388-394,398-411,431-439,496-507
> #2/*:39-42,46-48,54-60,76-85,89-92,135-143,156-163,192-200,202-206,217-219,250-266,284-292,297-320,340-345,355-370,388-394,398-411,431-439,496-507
2818 atoms, 2820 bonds, 352 residues, 2 models selected
> select #1/*:78 #2/*:78
12 atoms, 10 bonds, 2 residues, 2 models selected
> select #1/*:78-79 #2/*:78-79
22 atoms, 20 bonds, 4 residues, 2 models selected
1 [ID: 1] region 2 chains [57-58] RMSD: 0.001
> select #1/*:77 #2/*:77
10 atoms, 8 bonds, 2 residues, 2 models selected
> select #1/*:74-77 #2/*:74-77
62 atoms, 60 bonds, 8 residues, 2 models selected
1 [ID: 1] region 2 chains [53-56] RMSD: 0.001
> select #1/*:74 #2/*:74
14 atoms, 12 bonds, 2 residues, 2 models selected
> select #1/*:74 #2/*:74
14 atoms, 12 bonds, 2 residues, 2 models selected
1 [ID: 1] region 2 chains [53] RMSD: 0.001
> select #1/*:76 #2/*:76
22 atoms, 20 bonds, 2 residues, 2 models selected
> select #1/*:76 #2/*:76
22 atoms, 20 bonds, 2 residues, 2 models selected
1 [ID: 1] region 2 chains [55] RMSD: 0.000
> style sel & #1 stick
Changed 11 atom styles
> show sel & #1 atoms
> select #1/*:75 #2/*:75
16 atoms, 14 bonds, 2 residues, 2 models selected
> select #1/*:75 #2/*:75
16 atoms, 14 bonds, 2 residues, 2 models selected
1 [ID: 1] region 2 chains [54] RMSD: 0.001
> style sel & #1 stick
Changed 8 atom styles
> show sel & #1 atoms
> hide sel & #1 atoms
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!6 models
> show #!6 models
> hide #!5 models
> show #!5 models
> select #1/*:119 #2/*:119
16 atoms, 14 bonds, 2 residues, 2 models selected
> select #1/*:119 #2/*:119
16 atoms, 14 bonds, 2 residues, 2 models selected
1 [ID: 1] region 2 chains [98] RMSD: 0.000
> select #1/*:109 #2/*:109
16 atoms, 14 bonds, 2 residues, 2 models selected
> select #1/*:108-109 #2/*:108-109
34 atoms, 32 bonds, 4 residues, 2 models selected
1 [ID: 1] region 2 chains [87-88] RMSD: 0.001
> select #1/*:112 #2/*:112
16 atoms, 14 bonds, 2 residues, 2 models selected
> select #1/*:105-112 #2/*:105-112
128 atoms, 128 bonds, 16 residues, 2 models selected
1 [ID: 1] region 2 chains [84-91] RMSD: 0.001
> select #1/*:100-101 #2/*:100-101
38 atoms, 38 bonds, 4 residues, 2 models selected
> select #1/*:98-101 #2/*:98-101
88 atoms, 92 bonds, 8 residues, 2 models selected
1 [ID: 1] region 2 chains [77-80] RMSD: 0.000
> select #1/*:93 #2/*:93
8 atoms, 6 bonds, 2 residues, 2 models selected
> select #1/*:93-97 #2/*:93-97
68 atoms, 66 bonds, 10 residues, 2 models selected
1 [ID: 1] region 2 chains [72-76] RMSD: 0.000
> select #1/*:92 #2/*:92
16 atoms, 14 bonds, 2 residues, 2 models selected
> hide #!5 models
> select #1/*:94-95 #2/*:94-95
32 atoms, 30 bonds, 4 residues, 2 models selected
> select #1/*:94-97 #2/*:94-97
60 atoms, 58 bonds, 8 residues, 2 models selected
1 [ID: 1] region 2 chains [73-76] RMSD: 0.000
> select #1/*:97 #2/*:97
18 atoms, 16 bonds, 2 residues, 2 models selected
> select #1/*:97 #2/*:97
18 atoms, 16 bonds, 2 residues, 2 models selected
1 [ID: 1] region 2 chains [76] RMSD: 0.000
> style sel & #1 stick
Changed 9 atom styles
> show sel & #1 atoms
> show #!5 models
> hide #!5 models
> show #!5 models
> select #6/A-B:179
22 atoms, 20 bonds, 2 residues, 1 model selected
> select #6/A-B:179-184
104 atoms, 102 bonds, 12 residues, 1 model selected
> select #5/A:162
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/A:162-164
28 atoms, 27 bonds, 3 residues, 1 model selected
> hide #1 models
> select #5/A:162
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/A:162-164
28 atoms, 27 bonds, 3 residues, 1 model selected
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> select #6/A-B:139
14 atoms, 14 bonds, 2 residues, 1 model selected
> select #6/A-B:139-147
140 atoms, 144 bonds, 18 residues, 1 model selected
> hide #!5 models
> show #!5 models
> hide #!5 models
> select #6/A-B:90-91
36 atoms, 36 bonds, 4 residues, 1 model selected
> select #6/A-B:90-91
36 atoms, 36 bonds, 4 residues, 1 model selected
> color sel byhetero
> color sel byelement
> color sel #a9ffbdff
> color sel byhetero
> select #6/A-B:205
24 atoms, 24 bonds, 2 residues, 1 model selected
> select #6/A-B:205
24 atoms, 24 bonds, 2 residues, 1 model selected
> style sel stick
Changed 24 atom styles
> show sel atoms
> select #6/A-B:123
16 atoms, 14 bonds, 2 residues, 1 model selected
> select #6/A-B:123
16 atoms, 14 bonds, 2 residues, 1 model selected
> style sel stick
Changed 16 atom styles
> show sel atoms
> color sel byhetero
> select #6/A-B:205
24 atoms, 24 bonds, 2 residues, 1 model selected
> select #6/A-B:205
24 atoms, 24 bonds, 2 residues, 1 model selected
> color sel byhetero
> select
> #6/A-B:57-63,66-76,89-100,102-107,125-135,139-147,162-166,179-197,207-217,220-244,246-248,271-275,297-306,318-325,347-354,369-373,396-406,419-423
2654 atoms, 2678 bonds, 342 residues, 1 model selected
> select #6/A-B:54
16 atoms, 14 bonds, 2 residues, 1 model selected
> select #6/A-B:54
16 atoms, 14 bonds, 2 residues, 1 model selected
> style sel stick
Changed 16 atom styles
> show sel atoms
> select #1/*:35 #2/*:35
16 atoms, 14 bonds, 2 residues, 2 models selected
> style #!6 stick
Changed 6624 atom styles
> show #!6 atoms
> hide #!6 atoms
> select #6/A-B:54
16 atoms, 14 bonds, 2 residues, 1 model selected
> select #6/A-B:54
16 atoms, 14 bonds, 2 residues, 1 model selected
> show sel atoms
> hide sel atoms
> show sel atoms
> select #6/A-B:54-55
24 atoms, 22 bonds, 4 residues, 1 model selected
> select #6/A-B:54
16 atoms, 14 bonds, 2 residues, 1 model selected
> show sel atoms
> hide sel atoms
> show sel atoms
> select #6/A-B:54
16 atoms, 14 bonds, 2 residues, 1 model selected
> select #6/A-B:54-55
24 atoms, 22 bonds, 4 residues, 1 model selected
> hide sel atoms
> show sel atoms
> hide sel atoms
> show sel atoms
> select #6/A-B:54
16 atoms, 14 bonds, 2 residues, 1 model selected
> select #6/A-B:54
16 atoms, 14 bonds, 2 residues, 1 model selected
> select #6/A-B:55
8 atoms, 6 bonds, 2 residues, 1 model selected
> select #6/A-B:54-55
24 atoms, 22 bonds, 4 residues, 1 model selected
> hide sel cartoons
> show sel cartoons
> hide sel atoms
> select #6/A-B:54
16 atoms, 14 bonds, 2 residues, 1 model selected
> select #6/A-B:54
16 atoms, 14 bonds, 2 residues, 1 model selected
> show sel atoms
> select #1/*:35 #2/*:35
16 atoms, 14 bonds, 2 residues, 2 models selected
> select #1/*:35 #2/*:35
16 atoms, 14 bonds, 2 residues, 2 models selected
1 [ID: 1] region 2 chains [14] RMSD: 0.000
> show #!6 atoms
> hide #!6 atoms
> show #!5 models
> hide #!5 models
> show #!5 models
> select #6/A-B:54-55
24 atoms, 22 bonds, 4 residues, 1 model selected
> select #6/A-B:54
16 atoms, 14 bonds, 2 residues, 1 model selected
> show sel atoms
> color sel byhetero
> hide #!6 models
> select #6/A-B:257
16 atoms, 14 bonds, 2 residues, 1 model selected
> select #5/A:352
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/A:352
8 atoms, 7 bonds, 1 residue, 1 model selected
> show #!6 models
> select #6/A-B:257
16 atoms, 14 bonds, 2 residues, 1 model selected
> select #6/A-B:257
16 atoms, 14 bonds, 2 residues, 1 model selected
> style sel stick
Changed 16 atom styles
> show sel atoms
> color sel byhetero
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> select #6/A-B:90
14 atoms, 12 bonds, 2 residues, 1 model selected
> select #6/A-B:90
14 atoms, 12 bonds, 2 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 14 atom styles
> color sel byhetero
> select
> #5/A:31-37,65-67,70-71,101-104,109-112,121-122,156-159,176-180,187-190,295-301,345-350,370-371,394-398,401-404,433-438,467-471,475-476,495-496,498-502,508-510,514-515
682 atoms, 685 bonds, 84 residues, 1 model selected
> select #5/A:353
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #5/A:353
10 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select #6/A-B:246
14 atoms, 12 bonds, 2 residues, 1 model selected
> select #6/A-B:246-247
36 atoms, 34 bonds, 4 residues, 1 model selected
> select #6/A-B:257
16 atoms, 14 bonds, 2 residues, 1 model selected
> select #6/A-B:257-258
36 atoms, 36 bonds, 4 residues, 1 model selected
> select #6/A-B:259-260
24 atoms, 22 bonds, 4 residues, 1 model selected
> select #6/A-B:259-260
24 atoms, 22 bonds, 4 residues, 1 model selected
> select #6/A-B:258
20 atoms, 20 bonds, 2 residues, 1 model selected
> select #6/A-B:258
20 atoms, 20 bonds, 2 residues, 1 model selected
> style sel stick
Changed 20 atom styles
> show sel atoms
> color sel byhetero
> select #6/A-B:340-341
38 atoms, 38 bonds, 4 residues, 1 model selected
> select #6/A-B:340
20 atoms, 20 bonds, 2 residues, 1 model selected
> select #6/A-B:309
20 atoms, 20 bonds, 2 residues, 1 model selected
> select #6/A-B:309
20 atoms, 20 bonds, 2 residues, 1 model selected
> style sel stick
Changed 20 atom styles
> show sel atoms
> color sel byhetero
> hide sel atoms
> show sel atoms
> hide sel atoms
> show sel atoms
> hide sel atoms
> show sel atoms
> select #6/A-B:309
20 atoms, 20 bonds, 2 residues, 1 model selected
> select #6/A-B:309-311
56 atoms, 58 bonds, 6 residues, 1 model selected
> hide #!5 models
> select
> #6/A-B:57-63,66-76,89-100,102-107,125-135,139-147,162-166,179-197,207-217,220-244,246-248,271-275,297-306,318-325,347-354,369-373,396-406,419-423
2654 atoms, 2678 bonds, 342 residues, 1 model selected
> select #6/A-B:309
20 atoms, 20 bonds, 2 residues, 1 model selected
> select #6/A-B:309
20 atoms, 20 bonds, 2 residues, 1 model selected
> hide sel atoms
> show sel atoms
> hide sel atoms
> show #!5 models
> select #6/A-B:363
20 atoms, 20 bonds, 2 residues, 1 model selected
> select #6/A-B:363
20 atoms, 20 bonds, 2 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 20 atom styles
> color sel byhetero
> select #6/A-B:208
20 atoms, 20 bonds, 2 residues, 1 model selected
> select #6/A-B:208-214
106 atoms, 108 bonds, 14 residues, 1 model selected
> select #6/A-B:214
20 atoms, 20 bonds, 2 residues, 1 model selected
> select #6/A-B:214
20 atoms, 20 bonds, 2 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 20 atom styles
> color sel byhetero
> hide #!6 models
> show #1 models
> select #1/*:289 #2/*:289
20 atoms, 20 bonds, 2 residues, 2 models selected
> select #1/*:289 #2/*:289
20 atoms, 20 bonds, 2 residues, 2 models selected
1 [ID: 1] region 2 chains [268] RMSD: 0.001
> select #1/*:288 #2/*:288
16 atoms, 14 bonds, 2 residues, 2 models selected
> select #1/*:288 #2/*:288
16 atoms, 14 bonds, 2 residues, 2 models selected
1 [ID: 1] region 2 chains [267] RMSD: 0.001
> select #1/*:290-291 #2/*:290-291
34 atoms, 32 bonds, 4 residues, 2 models selected
> select #1/*:290 #2/*:290
22 atoms, 20 bonds, 2 residues, 2 models selected
1 [ID: 1] region 2 chains [269] RMSD: 0.000
> select #1/*:289 #2/*:289
20 atoms, 20 bonds, 2 residues, 2 models selected
> select #1/*:289 #2/*:289
20 atoms, 20 bonds, 2 residues, 2 models selected
1 [ID: 1] region 2 chains [268] RMSD: 0.001
> show sel & #1 atoms
> select #1/*:291 #2/*:291
12 atoms, 10 bonds, 2 residues, 2 models selected
> select #1/*:290-291 #2/*:290-291
34 atoms, 32 bonds, 4 residues, 2 models selected
1 [ID: 1] region 2 chains [269-270] RMSD: 0.000
> select #1/*:290 #2/*:290
22 atoms, 20 bonds, 2 residues, 2 models selected
> select #1/*:290 #2/*:290
22 atoms, 20 bonds, 2 residues, 2 models selected
1 [ID: 1] region 2 chains [269] RMSD: 0.000
> show sel & #1 atoms
> select #1/*:289 #2/*:289
20 atoms, 20 bonds, 2 residues, 2 models selected
> select #1/*:289 #2/*:289
20 atoms, 20 bonds, 2 residues, 2 models selected
1 [ID: 1] region 2 chains [268] RMSD: 0.001
> hide sel & #1 atoms
> select #1/*:466 #2/*:466
16 atoms, 14 bonds, 2 residues, 2 models selected
> select #1/*:466 #2/*:466
16 atoms, 14 bonds, 2 residues, 2 models selected
1 [ID: 1] region 2 chains [445] RMSD: 0.000
> show sel & #1 atoms
> color sel & #1 byhetero
> select #1/*:146 #2/*:146
10 atoms, 8 bonds, 2 residues, 2 models selected
> select #1/*:146-147 #2/*:146-147
20 atoms, 18 bonds, 4 residues, 2 models selected
1 [ID: 1] region 2 chains [125-126] RMSD: 0.001
> select #1/*:151 #2/*:151
10 atoms, 8 bonds, 2 residues, 2 models selected
> select #1/*:151 #2/*:151
10 atoms, 8 bonds, 2 residues, 2 models selected
1 [ID: 1] region 2 chains [130] RMSD: 0.000
> select #1/*:151 #2/*:151
10 atoms, 8 bonds, 2 residues, 2 models selected
> select #1/*:146-151 #2/*:146-151
84 atoms, 84 bonds, 12 residues, 2 models selected
1 [ID: 1] region 2 chains [125-130] RMSD: 0.001
> select #1/*:158 #2/*:158
10 atoms, 8 bonds, 2 residues, 2 models selected
> select #1/*:158-159 #2/*:158-159
20 atoms, 18 bonds, 4 residues, 2 models selected
1 [ID: 1] region 2 chains [137-138] RMSD: 0.001
> select #1/*:157 #2/*:157
16 atoms, 14 bonds, 2 residues, 2 models selected
> select #1/*:157-159 #2/*:157-159
36 atoms, 34 bonds, 6 residues, 2 models selected
1 [ID: 1] region 2 chains [136-138] RMSD: 0.000
> select #1/*:157 #2/*:157
16 atoms, 14 bonds, 2 residues, 2 models selected
> select #1/*:157 #2/*:157
16 atoms, 14 bonds, 2 residues, 2 models selected
1 [ID: 1] region 2 chains [136] RMSD: 0.000
> style sel & #1 stick
Changed 8 atom styles
> show sel & #1 atoms
> color sel & #1 byhetero
> select
> #5/A:43-52,56-64,78-89,91-96,126-131,141-150,162-171,198-214,223-227,253-286,302-312,315-340,358-365,376-389,405-413,415-429,450-459,490-494,518-528
1781 atoms, 1797 bonds, 228 residues, 1 model selected
> select #5/A:163
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/A:163
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #5/A:162
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/A:162
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/A:164
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #5/A:164
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/*:75 #2/*:75
16 atoms, 14 bonds, 2 residues, 2 models selected
> select #1/*:75 #2/*:75
16 atoms, 14 bonds, 2 residues, 2 models selected
1 [ID: 1] region 2 chains [54] RMSD: 0.001
> select #1/*:74 #2/*:74
14 atoms, 12 bonds, 2 residues, 2 models selected
> select #1/*:74 #2/*:74
14 atoms, 12 bonds, 2 residues, 2 models selected
1 [ID: 1] region 2 chains [53] RMSD: 0.001
> select #1/*:74-75 #2/*:74-75
30 atoms, 28 bonds, 4 residues, 2 models selected
> select #1/*:74-77 #2/*:74-77
62 atoms, 60 bonds, 8 residues, 2 models selected
1 [ID: 1] region 2 chains [53-56] RMSD: 0.001
> select
> #1/*:39-42,46-48,54-60,76-85,89-92,135-143,156-163,192-200,202-206,217-219,250-266,284-292,297-320,340-345,355-370,388-394,398-411,431-439,496-507
> #2/*:39-42,46-48,54-60,76-85,89-92,135-143,156-163,192-200,202-206,217-219,250-266,284-292,297-320,340-345,355-370,388-394,398-411,431-439,496-507
2818 atoms, 2820 bonds, 352 residues, 2 models selected
> select #1/*:77-78 #2/*:77-78
22 atoms, 20 bonds, 4 residues, 2 models selected
> select #1/*:74-78 #2/*:74-78
74 atoms, 72 bonds, 10 residues, 2 models selected
1 [ID: 1] region 2 chains [53-57] RMSD: 0.001
> select #1/*:155 #2/*:155
22 atoms, 22 bonds, 2 residues, 2 models selected
> select #1/*:155 #2/*:155
22 atoms, 22 bonds, 2 residues, 2 models selected
1 [ID: 1] region 2 chains [134] RMSD: 0.001
> show sel & #1 atoms
> color sel & #1 byhetero
> style sel & #1 stick
Changed 11 atom styles
> show #!6 models
> hide #!5 models
> hide #!6 models
> show #!6 models
> hide #1 models
> select #6/A-B:123
16 atoms, 14 bonds, 2 residues, 1 model selected
> select #6/A-B:123
16 atoms, 14 bonds, 2 residues, 1 model selected
> style sel stick
Changed 16 atom styles
> color sel byhetero
> show sel atoms
> color sel byhetero
> select #6/A-B:205
24 atoms, 24 bonds, 2 residues, 1 model selected
> select #6/A-B:205
24 atoms, 24 bonds, 2 residues, 1 model selected
> show sel atoms
> show #1 models
> show #!5 models
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 INTEL-20.2.48
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics OpenGL Engine
OpenGL vendor: Intel Inc.
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro16,2
Processor Name: Quad-Core Intel Core i7
Processor Speed: 2.3 GHz
Number of Processors: 1
Total Number of Cores: 4
L2 Cache (per Core): 512 KB
L3 Cache: 8 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
System Firmware Version: 1916.60.2.0.0 (iBridge: 20.16.2059.0.0,0)
OS Loader Version: 564.40.4~55
Software:
System Software Overview:
System Version: macOS 13.1 (22C65)
Kernel Version: Darwin 22.2.0
Time since boot: 31 days, 21 hours, 18 minutes
Graphics/Displays:
Intel Iris Plus Graphics:
Chipset Model: Intel Iris Plus Graphics
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x8a53
Revision ID: 0x0007
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
DELL P2719HC:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Display Serial Number: 5VCLY13
Mirror: Off
Online: Yes
Rotation: Supported
Connection Type: Thunderbolt/DisplayPort
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.2.1
Babel: 2.12.1
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
build: 0.10.0
certifi: 2021.10.8
cftime: 1.6.2
charset-normalizer: 3.1.0
ChimeraX-AddCharge: 1.5.9.1
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.3.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.9.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.43.10
ChimeraX-AtomicLibrary: 10.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.8
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3.1
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.3
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.6.1
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.1
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-Label: 1.1.7
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
ChimeraX-Map: 1.1.4
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.0.12
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.9
ChimeraX-ModelPanel: 1.3.7
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.0
ChimeraX-NRRD: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.10.1
ChimeraX-PDB: 2.7.2
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 3.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.1
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.8.3
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.10.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Topography: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.28.4
ChimeraX-uniprot: 2.2.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.1
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.1.3
contourpy: 1.0.7
cxservices: 1.2.2
cycler: 0.11.0
Cython: 0.29.33
debugpy: 1.6.7
decorator: 5.1.1
docutils: 0.19
executing: 1.2.0
filelock: 3.9.0
fonttools: 4.39.3
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.8.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.35
imagecodecs: 2022.2.22
imagesize: 1.4.1
importlib-metadata: 6.6.0
ipykernel: 6.21.1
ipython: 8.10.0
ipython-genutils: 0.2.0
ipywidgets: 8.0.6
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.0.2
jupyter-core: 5.3.0
jupyterlab-widgets: 3.0.7
kiwisolver: 1.4.4
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.2
matplotlib: 3.6.3
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.2
networkx: 2.8.8
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.4
numpy: 1.23.5
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.3.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 3.5.0
prompt-toolkit: 3.0.38
psutil: 5.9.4
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.14.0
pynrrd: 1.0.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.4.2
PyQt6-Qt6: 6.4.3
PyQt6-sip: 13.4.1
PyQt6-WebEngine-commercial: 6.4.0
PyQt6-WebEngine-Qt6: 6.4.3
python-dateutil: 2.8.2
pytz: 2023.3
pyzmq: 25.0.2
qtconsole: 5.4.0
QtPy: 2.3.1
RandomWords: 0.4.0
requests: 2.28.2
scipy: 1.9.3
setuptools: 67.4.0
setuptools-scm: 7.0.5
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.4.1
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.4
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.1
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tcia-utils: 1.2.0
tifffile: 2022.10.10
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.3.1
traitlets: 5.9.0
typing-extensions: 4.5.0
tzdata: 2023.3
urllib3: 1.26.15
wcwidth: 0.2.6
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.7
zipp: 3.15.0
Change History (2)
comment:1 by , 2 years ago
| Component: | Unassigned → Graphics |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Graphics hardware encountered an error and was reset |
comment:2 by , 2 years ago
| Resolution: | → nonchimerax |
|---|---|
| Status: | assigned → closed |
| Summary: | Graphics hardware encountered an error and was reset → Graphics crash, macOS 13.1, Intel Iris Plus Graphics |
Apple Intel graphics driver crash. Unfortunately Apple's Intel OpenGL graphics drivers are not very stable and crash often (we have hundreds of reports over years). The Apple Silicon Macs have stable OpenGL graphics drivers. Nothing we can do to fix this. More details here: https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#maccrash
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Reported by Ian Lidbury