![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 3 years ago
Closed 3 years ago
#8546 closed defect (can't reproduce)
Crash in event loop
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | 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: 1.5 (2022-11-24 00:03:27 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Current thread 0x0000000117e9a600 (most recent call first):
File "/private/var/folders/fk/sy3ybnfx0ylcf2lsb3p9myzstb7rgs/T/AppTranslocation/461EDB8C-24A2-4DBB-822E-2298967B0436/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 283 in event_loop
File "/private/var/folders/fk/sy3ybnfx0ylcf2lsb3p9myzstb7rgs/T/AppTranslocation/461EDB8C-24A2-4DBB-822E-2298967B0436/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 884 in init
File "/private/var/folders/fk/sy3ybnfx0ylcf2lsb3p9myzstb7rgs/T/AppTranslocation/461EDB8C-24A2-4DBB-822E-2298967B0436/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 1035 in
File "/private/var/folders/fk/sy3ybnfx0ylcf2lsb3p9myzstb7rgs/T/AppTranslocation/461EDB8C-24A2-4DBB-822E-2298967B0436/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
File "/private/var/folders/fk/sy3ybnfx0ylcf2lsb3p9myzstb7rgs/T/AppTranslocation/461EDB8C-24A2-4DBB-822E-2298967B0436/d/ChimeraX-1.5.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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"procLaunch" : "2023-02-22 16:23:12.4615 -0500",
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"incident" : "13B4A196-8390-4B1D-94A7-6EC66B87D688",
"bug_type" : "309",
"pid" : 21592,
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"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "46617AF6-E1CB-FA87-331D-F1FD4FD24E64",
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"exception" : {"codes":"0x000000000000000d, 0x0000000000000000","rawCodes":[13,0],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"UNKNOWN_0xD at 0x0000000000000000"},
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"path" : "\/Volumes\/VOLUME\/*\/ChimeraX-1.5.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/numpy\/.dylibs\/libopenblas64_.0.dylib",
"name" : "libopenblas64_.0.dylib"
},
{
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"arch" : "x86_64",
"base" : 140703575085056,
"size" : 49152,
"uuid" : "b5454e27-e8c7-3fdb-b77f-714f1e82e70b",
"path" : "\/usr\/lib\/system\/libsystem_pthread.dylib",
"name" : "libsystem_pthread.dylib"
},
{
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"base" : 5182238720,
"size" : 165052416,
"uuid" : "4aa1de3e-464c-340c-ab61-bcd39bfc7658",
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"name" : "QtWebEngineCore"
},
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"CFBundleIdentifier" : "com.apple.CoreFoundation",
"size" : 5255168,
"uuid" : "93c48919-68af-367e-9a67-db4159bc962c",
"path" : "\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation",
"name" : "CoreFoundation",
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"CFBundleIdentifier" : "com.apple.AppKit",
"size" : 15269888,
"uuid" : "af3d9501-0abf-3c79-955c-c42c29af6351",
"path" : "\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit",
"name" : "AppKit",
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"sharedCache" : {
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"vmSummary" : "ReadOnly portion of Libraries: Total=1.4G resident=0K(0%) swapped_out_or_unallocated=1.4G(100%)\nWritable regions: Total=3.0G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=3.0G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 384K 3 \nActivity Tracing 256K 1 \nCG backing stores 2160K 4 \nCG image 2188K 51 \nColorSync 232K 28 \nCoreAnimation 10.1M 90 \nCoreGraphics 12K 2 \nCoreUI image data 5304K 40 \nFoundation 32K 2 \nKernel Alloc Once 8K 1 \nMALLOC 2.6G 1738 \nMALLOC guard page 32K 8 \nMALLOC_LARGE (reserved) 384K 1 reserved VM address space (unallocated)\nOpenGL GLSL 384K 4 \nSTACK GUARD 112K 28 \nStack 164.7M 29 \nStack Guard 56.0M 1 \nVM_ALLOCATE 261.3M 125 \nVM_ALLOCATE (reserved) 32.0M 1 reserved VM address space (unallocated)\n__CTF 756 1 \n__DATA 44.9M 673 \n__DATA_CONST 32.5M 343 \n__DATA_DIRTY 1641K 213 \n__FONT_DATA 4K 1 \n__GLSLBUILTINS 5176K 1 \n__LINKEDIT 676.4M 147 \n__TEXT 806.7M 672 \n__UNICODE 592K 1 \ndyld private memory 1184K 3 \nmapped file 198.1M 50 \nshared memory 848K 33 \n=========== ======= ======= \nTOTAL 4.8G 4295 \nTOTAL, minus reserved VM space 4.8G 4295 \n",
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===== Log before crash start =====
UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
> open /Users/wt296/Downloads/66bp_15TnsC_1.cxs
Opened csparc_J392_localrefineC_sharp.mrc as #2.1, grid size 512,512,512,
pixel 1.07, shown at level 0.475, step 1, values float32
Opened csparc_J392_localrefineC.mrc as #2.2, grid size 512,512,512, pixel
1.07, shown at level 0.35, step 1, values float32
Log from Tue Feb 21 21:26:19 2023UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
> open /Users/wt296/Downloads/66bp_15TnsC.cxs
Opened csparc_J392_localrefineC_sharp.mrc as #2.1, grid size 512,512,512,
pixel 1.07, shown at level 0.475, step 1, values float32
Opened csparc_J392_localrefineC.mrc as #2.2, grid size 512,512,512, pixel
1.07, shown at level 0.35, step 1, values float32
Log from Thu Feb 16 01:40:01 2023UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/wt296/Downloads/15TnsCmodel_J373-coot-chainA.pdb
Chain information for 15TnsCmodel_J373-coot-chainA.pdb #1
---
Chain | Description
1 | No description available
2 | No description available
3 | No description available
4 | No description available
5 | No description available
6 | No description available
7 | No description available
A B C D E F G H I J K L M N U | No description available
O | No description available
Q | No description available
S | No description available
W | No description available
X | No description available
Y | No description available
Z | No description available
w x y z | No description available
> set bgColor white
> lighting soft
> set bgColor white
> lighting soft
> color /A/C/E/G/I/K #A3C46A
> color /B/D/F/H/J/L #65c18f
> color /Q #F16823
> color /Y/Z/y/z #a797c1
> color /W/X/w/x #6A3D9A
> color /O #Fc94AF
> color /S #f2be78
> color /1-6 #44A7e3
> color /7 #b2b2b2
> color /1:-30--1 #5364ae
> color /4:-30--1 #5364ae
> color /2/5 #5364ae
> hide atoms
> show cartoons
> graphics silhouettes true
> hide pseudobonds
> select /1-7
7570 atoms, 8477 bonds, 1 pseudobond, 366 residues, 2 models selected
> show sel atoms
> nucleotides ladder
> select clear
> color /M/U
> select /M/U
4196 atoms, 4260 bonds, 2 pseudobonds, 518 residues, 2 models selected
> color sel #A3C46A
> select /N
2098 atoms, 2130 bonds, 259 residues, 1 model selected
> color sel #65c18f
> select clear
> open /Users/wt296/Desktop/csparc_J392_localrefineC_sharp.mrc
> /Users/wt296/Desktop/csparc_J392_localrefineC.mrc
Opened csparc_J392_localrefineC_sharp.mrc as #2.1, grid size 512,512,512,
pixel 1.07, shown at level 0.157, step 2, values float32
Opened csparc_J392_localrefineC.mrc as #2.2, grid size 512,512,512, pixel
1.07, shown at level 0.0762, step 2, values float32
> volume #2.1 step 1
> volume #2.2 step 1
> volume #2.1 level 0.6837
> volume #2.2 level 0.3192
> transparency #1#2.2#!2 70
> transparency #1#2.2#!2 60
> ui tool show "Side View"
> hide #!2.2 models
> select #1/A-N,U:103,121
240 atoms, 210 bonds, 30 residues, 1 model selected
> show sel target ab
> hide sel target a
> show (sel-residues & sidechain) target ab
> hide sel target a
> show sel target ab
> style sel stick
Changed 240 atom styles
> color sel byelement
> select #1/A-N,U:119
135 atoms, 120 bonds, 15 residues, 1 model selected
> show sel target ab
> style sel stick
Changed 135 atom styles
> select #1/A-N,U:182
165 atoms, 150 bonds, 15 residues, 1 model selected
> show sel target ab
> style sel stick
Changed 165 atom styles
> color sel byelement
> select #1/A-N,U:119
135 atoms, 120 bonds, 15 residues, 1 model selected
> color sel byelement
> select clear
> cartoon style nucleic xsection oval width 2 thickness 2
> select /1:10
22 atoms, 24 bonds, 1 residue, 1 model selected
> select add /1:11
43 atoms, 47 bonds, 2 residues, 1 model selected
> select add /1:12
63 atoms, 68 bonds, 3 residues, 1 model selected
> select add /1:13
85 atoms, 92 bonds, 4 residues, 1 model selected
> select add /1:14
104 atoms, 112 bonds, 5 residues, 1 model selected
> hide (sel-residues & (protein|nucleic)) target a
> cartoon hide sel-residues
> show (sel-residues & backbone) target ab
> style sel stick
Changed 104 atom styles
> color sel byelement
> select clear
> select /1:15
22 atoms, 24 bonds, 1 residue, 1 model selected
> select add /1:16
41 atoms, 44 bonds, 2 residues, 1 model selected
> hide (sel-residues & (protein|nucleic)) target a
> cartoon hide sel-residues
> show (sel-residues & backbone) target ab
> style sel stick
Changed 41 atom styles
> color sel byelement
> select clear
> select /A:182@NH1
1 atom, 1 residue, 1 model selected
> select add /1:12@OP1
2 atoms, 2 residues, 1 model selected
> ui tool show Distances
> distance /A:182@NH1 /1:12@OP1
Distance between /A ARG 182 NH1 and /1 DT 12 OP1: 3.458Å
> distance style color #fadc48
[Repeated 2 time(s)]
> distance style color #1f1b09
[Repeated 2 time(s)]
> distance style color black
[Repeated 2 time(s)]
> distance style decimalPlaces 1
[Repeated 2 time(s)]
> distance style dashes 4
[Repeated 2 time(s)]
> distance style symbol false
[Repeated 2 time(s)]
> distance style symbol true
[Repeated 2 time(s)]
> distance style dashes 3
[Repeated 2 time(s)]
> distance style radius 0.2
[Repeated 2 time(s)]
> distance style dashes 4
[Repeated 2 time(s)]
> select /B:182@NH1
1 atom, 1 residue, 1 model selected
> select add /1:14@OP1
2 atoms, 2 residues, 1 model selected
> distance /B:182@NH1 /1:14@OP1
Distance between /B ARG 182 NH1 and /1 DC 14 OP1: 3.8Å
> distance style symbol false
[Repeated 2 time(s)]
> distance style symbol true
[Repeated 2 time(s)]
> distance style symbol false
[Repeated 2 time(s)]
> distance style symbol true
[Repeated 2 time(s)]
> select add /1:13@OP1
1 atom, 1 bond, 1 residue, 1 model selected
> select add /B:182@NH2
2 atoms, 2 residues, 1 model selected
> distance /1:13@OP1 /B:182@NH2
Distance between /1 DG 13 OP1 and /B ARG 182 NH2: 4.7Å
> select clear
> ~distance /1:13@OP1 /B:182@NH2
> distance style color #0433ff
[Repeated 2 time(s)]
> distance style color black
[Repeated 2 time(s)]
> select /C:182@NH2
1 atom, 1 residue, 1 model selected
> select clear
> select /1:15@OP2
1 atom, 1 residue, 1 model selected
> select add /C:182@NH2
2 atoms, 2 residues, 1 model selected
> distance /1:15@OP2 /C:182@NH2
Distance between /1 DG 15 OP2 and /C ARG 182 NH2: 2.9Å
> distance style color #aa7942
[Repeated 2 time(s)]
> distance style color black
[Repeated 2 time(s)]
> select clear
> show #!2.2 models
> hide #!2.2 models
> show #!2.2 models
> hide #!2.2 models
> show #!2.1 models
> transparency #1,3#2.1#!2 60
> volume #2.1 level 0.6086
> hide #!2.1 models
> show #!2.2 models
> hide #!2.2 models
> save /Users/wt296/Desktop/image1.png supersample 3
> show #!2.2 models
> save /Users/wt296/Desktop/image2.png supersample 3
> hide #!2.2 models
> select /1:17
21 atoms, 23 bonds, 1 residue, 1 model selected
> select add /1:18
41 atoms, 44 bonds, 2 residues, 1 model selected
> select add /1:19
60 atoms, 64 bonds, 3 residues, 1 model selected
> select add /1:20
80 atoms, 85 bonds, 4 residues, 1 model selected
> select add /1:21
101 atoms, 108 bonds, 5 residues, 1 model selected
> hide (sel-residues & (protein|nucleic)) target a
> cartoon hide sel-residues
> show (sel-residues & backbone) target ab
> style sel stick
Changed 101 atom styles
> color sel byelement
> select clear
> show #!2.2 models
> hide #!2.2 models
> show #!2.1 models
> hide #!2.1 models
> show #!2.2 models
> hide #!2.1 models
> volume #2.2 level 0.3496
> select /1:19@OP1
1 atom, 1 residue, 1 model selected
> select add /E:182@NH2
2 atoms, 2 residues, 1 model selected
> distance /1:19@OP1 /E:182@NH2
Distance between /1 DC 19 OP1 and /E ARG 182 NH2: 4.2Å
> distance style color #ff2600
[Repeated 2 time(s)]
> distance style color #fffb00
[Repeated 2 time(s)]
> select clear
> select /D:182@NH2
1 atom, 1 residue, 1 model selected
> select add /1:17@OP1
2 atoms, 2 residues, 1 model selected
> distance /D:182@NH2 /1:17@OP1
Distance between /D ARG 182 NH2 and /1 DA 17 OP1: 5.2Å
> select clear
> hide #!2.2 models
> save /Users/wt296/Desktop/image3.png supersample 3
> show #!2.2 models
> save /Users/wt296/Desktop/image4.png supersample 3
> select #2.2
4 models selected
> select #2.2
4 models selected
> select /F:182@NH2
1 atom, 1 residue, 1 model selected
> hide #!2.2 models
> select /1:21@OP2
1 atom, 1 residue, 1 model selected
Exactly two atoms must be selected!
> select add /F:182@NH2
2 atoms, 2 residues, 1 model selected
> distance /1:21@OP2 /F:182@NH2
Distance between /1 DA 21 OP2 and /F ARG 182 NH2: 6.2Å
> select clear
> save /Users/wt296/Desktop/image5.png supersample 3
> show #!2.2 models
> hide #!2.2 models
> show #!2.1 models
> volume #2.1 level 0.5003
> save /Users/wt296/Desktop/image6.png supersample 3
> hide #!2.1 models
> select /3:140
20 atoms, 21 bonds, 1 residue, 1 model selected
> select add /3:139
41 atoms, 44 bonds, 2 residues, 1 model selected
> select add /3:137
62 atoms, 67 bonds, 3 residues, 1 model selected
> select add /3:138
84 atoms, 91 bonds, 4 residues, 1 model selected
> select add /3:136
104 atoms, 112 bonds, 5 residues, 1 model selected
> select add /3:135
125 atoms, 135 bonds, 6 residues, 1 model selected
> hide (sel-residues & (protein|nucleic)) target a
> cartoon hide sel-residues
> show (sel-residues & backbone) target ab
> style sel stick
Changed 125 atom styles
> color sel byelement
> select clear
[Repeated 1 time(s)]
> select /A:103@NZ
1 atom, 1 residue, 1 model selected
> select add /3:139@OP1
2 atoms, 2 residues, 1 model selected
> distance /A:103@NZ /3:139@OP1
Distance between /A LYS 103 NZ and /3 DA 139 OP1: 6.1Å
> show #!2.2 models
> hide #!2.2 models
> show #!2.1 models
> hide #!2.1 models
> select clear
> select /B:103@NZ
1 atom, 1 residue, 1 model selected
> select add /3:138@OP1
2 atoms, 2 residues, 1 model selected
> distance /B:103@NZ /3:138@OP1
Distance between /B LYS 103 NZ and /3 DG 138 OP1: 4.0Å
> select /B:121@OG1
1 atom, 1 residue, 1 model selected
> select add /3:137@OP1
2 atoms, 2 residues, 1 model selected
> distance /B:121@OG1 /3:137@OP1
Distance between /B THR 121 OG1 and /3 DA 137 OP1: 2.1Å
> show #!2.1 models
> hide #!2.1 models
> show #!2.1 models
> hide #!2.1 models
> show #!2.1 models
> distance style color black
[Repeated 2 time(s)]
> select clear
> save /Users/wt296/Desktop/image7.png supersample 3
> hide #!2.1 models
> save /Users/wt296/Desktop/image8.png supersample 3
> select /3:134
20 atoms, 21 bonds, 1 residue, 1 model selected
> select add /3:133
41 atoms, 44 bonds, 2 residues, 1 model selected
> select add /3:132
61 atoms, 65 bonds, 3 residues, 1 model selected
> hide (sel-residues & (protein|nucleic)) target a
> cartoon hide sel-residues
> show (sel-residues & backbone) target ab
> style sel stick
Changed 61 atom styles
> color sel byelement
> select clear
> select /C:103@NZ
1 atom, 1 residue, 1 model selected
> select add /3:136@OP1
2 atoms, 2 residues, 1 model selected
> distance /C:103@NZ /3:136@OP1
Distance between /C LYS 103 NZ and /3 DT 136 OP1: 4.2Å
> select /C:121@OG1
1 atom, 1 residue, 1 model selected
> select add /3:135@OP1
2 atoms, 2 residues, 1 model selected
> distance /C:121@OG1 /3:135@OP1
Distance between /C THR 121 OG1 and /3 DA 135 OP1: 2.2Å
> select /D:103@NZ
1 atom, 1 residue, 1 model selected
> select add /3:134@OP1
2 atoms, 2 residues, 1 model selected
> distance /D:103@NZ /3:134@OP1
Distance between /D LYS 103 NZ and /3 DT 134 OP1: 3.4Å
> show #!2.2 models
> hide #!2.2 models
> show #!2.1 models
> hide #!2.1 models
> select /3:131
21 atoms, 23 bonds, 1 residue, 1 model selected
> select add /3:130
41 atoms, 44 bonds, 2 residues, 1 model selected
> hide (sel-residues & (protein|nucleic)) target a
> cartoon hide sel-residues
> show (sel-residues & backbone) target ab
> style sel stick
Changed 41 atom styles
> color sel byelement
> select clear
> select /E:103@NZ
1 atom, 1 residue, 1 model selected
> select add /3:132@OP1
2 atoms, 2 residues, 1 model selected
> distance /E:103@NZ /3:132@OP1
Distance between /E LYS 103 NZ and /3 DT 132 OP1: 3.0Å
> select /E:121@OG1
1 atom, 1 residue, 1 model selected
> select add /3:131@OP1
2 atoms, 2 residues, 1 model selected
> distance /E:121@OG1 /3:131@OP1
Distance between /E THR 121 OG1 and /3 DA 131 OP1: 2.5Å
> select clear
> show #!2.1 models
> hide #!2.1 models
> show #!2.2 models
> hide #!2.2 models
> show #!2.1 models
> distance style color #aa7942
[Repeated 2 time(s)]
> distance style color black
[Repeated 2 time(s)]
> hide #!2.1 models
> save /Users/wt296/Desktop/image9.png supersample 3
> show #!2.1 models
> save /Users/wt296/Desktop/image10.png supersample 3
> hide #!2.1 models
> save /Users/wt296/Desktop/image11.png supersample 3
> show #!2.1 models
> save /Users/wt296/Desktop/image12.png supersample 3
> hide #!2.1 models
> select /3:129
21 atoms, 23 bonds, 1 residue, 1 model selected
> select add /3:128
41 atoms, 44 bonds, 2 residues, 1 model selected
> select add /3:127
62 atoms, 67 bonds, 3 residues, 1 model selected
> select add /3:126
82 atoms, 88 bonds, 4 residues, 1 model selected
> hide (sel-residues & (protein|nucleic)) target a
> cartoon hide sel-residues
> show (sel-residues & backbone) target ab
> style sel stick
Changed 82 atom styles
> color sel byelement
> select clear
> select /F:121@OG1
1 atom, 1 residue, 1 model selected
> select add /3:129@OP1
2 atoms, 2 residues, 1 model selected
> distance /F:121@OG1 /3:129@OP1
Distance between /F THR 121 OG1 and /3 DA 129 OP1: 3.0Å
> select clear
> select /F:103@NZ
1 atom, 1 residue, 1 model selected
> select add /3:130@OP1
2 atoms, 2 residues, 1 model selected
> distance /F:103@NZ /3:130@OP1
Distance between /F LYS 103 NZ and /3 DT 130 OP1: 5.1Å
> select /G:103@NZ
1 atom, 1 residue, 1 model selected
> select add /3:128@OP1
2 atoms, 2 residues, 1 model selected
> distance /G:103@NZ /3:128@OP1
Distance between /G LYS 103 NZ and /3 DT 128 OP1: 2.5Å
> select /G:121@OG1
1 atom, 1 residue, 1 model selected
> select add /3:127@OP1
2 atoms, 2 residues, 1 model selected
> distance /G:121@OG1 /3:127@OP1
Distance between /G THR 121 OG1 and /3 DA 127 OP1: 2.9Å
> distance style color #0433ff
[Repeated 2 time(s)]
> distance style color black
[Repeated 2 time(s)]
> select clear
> save /Users/wt296/Desktop/image13.png supersample 3
> show #!2.1 models
> hide #!2.1 models
> select /3:125
20 atoms, 21 bonds, 1 residue, 1 model selected
> select add /3:124
41 atoms, 44 bonds, 2 residues, 1 model selected
> hide (sel-residues & (protein|nucleic)) target a
> cartoon hide sel-residues
> show (sel-residues & backbone) target ab
> style sel stick
Changed 41 atom styles
> color sel byelement
> select clear
> select /H:103@NZ
1 atom, 1 residue, 1 model selected
> select /H:103@NZ
1 atom, 1 residue, 1 model selected
> select add /3:126@OP1
2 atoms, 2 residues, 1 model selected
> distance /H:103@NZ /3:126@OP1
Distance between /H LYS 103 NZ and /3 DT 126 OP1: 2.6Å
> select /3:125@OP1
1 atom, 1 residue, 1 model selected
> select add /H:121@OG1
2 atoms, 2 residues, 1 model selected
> distance /3:125@OP1 /H:121@OG1
Distance between /3 DT 125 OP1 and /H THR 121 OG1: 4.3Å
> show #!2.1 models
> select clear
> hide #!2.1 models
> select /I:103@NZ
1 atom, 1 residue, 1 model selected
> select add /3:124@OP1
2 atoms, 2 residues, 1 model selected
> distance /I:103@NZ /3:124@OP1
Distance between /I LYS 103 NZ and /3 DA 124 OP1: 6.2Å
> select /3:123
19 atoms, 20 bonds, 1 residue, 1 model selected
> select add /3:122
41 atoms, 44 bonds, 2 residues, 1 model selected
> select add /3:121
61 atoms, 65 bonds, 3 residues, 1 model selected
> hide (sel-residues & (protein|nucleic)) target a
> cartoon hide sel-residues
> show (sel-residues & backbone) target ab
> style sel stick
Changed 61 atom styles
> color sel byelement
> select clear
> show #!2.1 models
> hide #!2.1 models
> show #!2.1 models
> volume #2.1 level 0.5503
> hide #!2.1 models
> show #!2.1 models
> hide #!2.1 models
> select /3:120
20 atoms, 21 bonds, 1 residue, 1 model selected
> select add /3:119
40 atoms, 42 bonds, 2 residues, 1 model selected
> select add /3:118
61 atoms, 65 bonds, 3 residues, 1 model selected
> hide (sel-residues & (protein|nucleic)) target a
> cartoon hide sel-residues
> show (sel-residues & backbone) target ab
> style sel stick
Changed 61 atom styles
> color sel byelement
> select clear
> show #!2.1 models
> select /K:121@OG1
1 atom, 1 residue, 1 model selected
> select add /3:120@OP1
2 atoms, 2 residues, 1 model selected
> distance /K:121@OG1 /3:120@OP1
Distance between /K THR 121 OG1 and /3 DT 120 OP1: 3.1Å
> select clear
> hide #!2.1 models
> select /3:117
21 atoms, 23 bonds, 1 residue, 1 model selected
> select add /3:116
40 atoms, 43 bonds, 2 residues, 1 model selected
> select add /3:115
60 atoms, 64 bonds, 3 residues, 1 model selected
> hide (sel-residues & (protein|nucleic)) target a
> cartoon hide sel-residues
> show (sel-residues & backbone) target ab
> style sel stick
Changed 60 atom styles
> color sel byelement
> select clear
> show #!2.1 models
> hide #!2.1 models
> select /1:45
22 atoms, 24 bonds, 1 residue, 1 model selected
> select add /1:46
44 atoms, 48 bonds, 2 residues, 1 model selected
> select add /1:47
63 atoms, 68 bonds, 3 residues, 1 model selected
> hide (sel-residues & (protein|nucleic)) target a
> cartoon hide sel-residues
> show (sel-residues & backbone) target ab
> style sel stick
Changed 63 atom styles
> color sel byelement
> select clear
> select /3:114
19 atoms, 20 bonds, 1 residue, 1 model selected
> select add /3:113
40 atoms, 43 bonds, 2 residues, 1 model selected
> select subtract /3:113
19 atoms, 20 bonds, 1 residue, 1 model selected
> select add /3:113
40 atoms, 43 bonds, 2 residues, 1 model selected
> select add /3:112
59 atoms, 63 bonds, 3 residues, 1 model selected
> hide (sel-residues & (protein|nucleic)) target a
> cartoon hide sel-residues
> show (sel-residues & backbone) target ab
> style sel stick
Changed 59 atom styles
> color sel byelement
> select clear
> select /3:116@OP1
1 atom, 1 residue, 1 model selected
> select add /M:121@OG1
2 atoms, 2 residues, 1 model selected
> distance /3:116@OP1 /M:121@OG1
Distance between /3 DC 116 OP1 and /M THR 121 OG1: 5.3Å
> show #!2.1 models
> select clear
> select /U:103@NZ
1 atom, 1 residue, 1 model selected
> select add /3:113@OP1
2 atoms, 2 residues, 1 model selected
> distance /U:103@NZ /3:113@OP1
Distance between /U LYS 103 NZ and /3 DA 113 OP1: 4.7Å
> select clear
> hide #!2.1 models
> show #!2.1 models
> volume #2.1 level 0.4753
> save /Users/wt296/Downloads/66bp_15TnsC.cxs
> save /Users/wt296/Downloads/66bp_15TnsC.cxs includeMaps true
——— End of log from Thu Feb 16 01:40:01 2023 ———
opened ChimeraX session
> open /Users/wt296/Downloads/66bp_DNAonlymodel_real_space_refined_002.pdb
Chain information for 66bp_DNAonlymodel_real_space_refined_002.pdb #4
---
Chain | Description
1 | No description available
3 | No description available
> hide #!1 models
> hide #!3 models
> ui tool show "Side View"
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2.1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> color #4.1 #44A7e3
> color #4/1 #44A7e3
> color #4/3 #5364ae
> select add #4
1804 atoms, 2022 bonds, 88 residues, 1 model selected
> cartoon style nucleic xsection oval width 2 thickness 2
> nucleotides ladder
> select subtract #4
Nothing selected
> show #!2.2 models
> hide #!2.2 models
> show #!2.1 models
> hide #4 models
> show #4 models
> hide #!2.1 models
> show #!1 models
> hide #4 models
> select #1/1,3
3217 atoms, 3606 bonds, 157 residues, 1 model selected
> hide sel target a
> cartoon hide sel
> hide #!1 models
> show #!1 models
> show #4 models
> select add #1
59483 atoms, 61245 bonds, 44 pseudobonds, 6784 residues, 4 models selected
> select subtract #1
Nothing selected
> select #4/1:13
22 atoms, 24 bonds, 1 residue, 1 model selected
> select add #4/1:12
42 atoms, 45 bonds, 2 residues, 1 model selected
> select add #4/1:11
63 atoms, 68 bonds, 3 residues, 1 model selected
> cartoon hide sel
> color sel byelement
> color sel #44A7e3
> color sel byelement
> color sel #44A7e3 target c
> color sel #44A7e3 target a
> color sel #44A7e3 target c
> color sel #44A7e3 target s
> color sel byhetero
> select add #4/1:12@OP1
1 atom, 1 bond, 1 residue, 2 models selected
> ui tool show Distances
Exactly two atoms must be selected!
> select #4/1:12@OP1
1 atom, 1 residue, 1 model selected
> select add #1/A:182@NH1
2 atoms, 2 residues, 2 models selected
> distance #4/1:12@OP1 #1/A:182@NH1
Distance between 66bp_DNAonlymodel_real_space_refined_002.pdb #4/1 DT 12 OP1
and 15TnsCmodel_J373-coot-chainA.pdb #1/A ARG 182 NH1: 3.323Å
> distance #4/1:12@OP1 #1/A:182@NH1
Distance already exists; modify distance properties with 'distance style'
> ~distance #1/B:103@NZ #1/3:138@OP1
> ~distance #1/F:121@OG1 #1/3:129@OP1
> ~distance #1/I:103@NZ #1/3:124@OP1
> ~distance #1/G:121@OG1 #1/3:127@OP1
> ~distance #1/F:103@NZ #1/3:130@OP1
> ~distance #1/C:121@OG1 #1/3:135@OP1
> ~distance #1/E:121@OG1 #1/3:131@OP1
> ~distance #1/D:182@NH2 #1/1:17@OP1
> ~distance #1/1:19@OP1 #1/E:182@NH2
> ~distance #1/U:103@NZ #1/3:113@OP1
> ~distance #1/1:21@OP2 #1/F:182@NH2
> ~distance #1/A:103@NZ #1/3:139@OP1
> ~distance #1/C:103@NZ #1/3:136@OP1
> ~distance #1/D:103@NZ #1/3:134@OP1
> ~distance #1/K:121@OG1 #1/3:120@OP1
> ~distance #1/3:125@OP1 #1/H:121@OG1
> ~distance #1/E:103@NZ #1/3:132@OP1
> ~distance #1/B:182@NH1 #1/1:14@OP1
> ~distance #1/A:182@NH1 #1/1:12@OP1
> ~distance #1/1:15@OP2 #1/C:182@NH2
> ~distance #1/3:116@OP1 #1/M:121@OG1
> ~distance #1/B:121@OG1 #1/3:137@OP1
> ~distance #1/G:103@NZ #1/3:128@OP1
> ~distance #1/H:103@NZ #1/3:126@OP1
> distance style color black
[Repeated 2 time(s)]
> show #!3 models
> distance style decimalPlaces 2
[Repeated 2 time(s)]
> distance style decimalPlaces 1
[Repeated 2 time(s)]
> distance style symbol false
[Repeated 2 time(s)]
> distance style symbol true
[Repeated 2 time(s)]
> distance style decimalPlaces 0
[Repeated 2 time(s)]
> distance style decimalPlaces -1
Invalid "decimalPlaces" argument: Must be greater than or equal to 0
> distance style decimalPlaces 0
> hide #3.1 models
> distance style dashes 8
[Repeated 2 time(s)]
> distance style dashes 7
[Repeated 2 time(s)]
> distance style dashes 6
[Repeated 2 time(s)]
> distance style dashes 5
[Repeated 2 time(s)]
> distance style dashes 4
[Repeated 2 time(s)]
> distance style dashes 3
[Repeated 2 time(s)]
> distance style dashes 2
[Repeated 2 time(s)]
> distance style dashes 1
[Repeated 2 time(s)]
> distance style dashes 0
[Repeated 2 time(s)]
> distance style dashes -1
Invalid "dashes" argument: Must be greater than or equal to 0
> distance style dashes 0
> distance style dashes 1
[Repeated 2 time(s)]
> distance style dashes 2
[Repeated 2 time(s)]
> distance style dashes 3
[Repeated 2 time(s)]
> distance style dashes 4
[Repeated 2 time(s)]
> distance style dashes 5
[Repeated 2 time(s)]
> select clear
> select #4/1:14
19 atoms, 20 bonds, 1 residue, 1 model selected
> select add #4/1:15
41 atoms, 44 bonds, 2 residues, 1 model selected
> select add #4/1:16
60 atoms, 64 bonds, 3 residues, 1 model selected
> select add #4/1:17
81 atoms, 87 bonds, 4 residues, 1 model selected
> cartoon hide sel
> color sel byhetero
> select #1/B:182@NH1
1 atom, 1 residue, 1 model selected
> select add #4/1:14@OP1
2 atoms, 2 residues, 2 models selected
> distance #1/B:182@NH1 #4/1:14@OP1
Distance between 15TnsCmodel_J373-coot-chainA.pdb #1/B ARG 182 NH1 and
66bp_DNAonlymodel_real_space_refined_002.pdb #4/1 DC 14 OP1: 4Å
> show #3.1 models
> hide #3.1 models
> show #3.1 models
> hide #3.1 models
> distance style color #0433ff
[Repeated 2 time(s)]
> distance style color black
[Repeated 2 time(s)]
> select add #4/3:147
21 atoms, 20 bonds, 3 residues, 2 models selected
> select #1/B:182@NH2
1 atom, 1 residue, 1 model selected
> select add #4/1:13@OP1
2 atoms, 2 residues, 2 models selected
> distance #1/B:182@NH2 #4/1:13@OP1
Distance between 15TnsCmodel_J373-coot-chainA.pdb #1/B ARG 182 NH2 and
66bp_DNAonlymodel_real_space_refined_002.pdb #4/1 DG 13 OP1: 4Å
> distance style color #0433ff
[Repeated 2 time(s)]
> distance style color black
[Repeated 2 time(s)]
> show #3.1 models
> hide #3.1 models
> select #1/C:182@NH2
1 atom, 1 residue, 1 model selected
> select add #4/1:15@OP2
2 atoms, 2 residues, 2 models selected
> distance #1/C:182@NH2 #4/1:15@OP2
Distance between 15TnsCmodel_J373-coot-chainA.pdb #1/C ARG 182 NH2 and
66bp_DNAonlymodel_real_space_refined_002.pdb #4/1 DG 15 OP2: 4Å
> show #3.1 models
> distance style decimalPlaces 1
[Repeated 2 time(s)]
> distance style decimalPlaces 2
[Repeated 2 time(s)]
> distance style decimalPlaces 3
[Repeated 2 time(s)]
> select #1/D:182@NH2
1 atom, 1 residue, 1 model selected
> select add #1/W:425
10 atoms, 8 bonds, 2 residues, 1 model selected
> select subtract #1/W:425
1 atom, 1 residue, 1 model selected
> select add #4/1:17@OP1
2 atoms, 2 residues, 2 models selected
> distance #1/D:182@NH2 #4/1:17@OP1
Distance between 15TnsCmodel_J373-coot-chainA.pdb #1/D ARG 182 NH2 and
66bp_DNAonlymodel_real_space_refined_002.pdb #4/1 DA 17 OP1: 5.329Å
> ~distance #1/C:182@NH2 #4/1:15@OP2
> ~distance #1/D:182@NH2 #4/1:17@OP1
> ~distance #1/B:182@NH2 #4/1:13@OP1
> select add #1/C:182@NH1
3 atoms, 3 residues, 2 models selected
> select add #4/1:16@OP1
4 atoms, 4 residues, 2 models selected
Exactly two atoms must be selected!
> select #4/1:16@OP1
1 atom, 1 residue, 1 model selected
> select add #1/C:182@NH1
2 atoms, 2 residues, 2 models selected
> distance #4/1:16@OP1 #1/C:182@NH1
Distance between 66bp_DNAonlymodel_real_space_refined_002.pdb #4/1 DC 16 OP1
and 15TnsCmodel_J373-coot-chainA.pdb #1/C ARG 182 NH1: 4.578Å
> ui tool show Distances
Traceback (most recent call last):
File
"/private/var/folders/fk/sy3ybnfx0ylcf2lsb3p9myzstb7rgs/T/AppTranslocation/159E4D5D-BA70-42B9-BD95-5DE23F9115D0/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/struct_measure/tool.py", line 626, in clear_status
if s.apc_status_label.text() == s.apc_status_tip:
RuntimeError: wrapped C/C++ object of type QLabel has been deleted
RuntimeError: wrapped C/C++ object of type QLabel has been deleted
File
"/private/var/folders/fk/sy3ybnfx0ylcf2lsb3p9myzstb7rgs/T/AppTranslocation/159E4D5D-BA70-42B9-BD95-5DE23F9115D0/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/struct_measure/tool.py", line 626, in clear_status
if s.apc_status_label.text() == s.apc_status_tip:
See log for complete Python traceback.
> ~distance #4/1:16@OP1 #1/C:182@NH1
> select clear
> select #1/C:182@NH2
1 atom, 1 residue, 1 model selected
> select add #4/1:15@OP2
2 atoms, 2 residues, 2 models selected
> distance #1/C:182@NH2 #4/1:15@OP2
Distance between 15TnsCmodel_J373-coot-chainA.pdb #1/C ARG 182 NH2 and
66bp_DNAonlymodel_real_space_refined_002.pdb #4/1 DG 15 OP2: 4.227Å
> distance style color #0433ff
[Repeated 2 time(s)]
> distance style color black
[Repeated 2 time(s)]
> hide #3.1 models
> select clear
> show #!2.2 models
> hide #!2 models
> show #!2 models
> hide #!2.2 models
> show #!2.1 models
> hide #!2.1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> select #1/A-C
6294 atoms, 6390 bonds, 2 pseudobonds, 777 residues, 2 models selected
> transparency 60% target C
Missing or invalid "percent" argument: Expected a number
> transparency 60 target C
Invalid "target" argument: Character 'C' is not an allowed target, must be one
of acrsbmpfl
> transparency 60 target c
> transparency 100 target c
> transparency 0 target c
> select transparency 60 target c
Expected an objects specifier or a keyword
> select #1/A-C transparency 60 target c
Expected a keyword
> transparency 60 target c #1/A-C
Expected a keyword
> transparency 60 target c
> transparency 0 target c
> select clear
> select #1/A-C
6294 atoms, 6390 bonds, 2 pseudobonds, 777 residues, 2 models selected
> transparency 60 target c sel
Expected a keyword
> set sel transparency 60 target c
Expected keyword "selectionColor" or "selectionWidth"
> select transparency 60 target c
Expected an objects specifier or a keyword
> transparency sel 60 target c
> transparency sel 70 target c
> transparency sel 40 target c
> transparency sel 50 target c
> select clear
> select #1/A-C
6294 atoms, 6390 bonds, 2 pseudobonds, 777 residues, 2 models selected
> transparency sel 60 target c
> select clear
> select #1/A-C
6294 atoms, 6390 bonds, 2 pseudobonds, 777 residues, 2 models selected
> transparency sel 70 target c
> select clear
> save /Users/wt296/Desktop/image19.png supersample 3
> select #1/A-C:182
33 atoms, 30 bonds, 3 residues, 1 model selected
> select #1/A,C:182
22 atoms, 20 bonds, 2 residues, 1 model selected
> color sel #A3C46A target a
> color sel byhetero
> select radius 1
Expected an objects specifier or a keyword
> size sel stickRadius 1
Changed 20 bond radii
> size sel stickRadius 0.5
Changed 20 bond radii
> select clear
> select #1/B:182
11 atoms, 10 bonds, 1 residue, 1 model selected
> color sel #65c18f target a
> color sel byhetero
> size sel stickRadius 0.5
Changed 10 bond radii
> select clear
> save /Users/wt296/Desktop/image20.png supersample 3
> select #1/A-C:121
21 atoms, 18 bonds, 3 residues, 1 model selected
> size sel stickRadius 0.5
Changed 18 bond radii
> select #1/A-C:101,119
39 atoms, 33 bonds, 6 residues, 1 model selected
> select #1/A-C:103,119
54 atoms, 48 bonds, 6 residues, 1 model selected
> hide sel target a
> select clear
> select #4/3:138
22 atoms, 24 bonds, 1 residue, 1 model selected
> select add #4/3:137
43 atoms, 47 bonds, 2 residues, 1 model selected
> select add #4/3:136
63 atoms, 68 bonds, 3 residues, 1 model selected
> select add #4/3:135
84 atoms, 91 bonds, 4 residues, 1 model selected
> select add #4/3:134
104 atoms, 112 bonds, 5 residues, 1 model selected
> cartoon hide sel
> color sel byhetero
> select clear
> select #4/3:139
21 atoms, 23 bonds, 1 residue, 1 model selected
> cartoon hide sel
> color sel byhetero
> select clear
> select #1/A:121@CG2
1 atom, 1 residue, 1 model selected
> select add #4/3:139@OP1
2 atoms, 2 residues, 2 models selected
> distance #1/A:121@CG2 #4/3:139@OP1
Distance between 15TnsCmodel_J373-coot-chainA.pdb #1/A THR 121 CG2 and
66bp_DNAonlymodel_real_space_refined_002.pdb #4/3 DA 139 OP1: 4.170Å
> show #3.1 models
> hide #3.1 models
> distance style color #0433ff
[Repeated 2 time(s)]
> distance style color black
[Repeated 2 time(s)]
> ui tool show Distances
> ~distance #1/A:121@CG2 #4/3:139@OP1
> select #1/B:121@OG1
1 atom, 1 residue, 1 model selected
> select add #4/3:137@OP1
2 atoms, 2 residues, 2 models selected
> distance #1/B:121@OG1 #4/3:137@OP1
Distance between 15TnsCmodel_J373-coot-chainA.pdb #1/B THR 121 OG1 and
66bp_DNAonlymodel_real_space_refined_002.pdb #4/3 DA 137 OP1: 2.343Å
> show #3.1 models
> hide #3.1 models
> distance style color #0433ff
[Repeated 2 time(s)]
> distance style color black
[Repeated 2 time(s)]
> select #1/C:121@OG1
1 atom, 1 residue, 1 model selected
> select add #4/3:135@OP1
2 atoms, 2 residues, 2 models selected
> distance #1/C:121@OG1 #4/3:135@OP1
Distance between 15TnsCmodel_J373-coot-chainA.pdb #1/C THR 121 OG1 and
66bp_DNAonlymodel_real_space_refined_002.pdb #4/3 DA 135 OP1: 2.408Å
> show #3.1 models
> hide #3.1 models
> distance style color #aa7942
[Repeated 2 time(s)]
> distance style color black
[Repeated 2 time(s)]
> show #!2.1 models
> hide #!2.1 models
> select clear
> select #1/D:121
7 atoms, 6 bonds, 1 residue, 1 model selected
> size sel stickRadius 0.5
Changed 6 bond radii
> select #1/D:103,119
18 atoms, 16 bonds, 2 residues, 1 model selected
> hide sel target a
> select clear
> select #1/D
2098 atoms, 2130 bonds, 259 residues, 1 model selected
> transparency sel 70 target c
> select clear
> select #4/3:133
21 atoms, 23 bonds, 1 residue, 1 model selected
> select add #4/3:132
41 atoms, 44 bonds, 2 residues, 1 model selected
> cartoon hide sel
> color sel byhetero
> select clear
> show #!2.1 models
> hide #!2.1 models
> show #!2.1 models
> hide #!2.1 models
> select clear
> select #1/D:121@CG2
1 atom, 1 residue, 1 model selected
> select add #4/3:133@OP1
2 atoms, 2 residues, 2 models selected
> distance #1/D:121@CG2 #4/3:133@OP1
Distance between 15TnsCmodel_J373-coot-chainA.pdb #1/D THR 121 CG2 and
66bp_DNAonlymodel_real_space_refined_002.pdb #4/3 DA 133 OP1: 5.055Å
> distance #1/D:121@CG2 #4/3:133@OP1
Distance already exists; modify distance properties with 'distance style'
> show #3.1 models
> hide #3.1 models
> select clear
> select #1/A,C:121
14 atoms, 12 bonds, 2 residues, 1 model selected
> color sel #A3C46A target a
> color sel byhetero
> select #1/B,D:121
14 atoms, 12 bonds, 2 residues, 1 model selected
> color sel #65c18f target a
> color sel byhetero
> select clear
> select #1/D-L
18882 atoms, 19170 bonds, 6 pseudobonds, 2331 residues, 2 models selected
> select #1/E-L
16784 atoms, 17040 bonds, 6 pseudobonds, 2072 residues, 2 models selected
> transparency sel 70 target c
> select #1/E-G:121
21 atoms, 18 bonds, 3 residues, 1 model selected
> size sel stickRadius 0.5
Changed 18 bond radii
> select #1/E-G:103,119
54 atoms, 48 bonds, 6 residues, 1 model selected
> hide sel target a
> select #1/E-G:182
33 atoms, 30 bonds, 3 residues, 1 model selected
> hide sel target a
> select #1/L:182
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel target a
> select clear
> select #1/K:182
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel target a
> select clear
> select #1/M:182
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel target a
> select clear
> select #4/3:131
21 atoms, 23 bonds, 1 residue, 1 model selected
> select add #4/3:130
41 atoms, 44 bonds, 2 residues, 1 model selected
> select add #4/3:129
62 atoms, 67 bonds, 3 residues, 1 model selected
> select add #4/3:128
82 atoms, 88 bonds, 4 residues, 1 model selected
> select add #4/3:127
103 atoms, 111 bonds, 5 residues, 1 model selected
> select add #4/3:126
123 atoms, 132 bonds, 6 residues, 1 model selected
> cartoon hide sel
> color sel byhetero
> select clear
> select #1/H:103,119
18 atoms, 16 bonds, 2 residues, 1 model selected
> hide sel target a
> select clear
> select #4/3:129@OP1
1 atom, 1 residue, 1 model selected
> select add #1/F:121@OG1
2 atoms, 2 residues, 2 models selected
> distance #4/3:129@OP1 #1/F:121@OG1
Distance between 66bp_DNAonlymodel_real_space_refined_002.pdb #4/3 DA 129 OP1
and 15TnsCmodel_J373-coot-chainA.pdb #1/F THR 121 OG1: 3.202Å
> show #3.1 models
> hide #3.1 models
> distance style color #0433ff
[Repeated 2 time(s)]
> distance style color black
[Repeated 2 time(s)]
> select #4/3:127@OP1
1 atom, 1 residue, 1 model selected
> select add #1/G:121@OG1
2 atoms, 2 residues, 2 models selected
> distance #4/3:127@OP1 #1/G:121@OG1
Distance between 66bp_DNAonlymodel_real_space_refined_002.pdb #4/3 DA 127 OP1
and 15TnsCmodel_J373-coot-chainA.pdb #1/G THR 121 OG1: 2.990Å
> show #3.1 models
> hide #3.1 models
> distance style color #aa7942
[Repeated 2 time(s)]
> distance style color black
[Repeated 2 time(s)]
> select #4/3:131@OP1
1 atom, 1 residue, 1 model selected
> select add #1/E:121@OG1
2 atoms, 2 residues, 2 models selected
> distance #4/3:131@OP1 #1/E:121@OG1
Distance between 66bp_DNAonlymodel_real_space_refined_002.pdb #4/3 DA 131 OP1
and 15TnsCmodel_J373-coot-chainA.pdb #1/E THR 121 OG1: 2.704Å
> show #3.1 models
> hide #3.1 models
> distance style color #0433ff
[Repeated 2 time(s)]
> distance style color black
[Repeated 2 time(s)]
> select clear
> save /Users/wt296/Desktop/image21.png supersample 3
> select #1/E,G:121
14 atoms, 12 bonds, 2 residues, 1 model selected
> color sel #A3C46A target a
> color sel byhetero
> select #1/F:121
7 atoms, 6 bonds, 1 residue, 1 model selected
> color sel #65c18f target a
> color sel byhetero
> select clear
> save /Users/wt296/Desktop/image22.png supersample 3
> show #3.1 models
> show #!2.2 models
> hide #!2.2 models
> show #!2.1 models
> hide #!2.1 models
> select #1/I:103,119
18 atoms, 16 bonds, 2 residues, 1 model selected
> select clear
> select #1/I:103,119
18 atoms, 16 bonds, 2 residues, 1 model selected
> hide sel target a
> select #1/J:103,119
18 atoms, 16 bonds, 2 residues, 1 model selected
> hide sel target a
> select clear
> select #1/N,U:182
22 atoms, 20 bonds, 2 residues, 1 model selected
> hide sel target a
> select clear
> select #1/K:103,119,182
29 atoms, 26 bonds, 3 residues, 1 model selected
> hide sel target a
> select #1/L:103,119,182
29 atoms, 26 bonds, 3 residues, 1 model selected
> hide sel target a
> select clear
> select #4/3:125
20 atoms, 21 bonds, 1 residue, 1 model selected
> select add #4/3:124
41 atoms, 44 bonds, 2 residues, 1 model selected
> select add #4/3:123
60 atoms, 64 bonds, 3 residues, 1 model selected
> select add #4/3:122
82 atoms, 88 bonds, 4 residues, 1 model selected
> select add #4/3:121
102 atoms, 109 bonds, 5 residues, 1 model selected
> cartoon hide sel
> color sel byhetero
> select clear
> select #1/H:121@OG1
1 atom, 1 residue, 1 model selected
> select add #4/3:125@OP1
2 atoms, 2 residues, 2 models selected
> distance #1/H:121@OG1 #4/3:125@OP1
Distance between 15TnsCmodel_J373-coot-chainA.pdb #1/H THR 121 OG1 and
66bp_DNAonlymodel_real_space_refined_002.pdb #4/3 DT 125 OP1: 5.407Å
> hide #3.1 models
> select add #4/3:120
22 atoms, 21 bonds, 3 residues, 2 models selected
> select add #4/3:119
42 atoms, 42 bonds, 4 residues, 2 models selected
> hide sel target ab
> show sel target ab
> cartoon hide sel
> color sel byhetero
> select clear
> select #1/K:121@OG1
1 atom, 1 residue, 1 model selected
> select add #4/3:120@OP1
2 atoms, 2 residues, 2 models selected
> distance #1/K:121@OG1 #4/3:120@OP1
Distance between 15TnsCmodel_J373-coot-chainA.pdb #1/K THR 121 OG1 and
66bp_DNAonlymodel_real_space_refined_002.pdb #4/3 DT 120 OP1: 4.186Å
> show #3.1 models
> hide #3.1 models
> select clear
> select #4/3:118
21 atoms, 23 bonds, 1 residue, 1 model selected
> select add #4/3:117
42 atoms, 46 bonds, 2 residues, 1 model selected
> cartoon hide sel
> color sel byhetero
> select clear
> select #1/M:103,119
18 atoms, 16 bonds, 2 residues, 1 model selected
> hide sel target a
> select clear
> select #4/3:116
19 atoms, 20 bonds, 1 residue, 1 model selected
> select add #4/3:115
39 atoms, 41 bonds, 2 residues, 1 model selected
> cartoon hide sel
> color sel byhetero
> select clear
> select #4/1:45
22 atoms, 24 bonds, 1 residue, 1 model selected
> select add #4/1:44
42 atoms, 45 bonds, 2 residues, 1 model selected
> hide sel target a
> show sel target ab
> cartoon hide sel
> color sel byhetero
> select clear
> select add #4/1:46
22 atoms, 24 bonds, 1 residue, 1 model selected
> select add #4/1:47
41 atoms, 44 bonds, 2 residues, 1 model selected
> cartoon hide sel
> color sel byhetero
> select clear
> select #1/N:103@NZ
1 atom, 1 residue, 1 model selected
> select add #4/1:46@OP1
2 atoms, 2 residues, 2 models selected
> distance #1/N:103@NZ #4/1:46@OP1
Distance between 15TnsCmodel_J373-coot-chainA.pdb #1/N LYS 103 NZ and
66bp_DNAonlymodel_real_space_refined_002.pdb #4/1 DG 46 OP1: 4.102Å
> show #3.1 models
> hide #3.1 models
> show #!2.2 models
> hide #!2.2 models
> show #!2.1 models
> hide #!1 models
> hide #!2.1 models
> select #4/3:114
19 atoms, 20 bonds, 1 residue, 1 model selected
> select add #4/3:113
40 atoms, 43 bonds, 2 residues, 1 model selected
> select add #4/3:112
59 atoms, 63 bonds, 3 residues, 1 model selected
> select add #4/3:111
78 atoms, 83 bonds, 4 residues, 1 model selected
> cartoon hide sel
> color sel byhetero
> select ~sel
61209 atoms, 63179 bonds, 32 pseudobonds, 6868 residues, 11 models selected
> select clear
> show #!2.1 models
> hide #!2.1 models
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> hide #4 models
> show #!2.1 models
> select #1/N:119
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
> select #1/N:119
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel target a
> select clear
> hide #!2.1 models
> show #4 models
> select #1/N:103@NZ
1 atom, 1 residue, 1 model selected
> select add #4/1:46@OP1
2 atoms, 2 residues, 2 models selected
> distance #1/N:103@NZ #4/1:46@OP1
Distance already exists; modify distance properties with 'distance style'
> select clear
> select #4/1:46@OP1
1 atom, 1 residue, 1 model selected
> select add #1/N:103@NZ
2 atoms, 2 residues, 2 models selected
> distance #4/1:46@OP1 #1/N:103@NZ
Distance already exists; modify distance properties with 'distance style'
> show #!3 models
> show #3.1 models
> select #4/3:115@OP2
1 atom, 1 residue, 1 model selected
> select add #1/N:103@NZ
2 atoms, 2 residues, 2 models selected
> distance #4/3:115@OP2 #1/N:103@NZ
Distance between 66bp_DNAonlymodel_real_space_refined_002.pdb #4/3 DT 115 OP2
and 15TnsCmodel_J373-coot-chainA.pdb #1/N LYS 103 NZ: 6.545Å
> select clear
> show #!2.1 models
> hide #3.1 models
> show #3.1 models
> hide #3.1 models
> hide #!2.1 models
> select #1/N:121@OG1
1 atom, 1 residue, 1 model selected
> select add #4/3:114@OP1
2 atoms, 2 residues, 2 models selected
> distance #1/N:121@OG1 #4/3:114@OP1
Distance between 15TnsCmodel_J373-coot-chainA.pdb #1/N THR 121 OG1 and
66bp_DNAonlymodel_real_space_refined_002.pdb #4/3 DC 114 OP1: 7.394Å
> show #3.1 models
> hide #3.1 models
> select clear
> show #3.1 models
> hide #3.1 models
> show #!2.1 models
> hide #!2.1 models
> select #1/N:150
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel target ab
> style sel stick
Changed 9 atom styles
> color sel byhetero
> show #!2.1 models
> hide #!2.1 models
> ui tool show "Side View"
> show #!2.1 models
> hide #!2.1 models
> select clear
> select #4/3:116@OP2
1 atom, 1 residue, 1 model selected
> select add #1/N:150@NZ
2 atoms, 2 residues, 2 models selected
> distance #4/3:116@OP2 #1/N:150@NZ
Distance between 66bp_DNAonlymodel_real_space_refined_002.pdb #4/3 DC 116 OP2
and 15TnsCmodel_J373-coot-chainA.pdb #1/N LYS 150 NZ: 2.341Å
> show #3.1 models
> ui tool show "Side View"
> show #!2.1 models
> save /Users/wt296/Downloads/66bp_15TnsC_1.cxs
——— End of log from Tue Feb 21 21:26:19 2023 ———
opened ChimeraX session
> hide #!2.1 models
> hide #3.1 models
> ui tool show "Side View"
> select #1/M:103
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel target ab
> color sel byhetero
> select clear
> select #1/M:103@NZ
1 atom, 1 residue, 1 model selected
> select add #4/1:44@OP2
2 atoms, 2 residues, 2 models selected
> ui tool show Distances
> distance #1/M:103@NZ #4/1:44@OP2
Distance between 15TnsCmodel_J373-coot-chainA.pdb #1/M LYS 103 NZ and
66bp_DNAonlymodel_real_space_refined_002.pdb #4/1 DT 44 OP2: 5.132Å
> show #3.1 models
> show #!2.2 models
> volume #2.1 level 0.4586
> hide #!2.2 models
> hide #!2.1 models
> select #4/1:43
22 atoms, 24 bonds, 1 residue, 1 model selected
> cartoon hide sel
> color sel byhetero
> select clear
> show #!2.1 models
> ui tool show "Side View"
> volume #2.1 level 0.2419
> hide #!2.1 models
> select #1/M:121
7 atoms, 6 bonds, 1 residue, 1 model selected
> ui tool show Rotamers
> swapaa interactive sel THR rotLib Dunbrack
15TnsCmodel_J373-coot-chainA.pdb #1/M THR 121: phi -85.0, psi 176.9 trans
Changed 12 bond radii
> volume #2.1 level 0.5503
> select clear
> select #1/M:119
9 atoms, 8 bonds, 1 residue, 1 model selected
> volume #2.1 level 0.592
> show sel target ab
> color sel byhetero
> hide sel target a
> select clear
> hide #!2.1 models
> show #!2.1 models
> select #1/M:150
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide #!2.1 models
> show sel target ab
> style sel stick
Changed 9 atom styles
> color sel byhetero
> show #!2.1 models
> select #1/M:150@NZ
1 atom, 1 residue, 1 model selected
> select add #4/3:118@OP2
2 atoms, 2 residues, 2 models selected
> distance #1/M:150@NZ #4/3:118@OP2
Distance between 15TnsCmodel_J373-coot-chainA.pdb #1/M LYS 150 NZ and
66bp_DNAonlymodel_real_space_refined_002.pdb #4/3 DA 118 OP2: 3.193Å
> hide #3.1 models
> distance style color #0433ff
> distance style color black
> hide #!3 models
> show #!3 models
> hide #!2.1 models
> view
Drag select of 136 atoms, 606 residues, 127 bonds, 4 pseudobonds, 66 shapes
> select clear
> ui mousemode right zoom
> select #1/U
2098 atoms, 2130 bonds, 1 pseudobond, 259 residues, 2 models selected
> cartoon hide (#!1 & sel)
> hide (#!1 & sel) target a
> select clear
> select #1/L:121
7 atoms, 6 bonds, 1 residue, 1 model selected
> hide #* target a
> show sel target ab
> hide sel target a
> select #1/M:150
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel target ab
> color sel byhetero
> select clear
> select #4/3:110
22 atoms, 24 bonds, 1 residue, 1 model selected
> show sel target ab
> select #4/3:111-118
159 atoms, 177 bonds, 8 residues, 1 model selected
> show sel target ab
> select clear
> select #4/3
898 atoms, 1005 bonds, 44 residues, 1 model selected
> show sel target ab
> select clear
> select #1/N:103
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel target ab
> color sel byhetero
> select clear
> select #1/N:121
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel target ab
> select #4/1
906 atoms, 1017 bonds, 44 residues, 1 model selected
> show sel target ab
> select clear
> select #1/N:103
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel target a
> show #!2.1 models
> hide #!2.1 models
> select #1/N:121
7 atoms, 6 bonds, 1 residue, 1 model selected
> hide sel target a
> select #1/N:150
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/N:150
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel target ab
> show #3.1 models
> hide #3.1 models
> show #3.1 models
> hide #3.1 models
> show #!2.1 models
> show #3.1 models
> hide #!3 models
> show #!3 models
> hide #!2.1 models
> select #1/N:182
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel target ab
> hide sel target a
> select #1/M,N
4196 atoms, 4260 bonds, 1 pseudobond, 518 residues, 2 models selected
> transparency sel 70 target c
> select clear
> select #1/M,N:150
18 atoms, 16 bonds, 2 residues, 1 model selected
> size sel stickRadius 0.5
Changed 16 bond radii
> select clear
> hide #3.1 models
> save /Users/wt296/Desktop/image23.png supersample 3
> view
Drag select of 184 residues
> select clear
> select #1/A:121
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel target ab
> swapaa interactive sel THR rotLib Dunbrack
15TnsCmodel_J373-coot-chainA.pdb #1/A THR 121: phi -114.7, psi 170.8 trans
Changed 12 bond radii
> show #!2.1 models
> swapaa #!1/A:121 THR criteria 2 rotLib Dunbrack retain false
Using Dunbrack library
15TnsCmodel_J373-coot-chainA.pdb #!1/A THR 121: phi -114.7, psi 170.8 trans
Applying THR rotamer (chi angles: -171.2) to 15TnsCmodel_J373-coot-chainA.pdb
#!1/A THR 121
> hide #!2.1 models
> select #4/3:139@OP1
1 atom, 1 residue, 1 model selected
> select add #1/A:121@OG1
2 atoms, 2 residues, 2 models selected
> distance #4/3:139@OP1 #1/A:121@OG1
Distance between 66bp_DNAonlymodel_real_space_refined_002.pdb #4/3 DA 139 OP1
and 15TnsCmodel_J373-coot-chainA.pdb #1/A THR 121 OG1: 2.300Å
> show #3.1 models
> hide #3.1 models
> hide sel target a
> select clear
> select #1/A:121@CA
1 atom, 1 residue, 1 model selected
> style sel stick
Changed 1 atom style
> show sel target ab
> style sel stick
Changed 1 atom style
> select #1/A:121
7 atoms, 6 bonds, 1 residue, 1 model selected
> cartoon sel
> style sel stick
Changed 7 atom styles
> style sel sphere
Changed 7 atom styles
> style sel ball
Changed 7 atom styles
> style sel stick
Changed 7 atom styles
> hide sel target a
> select #1/A:121
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel target ab
> style sel stick
Changed 7 atom styles
> style sel sphere
Changed 7 atom styles
> style sel stick
Changed 7 atom styles
> style sel ball
Changed 7 atom styles
> style sel ball
Changed 7 atom styles
> style sel stick
Changed 7 atom styles
> hide sel atoms
> show sel atoms
> select #1/A:121@OG1
1 atom, 1 residue, 1 model selected
> select add #4/3:139@OP2
2 atoms, 2 residues, 2 models selected
> distance #1/A:121@OG1 #4/3:139@OP2
Distance between 15TnsCmodel_J373-coot-chainA.pdb #1/A THR 121 OG1 and
66bp_DNAonlymodel_real_space_refined_002.pdb #4/3 DA 139 OP2: 4.211Å
> show #3.1 models
> hide #3.1 models
> select #1/A:121
7 atoms, 6 bonds, 1 residue, 1 model selected
> swapaa interactive sel THR rotLib Dunbrack
15TnsCmodel_J373-coot-chainA.pdb #1/A THR 121: phi -114.7, psi 170.8 trans
Changed 12 bond radii
> select #4/3:139@P
1 atom, 1 residue, 1 model selected
> select add #4/3:138@C3'
2 atoms, 2 residues, 1 model selected
> select add #4/3:139@C5'
3 atoms, 2 residues, 1 model selected
> hide sel target a
> show sel target ab
> select clear
> swapaa #!1/A:121 THR criteria 2 rotLib Dunbrack retain false
Using Dunbrack library
15TnsCmodel_J373-coot-chainA.pdb #!1/A THR 121: phi -114.7, psi 170.8 trans
Applying THR rotamer (chi angles: -171.2) to 15TnsCmodel_J373-coot-chainA.pdb
#!1/A THR 121
> select #4/3:139@P
1 atom, 1 residue, 1 model selected
> show sel target ab
> style sel stick
Changed 1 atom style
> style sel sphere
Changed 1 atom style
> style sel stick
Changed 1 atom style
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 INTEL-18.8.5
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 645
OpenGL vendor: Intel Inc.
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro15,4
Processor Name: Quad-Core Intel Core i5
Processor Speed: 1.4 GHz
Number of Processors: 1
Total Number of Cores: 4
L2 Cache (per Core): 256 KB
L3 Cache: 6 MB
Hyper-Threading Technology: Enabled
Memory: 8 GB
System Firmware Version: 1916.60.2.0.0 (iBridge: 20.16.2059.0.0,0)
OS Loader Version: 540.120.3~22
Software:
System Software Overview:
System Version: macOS 12.6.2 (21G320)
Kernel Version: Darwin 21.6.0
Time since boot: 35 days 19:41
Graphics/Displays:
Intel Iris Plus Graphics 645:
Chipset Model: Intel Iris Plus Graphics 645
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x3ea6
Revision ID: 0x0001
Metal Family: Supported, Metal GPUFamily macOS 2
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Framebuffer Depth: 24-Bit Color (ARGB8888)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.1.0
Babel: 2.11.0
backcall: 0.2.0
blockdiag: 3.0.0
build: 0.8.0
certifi: 2021.10.8
cftime: 1.6.2
charset-normalizer: 2.1.1
ChimeraX-AddCharge: 1.4
ChimeraX-AddH: 2.2.1
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2.1
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.6
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.41.5
ChimeraX-AtomicLibrary: 8.0.3
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3
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: 2.7.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.1
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.2
ChimeraX-CommandLine: 1.2.4
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.5
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.1
ChimeraX-DistMonitor: 1.3
ChimeraX-DockPrep: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.2
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 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: 1.1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.1
ChimeraX-MatchMaker: 2.0.9
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.8
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.6
ChimeraX-ModelPanel: 1.3.6
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.1
ChimeraX-MouseModes: 1.1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.9.1
ChimeraX-PDB: 2.6.8
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-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
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: 2.7.2
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
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.1.3
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.24.3
ChimeraX-uniprot: 2.2.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.1.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.1
ChimeraX-WebServices: 1.1.0
ChimeraX-Zone: 1.0.1
colorama: 0.4.5
cxservices: 1.2
cycler: 0.11.0
Cython: 0.29.32
debugpy: 1.6.4
decorator: 5.1.1
docutils: 0.19
entrypoints: 0.4
executing: 1.2.0
filelock: 3.7.1
fonttools: 4.38.0
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.7.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.33
imagecodecs: 2022.7.31
imagesize: 1.4.1
importlib-metadata: 5.1.0
ipykernel: 6.15.3
ipython: 8.4.0
ipython-genutils: 0.2.0
jedi: 0.18.1
Jinja2: 3.1.2
jupyter-client: 7.3.4
jupyter-core: 5.1.0
kiwisolver: 1.4.4
line-profiler: 3.5.1
lxml: 4.9.1
lz4: 4.0.2
MarkupSafe: 2.1.1
matplotlib: 3.5.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.0
networkx: 2.8.5
numexpr: 2.8.4
numpy: 1.23.1
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: 9.2.0
pip: 22.2.2
pkginfo: 1.8.3
platformdirs: 2.5.4
prompt-toolkit: 3.0.33
psutil: 5.9.1
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.12.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2022.6
pyzmq: 24.0.1
qtconsole: 5.3.1
QtPy: 2.3.0
RandomWords: 0.4.0
requests: 2.28.1
scipy: 1.9.0
setuptools: 65.1.1
setuptools-scm: 7.0.5
sfftk-rw: 0.7.2
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 5.1.1
sphinx-autodoc-typehints: 1.19.1
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
stack-data: 0.6.2
tables: 3.7.0
tifffile: 2022.7.31
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.2
traitlets: 5.3.0
typing-extensions: 4.4.0
urllib3: 1.26.13
wcwidth: 0.2.5
webcolors: 1.12
wheel: 0.37.1
wheel-filename: 1.4.1
zipp: 3.11.0
Change History (2)
comment:1 by , 3 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Core |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash in event loop |
comment:2 by , 3 years ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
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