![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 4 years ago
Closed 4 years ago
#6215 closed defect (can't reproduce)
Crash removing dock widget from main window
| Reported by: | Owned by: | pett | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | 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: 1.3 (2021-12-08 23:08:33 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Thread 0x000070000b3d9000 (most recent call first):
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 316 in wait
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 574 in wait
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 1284 in run
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x0000700012018000 (most recent call first):
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 316 in wait
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 574 in wait
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 1284 in run
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Current thread 0x000000010e7f5600 (most recent call first):
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 2285 in destroy
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 2156 in _destroy
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 787 in remove_tool
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 353 in remove_tool
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/tools.py", line 154 in delete
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/clashes/tool.py", line 54 in delete
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 301 in event_loop
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py", line 867 in init
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py", line 1018 in
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 197 in _run_module_as_main
{"app_name":"ChimeraX","timestamp":"2022-02-20 14:07:36.00 -0700","app_version":"1.3.0","slice_uuid":"9596eff5-d2be-396c-9c4e-6177235c3dae","build_version":"1.3.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":1,"is_first_party":0,"bug_type":"309","os_version":"macOS 12.1 (21C52)","incident_id":"6695A772-4A4F-4EE3-B59C-932F81053B28","name":"ChimeraX"}
{
"uptime" : 83000,
"procLaunch" : "2022-02-18 20:31:15.1589 -0700",
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookAir7,2",
"procStartAbsTime" : 67543257037123,
"coalitionID" : 5859,
"osVersion" : {
"train" : "macOS 12.1",
"build" : "21C52",
"releaseType" : "User"
},
"captureTime" : "2022-02-20 14:07:04.3925 -0700",
"incident" : "6695A772-4A4F-4EE3-B59C-932F81053B28",
"bug_type" : "309",
"pid" : 7792,
"procExitAbsTime" : 83154714503415,
"cpuType" : "X86-64",
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.3.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.3.0","CFBundleVersion":"1.3.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"104AC23F-3B17-56FF-AE17-DE90ED949486","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "85F5B6DD-6558-277E-C538-DC6AB21E3954",
"wakeTime" : 3898,
"sleepWakeUUID" : "21ACCFBD-61CD-458F-8381-A95888C439F2",
"sip" : "enabled",
"vmRegionInfo" : "0x46688285bc88 is not in any region. Bytes after previous region: 77408902126729 Bytes before following region: 28138435920760\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n VM_ALLOCATE 1583be000-15868a000 [ 2864K] rw-\/rwx SM=PRV \n---> GAP OF 0x5ffea7976000 BYTES\n MALLOC_NANO 600000000000-600008000000 [128.0M] rw-\/rwx SM=PRV ",
"isCorpse" : 1,
"exception" : {"codes":"0x0000000000000001, 0x000046688285bc88","rawCodes":[1,77414680345736],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x000046688285bc88"},
"ktriageinfo" : "VM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\n",
"vmregioninfo" : "0x46688285bc88 is not in any region. Bytes after previous region: 77408902126729 Bytes before following region: 28138435920760\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n VM_ALLOCATE 1583be000-15868a000 [ 2864K] rw-\/rwx SM=PRV \n---> GAP OF 0x5ffea7976000 BYTES\n MALLOC_NANO 600000000000-600008000000 [128.0M] rw-\/rwx SM=PRV ",
"extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
"faultingThread" : 0,
"threads" : 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"name" : "HIToolbox"
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"size" : 15265792,
"uuid" : "d23b9681-3764-3298-a716-fbb511dd5a7c",
"path" : "\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit",
"name" : "AppKit",
"CFBundleVersion" : "2113.20.111"
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"size" : 4096,
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"path" : "\/usr\/lib\/dyld",
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"size" : 131002368,
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"path" : "\/Applications\/ChimeraX-1.3.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/PyQt5\/Qt\/lib\/QtWebEngineCore.framework\/Versions\/5\/QtWebEngineCore",
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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=1.5G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=1.5G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 512K 4 \nActivity Tracing 256K 1 \nCG backing stores 544K 4 \nCG image 440K 56 \nColorSync 244K 29 \nCoreAnimation 1744K 127 \nCoreGraphics 12K 2 \nCoreUI image data 2180K 39 \nFoundation 36K 2 \nKernel Alloc Once 8K 1 \nMALLOC 1.0G 1839 \nMALLOC guard page 32K 8 \nMALLOC_LARGE (reserved) 384K 1 reserved VM address space (unallocated)\nMALLOC_NANO (reserved) 128.0M 1 reserved VM address space (unallocated)\nMach message 24K 4 \nOpenGL GLSL 384K 5 \nSTACK GUARD 88K 22 \nStack 170.2M 23 \nStack Guard 56.0M 1 \nVM_ALLOCATE 116.5M 216 \n__DATA 41.4M 667 \n__DATA_CONST 30.5M 343 \n__DATA_DIRTY 1641K 219 \n__FONT_DATA 4K 1 \n__GLSLBUILTINS 5176K 1 \n__LINKEDIT 732.5M 140 \n__OBJC_RO 81.8M 1 \n__OBJC_RW 3136K 2 \n__TEXT 728.8M 665 \n__UNICODE 588K 1 \ndyld private memory 1024K 1 \nmapped file 562.2M 75 \nshared memory 2972K 25 \n=========== ======= ======= \nTOTAL 3.7G 4526 \nTOTAL, minus reserved VM space 3.5G 4526 \n",
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{
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}
}
===== Log before crash start =====
UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/Cailin/Desktop/agonist_1.pdb
Chain information for agonist_1.pdb #1
---
Chain | Description
B | No description available
> hide #1.1 models
> show #1.1 models
> hide #1.1 models
> hbonds reveal true
241 hydrogen bonds found
Alignment identifier is 1/B
> label #1.2#!1 atoms
> label #1.2-3#!1 atoms attribute bfactor
> hide #1.3 models
Drag select of 1 residues
> hide #1.2 models
Drag select of 3 atoms, 6 bonds
> select /B:285
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /B:4@CE2
1 atom, 1 residue, 1 model selected
> select clear
Drag select of 2 bonds
> select clear
> select /B:4@CE3
1 atom, 1 residue, 1 model selected
Drag select of 1 residues, 1 bonds
> select /B:285
6 atoms, 5 bonds, 1 residue, 1 model selected
Drag select of 15 atoms, 4 residues, 14 bonds
> select /B:449
10 atoms, 10 bonds, 1 residue, 1 model selected
Drag select of 11 atoms, 2 residues, 14 bonds
Drag select of 5 atoms, 7 bonds
> select clear
Drag select of 1 bonds
Drag select of 2 bonds
> select clear
Drag select of 10 atoms, 1 residues, 13 bonds
> ui mousemode right select
> select clear
Drag select of 3 atoms, 2 bonds
> ui mousemode right select
> preset "molecular surfaces" "chain id coloring (opaque)"
Changed 0 atom styles
Preset expands to these ChimeraX commands:
style (protein|nucleic|solvent) & @@draw_mode=0 stick
surface
color bychain targ s trans 0
> undo
> hide #1.4 models
> ~select #1.4
2 atoms, 2 bonds, 1 residue, 2 models selected
> ui tool show "Color Actions"
> color sel bypolymer
> interfaces select & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
> select clear
> interfaces ~solvent
0 buried areas:
> coulombic
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for agonist_1.pdb_B SES surface #1.4: minimum, -17.89, mean
-1.45, maximum 12.60
To also show corresponding color key, enter the above coulombic command and
add key true
> transparency #1.4#!1 40
> transparency #1.4#!1 10
> transparency #1.4#!1 60
> interfaces ~solvent
0 buried areas:
> hide #1.4 models
> mlp
Map values for surface "agonist_1.pdb_B SES surface": minimum -27.25, mean
-3.469, maximum 22.53
To also show corresponding color key, enter the above mlp command and add key
true
> select /B:271@NE2
1 atom, 1 residue, 1 model selected
> select /B:271@NE2
1 atom, 1 residue, 1 model selected
> open /Users/Cailin/Desktop/agonist_2.pdb
Chain information for agonist_2.pdb #2
---
Chain | Description
A | No description available
B | No description available
> open /Users/Cailin/Desktop/antagonist.pdb
Chain information for antagonist.pdb #3
---
Chain | Description
A | No description available
D | No description available
> hide #!3 models
> hide #1.4 models
> hide #!1 models
> select add #2/B:3@C12
2 atoms, 3 bonds, 2 residues, 3 models selected
> select add #2/B:3@C15
3 atoms, 5 bonds, 2 residues, 3 models selected
> select add #2/B:3@C10
4 atoms, 6 bonds, 2 residues, 3 models selected
Drag select of 1 atoms
Drag select of 2 atoms, 2 residues
> select subtract #2/B:288
26 atoms, 24 bonds, 4 residues, 3 models selected
> color (#!2 & sel) hot pink
> undo
> select subtract #2/B:368
15 atoms, 25 bonds, 3 residues, 3 models selected
> select subtract #2/B:369
6 atoms, 24 bonds, 2 residues, 3 models selected
> color (#!2 & sel) purple
> select add #2/B:3@C4
1 atom, 2 bonds, 1 residue, 1 model selected
> color sel purple
> select #2/B:3@C17
1 atom, 1 residue, 1 model selected
> color sel purple
> undo
> select #2/B:3@C11
1 atom, 1 residue, 1 model selected
> select #2/B:3@C13
1 atom, 1 residue, 1 model selected
> select #2/B:3@C14
1 atom, 1 residue, 1 model selected
> select #2/B:3@C13
1 atom, 1 residue, 1 model selected
> select add #2/B:3@C14
2 atoms, 7 bonds, 1 residue, 1 model selected
> select add #2/B:3@C15
3 atoms, 7 bonds, 1 residue, 1 model selected
> select add #2/B:3@C12
4 atoms, 7 bonds, 1 residue, 1 model selected
> select add #2/B:3@C11
5 atoms, 7 bonds, 1 residue, 1 model selected
Drag select of 1 atoms, 1 residues, 1 bonds
> select subtract #2/A:350
6 atoms, 13 bonds, 1 residue, 1 model selected
> color: sti & C salmon
Unknown command: color: sti & C salmon
Drag select of 1 atoms, 3 residues, 1 bonds
> ui mousemode right translate
Drag select of 1 atoms, 1 residues
> ui mousemode right select
> ui mousemode right rotate
> ui mousemode right translate
> select #2/B:259
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/B:259
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/A:352
11 atoms, 11 bonds, 1 residue, 1 model selected
Drag select of 4 residues, 1 bonds
> ui mousemode right translate
> ui mousemode right rotate
> ui mousemode right translate
> ui mousemode right rotate
> select clear
> hbonds #!2 reveal true
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: agonist_2.pdb #2/A PRO 206 N; antagonist.pdb #3/A PRO 206 N;
antagonist.pdb #3/D ARG 357 NE
2267 hydrogen bonds found
Destroying pre-existing alignment with identifier 1/B
Alignment identifier is 1/B
Alignment identifier is 2/A
Alignment identifier is 2/B
Alignment identifier is 3/A
Alignment identifier is 3/D
> select #2/B:247-249,338-341,346-349
83 atoms, 82 bonds, 7 pseudobonds, 11 residues, 2 models selected
> select
> #2/B:208-225,230-238,252-263,277-302,306-308,311-333,350-354,360-362,365-377,381-392,403-424,431-457,467-472
1443 atoms, 1451 bonds, 161 pseudobonds, 179 residues, 2 models selected
> select #3/A:247-249,338-341,346-349
83 atoms, 82 bonds, 11 residues, 1 model selected
> select #3/D:449-475
152 atoms, 153 bonds, 1 pseudobond, 22 residues, 2 models selected
> select #3/D:449-475
152 atoms, 153 bonds, 1 pseudobond, 22 residues, 2 models selected
> color #!2 bynucleotide
> label #2,4 text "/{0.chain_id} {0.name} {0.number}{0.insertion_code}"
> undo
> label #2,4 attribute name
Drag select of 5 residues, 1 bonds
> ui mousemode right select
> ui mousemode right rotate
> ~label sel residues
> hide #2.2 models
> show #2.2 models
> hide #2.2 models
> show #2.2 models
> hide #2.2 models
> show #2.2 models
> hide #2.2 models
> hide (sel-residues & (protein|nucleic)) target ab
> cartoon hide sel-residues
> show (sel-residues & ((protein&@ca)|(nucleic&@p))) target ab
> undo
> hide #3.1 models
> style sel stick
Changed 43 atom styles
> label sel attribute label_specifier
No visible Surface models selected
> ui mousemode right select
> select #2/B:3@C11
1 atom, 1 residue, 1 model selected
> select clear
> ui mousemode right select
> ui mousemode right rotate
> show (#4#2.1#!2 & sidechain) target ab
> coulombic #!2
The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:
agonist_2.pdb #2/A GLN 203
agonist_2.pdb #2/A LEU 204
agonist_2.pdb #2/A ASN 205
agonist_2.pdb #2/A PRO 206
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for agonist_2.pdb_A SES surface #2.4: minimum, -18.03, mean
-2.09, maximum 13.21
Coulombic values for agonist_2.pdb_B SES surface #2.5: minimum, -20.97, mean
-1.16, maximum 11.06
To also show corresponding color key, enter the above coulombic command and
add key true
> hide #2.3 models
> show #2.3 models
> hide #2.5 models
> show #2.5 models
> hide #2.4 models
> show #2.4 models
> hide #2.4 models
> hide #2.3 models
> show #2.3 models
> hide #2.5 models
> hide #!2 models
> show #!3 models
> coulombic #!3
The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:
antagonist.pdb #3/A ASN 205
antagonist.pdb #3/A PRO 206
antagonist.pdb #3/A GLU 207
antagonist.pdb #3/A THR 242
antagonist.pdb #3/A GLU 259
antagonist.pdb #3/A ILE 262
antagonist.pdb #3/A LYS 263
antagonist.pdb #3/A SER 274
antagonist.pdb #3/A LYS 275
antagonist.pdb #3/A GLN 283
antagonist.pdb #3/A LYS 358
antagonist.pdb #3/A SER 428
antagonist.pdb #3/A GLN 430
antagonist.pdb #3/A LYS 434
antagonist.pdb #3/A GLN 444
antagonist.pdb #3/A LEU 452
antagonist.pdb #3/A LYS 474
antagonist.pdb #3/D SER 208
antagonist.pdb #3/D ARG 212
antagonist.pdb #3/D LYS 240
antagonist.pdb #3/D THR 242
antagonist.pdb #3/D LYS 263
antagonist.pdb #3/D THR 268
antagonist.pdb #3/D LYS 275
antagonist.pdb #3/D VAL 277
antagonist.pdb #3/D ARG 357
antagonist.pdb #3/D LYS 358
antagonist.pdb #3/D LYS 422
antagonist.pdb #3/D GLU 427
antagonist.pdb #3/D SER 429
antagonist.pdb #3/D GLN 430
antagonist.pdb #3/D THR 447
antagonist.pdb #3/D GLU 448
antagonist.pdb #3/D GLN 451
antagonist.pdb #3/D LEU 452
antagonist.pdb #3/D VAL 455
antagonist.pdb #3/D LYS 457
antagonist.pdb #3/D LYS 458
antagonist.pdb #3/D GLU 460
antagonist.pdb #3/D HIS 466
antagonist.pdb #3/D GLN 470
antagonist.pdb #3/D LYS 474
antagonist.pdb #3/D ASP 475
Using Amber 20 recommended default charges and atom types for standard
residues
Assigning partial charges to residue HIS (net charge -4) with am1-bcc method
Running ANTECHAMBER command:
/Applications/ChimeraX-1.3.app/Contents/bin/amber20/bin/antechamber -ek
qm_theory='AM1', -i
/var/folders/k9/52yp04c17k11ykf6bljvnrd40000gn/T/tmp_sjlghjp/ante.in.mol2 -fi
mol2 -o
/var/folders/k9/52yp04c17k11ykf6bljvnrd40000gn/T/tmp_sjlghjp/ante.out.mol2 -fo
mol2 -c bcc -nc -4 -j 5 -s 2 -dr n
(HIS) ``
(HIS) `Welcome to antechamber 20.0: molecular input file processor.`
(HIS) ``
(HIS) `Info: Finished reading file
(/var/folders/k9/52yp04c17k11ykf6bljvnrd40000gn/T/tmp_sjlghjp/ante.in.mol2);
atoms read (16), bonds read (15).`
(HIS) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(HIS) `Running:
/Applications/ChimeraX-1.3.app/Contents/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`
(HIS) ``
(HIS) ``
(HIS) `Running:
/Applications/ChimeraX-1.3.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`
(HIS) `Info: Total number of electrons: 64; net charge: -4`
(HIS) ``
(HIS) `Running: /Applications/ChimeraX-1.3.app/Contents/bin/amber20/bin/sqm -O
-i sqm.in -o sqm.out`
(HIS) `/Applications/ChimeraX-1.3.app/Contents/bin/amber20/bin/antechamber:
Fatal Error!`
(HIS) `Cannot properly run
"/Applications/ChimeraX-1.3.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o
sqm.out".`
Failure running ANTECHAMBER for residue HIS Check reply log for details
> ui mousemode right select
Drag select of 1 atoms, 1 residues
> select #3/D:340
8 atoms, 7 bonds, 1 residue, 1 model selected
> select subtract #3/D:340
1 bond, 1 model selected
> select add #3/D:501@C05
1 atom, 2 bonds, 1 residue, 1 model selected
> select subtract #3/D:501@C05
2 bonds, 1 model selected
> select add #3/D:501@C08
1 atom, 5 bonds, 1 residue, 1 model selected
> select add #3/D:501@C02
2 atoms, 9 bonds, 1 residue, 1 model selected
> select add #3/D:501@C03
3 atoms, 9 bonds, 1 residue, 1 model selected
> select add #3/D:501@C33
4 atoms, 17 bonds, 1 residue, 1 model selected
> select add #3/D:501@C34
5 atoms, 18 bonds, 1 residue, 1 model selected
> color sel red
> undo
> color sel lime
> select add #3/D:501@C20
6 atoms, 22 bonds, 1 residue, 1 model selected
> select add #3/D:501@C24
7 atoms, 22 bonds, 1 residue, 1 model selected
> select add #3/D:501@C22
8 atoms, 23 bonds, 1 residue, 1 model selected
> select add #3/D:501@C23
9 atoms, 24 bonds, 1 residue, 1 model selected
> color (#!3 & sel) cyan
> select add #3/D:501@C19
10 atoms, 33 bonds, 2 pseudobonds, 1 residue, 2 models selected
> select add #3/D:501@C05
11 atoms, 35 bonds, 2 pseudobonds, 1 residue, 2 models selected
> select add #3/D:501@C04
12 atoms, 35 bonds, 2 pseudobonds, 1 residue, 2 models selected
> color (#!3 & sel) cyan
> select add #3/D:501@C26
13 atoms, 36 bonds, 2 pseudobonds, 1 residue, 2 models selected
> select subtract #3/D:501@C26
12 atoms, 36 bonds, 2 pseudobonds, 1 residue, 2 models selected
> select add #3/D:501@C27
13 atoms, 36 bonds, 2 pseudobonds, 1 residue, 2 models selected
> select add #3/D:281
21 atoms, 43 bonds, 2 pseudobonds, 2 residues, 2 models selected
> select subtract #3/D:281@CG2
20 atoms, 41 bonds, 3 pseudobonds, 2 residues, 2 models selected
> select subtract #3/D:281@CG1
19 atoms, 39 bonds, 3 pseudobonds, 2 residues, 2 models selected
> select subtract #3/D:281@CB
18 atoms, 39 bonds, 3 pseudobonds, 2 residues, 2 models selected
> select subtract #3/D:281
13 atoms, 36 bonds, 4 pseudobonds, 1 residue, 2 models selected
> select add #3/D:501@C25
14 atoms, 37 bonds, 4 pseudobonds, 1 residue, 2 models selected
> select add #3/D:501@C13
15 atoms, 37 bonds, 4 pseudobonds, 1 residue, 2 models selected
> color (#!3 & sel) cyan
> select add #3/D:501@C12
16 atoms, 37 bonds, 4 pseudobonds, 1 residue, 2 models selected
> color (#!3 & sel) cyan
> select add #3/D:501@C26
17 atoms, 37 bonds, 4 pseudobonds, 1 residue, 2 models selected
> select subtract #3/D:501@C26
16 atoms, 37 bonds, 4 pseudobonds, 1 residue, 2 models selected
> select add #3/D:501@C01
17 atoms, 38 bonds, 4 pseudobonds, 1 residue, 2 models selected
> color (#!3 & sel) cyan
> select add #3/D:501@C06
18 atoms, 38 bonds, 4 pseudobonds, 1 residue, 2 models selected
> select add #3/D:501@C10
19 atoms, 38 bonds, 4 pseudobonds, 1 residue, 2 models selected
> color (#!3 & sel) cyan
> select add #3/D:501@C09
20 atoms, 39 bonds, 4 pseudobonds, 1 residue, 2 models selected
> color (#!3 & sel) cyan
> select add #3/D:501@C11
21 atoms, 39 bonds, 4 pseudobonds, 1 residue, 2 models selected
> select add #3/D:501@C14
22 atoms, 40 bonds, 4 pseudobonds, 1 residue, 2 models selected
> color (#!3 & sel) cyan
> select add #3/D:501@C21
23 atoms, 39 bonds, 4 pseudobonds, 1 residue, 2 models selected
> color (#!3 & sel) cyan
> select add #3/D:501@C17
24 atoms, 41 bonds, 4 pseudobonds, 1 residue, 2 models selected
> select add #3/D:501@C18
25 atoms, 41 bonds, 4 pseudobonds, 1 residue, 2 models selected
> select add #3/D:501@C31
26 atoms, 41 bonds, 4 pseudobonds, 1 residue, 2 models selected
> select subtract #3/D:501@C31
25 atoms, 41 bonds, 4 pseudobonds, 1 residue, 2 models selected
> select add #3/D:501@C32
26 atoms, 41 bonds, 4 pseudobonds, 1 residue, 2 models selected
> color (#!3 & sel) cyan
> select add #3/D:501@C31
27 atoms, 41 bonds, 4 pseudobonds, 1 residue, 2 models selected
> select add #3/D:501@C35
28 atoms, 41 bonds, 4 pseudobonds, 1 residue, 2 models selected
> select subtract #3/D:501@C35
27 atoms, 41 bonds, 4 pseudobonds, 1 residue, 2 models selected
> color (#!3 & sel) cyan
> select add #3/D:501@C35
28 atoms, 41 bonds, 4 pseudobonds, 1 residue, 2 models selected
> color (#!3 & sel) cyan
> select add #3/D:501@C26
29 atoms, 41 bonds, 4 pseudobonds, 1 residue, 2 models selected
> select subtract #3/D:501@C25
28 atoms, 40 bonds, 4 pseudobonds, 1 residue, 2 models selected
> select add #3/D:501@C25
29 atoms, 40 bonds, 4 pseudobonds, 1 residue, 2 models selected
> select add #3/D:501@C39
30 atoms, 39 bonds, 4 pseudobonds, 1 residue, 2 models selected
> select subtract #3/D:501@C39
29 atoms, 40 bonds, 4 pseudobonds, 1 residue, 2 models selected
> select add #3/D:501@C28
30 atoms, 40 bonds, 4 pseudobonds, 1 residue, 2 models selected
> select add #3/D:501@C29
31 atoms, 40 bonds, 4 pseudobonds, 1 residue, 2 models selected
> color (#!3 & sel) cyan
> select add #3/D:501@C30
32 atoms, 40 bonds, 4 pseudobonds, 1 residue, 2 models selected
> color (#!3 & sel) cyan
> select add #3/D:501@C39
33 atoms, 40 bonds, 4 pseudobonds, 1 residue, 2 models selected
> color (#!3 & sel) cyan
> hide #4 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> select clear
> select add #2/B:3@C13
1 atom, 1 bond, 1 residue, 1 model selected
> select add #2/B:3@C14
2 atoms, 3 bonds, 1 residue, 1 model selected
> color sel purple
> select add #2/B:3@C11
3 atoms, 5 bonds, 1 residue, 1 model selected
> select add #2/B:3@C9
4 atoms, 6 bonds, 1 residue, 1 model selected
> color sel purple
> select add #2/B:3@C8
5 atoms, 9 bonds, 1 residue, 1 model selected
> select add #2/B:3@C16
6 atoms, 10 bonds, 1 residue, 1 model selected
> select add #2/B:3@C7
7 atoms, 12 bonds, 1 residue, 1 model selected
> select add #2/B:3@C17
8 atoms, 13 bonds, 1 residue, 1 model selected
> select add #2/B:3@C18
9 atoms, 14 bonds, 1 residue, 1 model selected
> select add #2/B:3@C2
10 atoms, 20 bonds, 1 residue, 1 model selected
> select add #2/B:3@C5
11 atoms, 21 bonds, 1 residue, 1 model selected
> select add #2/B:442
19 atoms, 29 bonds, 2 residues, 1 model selected
> select subtract #2/B:442
11 atoms, 22 bonds, 1 residue, 1 model selected
> color sel purple
> select add #2/B:3@C1
12 atoms, 22 bonds, 1 residue, 1 model selected
> select subtract #2/B:3@C1
11 atoms, 22 bonds, 1 residue, 1 model selected
> color sel purple
> select add #2/B:3@C4
12 atoms, 24 bonds, 1 residue, 1 model selected
> select add #2/B:3@C1
13 atoms, 24 bonds, 1 residue, 1 model selected
> select add #2/B:3@C6
14 atoms, 25 bonds, 1 residue, 1 model selected
> color sel purple
> select add #2/B:3@C3
15 atoms, 25 bonds, 1 residue, 1 model selected
> select subtract #2/B:3@C3
14 atoms, 25 bonds, 1 residue, 1 model selected
> color sel purple
> select add #2/B:3@C3
15 atoms, 25 bonds, 1 residue, 1 model selected
> select subtract #2/B:3@C3
14 atoms, 25 bonds, 1 residue, 1 model selected
> select add #2/B:3@C3
15 atoms, 25 bonds, 1 residue, 1 model selected
> select subtract #2/B:3@C3
14 atoms, 25 bonds, 1 residue, 1 model selected
> color sel purple
> select subtract #2/B:3@C2
13 atoms, 25 bonds, 1 residue, 1 model selected
> select add #2/B:3@C2
14 atoms, 25 bonds, 1 residue, 1 model selected
> select subtract #2/B:3@C4
13 atoms, 25 bonds, 1 residue, 1 model selected
> select add #2/B:3@C4
14 atoms, 25 bonds, 1 residue, 1 model selected
> select add #2/B:3@C3
15 atoms, 25 bonds, 1 residue, 1 model selected
> color sel purple
> select ~sel
10599 atoms, 10498 bonds, 2280 pseudobonds, 1563 residues, 10 models selected
> select subtract #2/B:3@N
10598 atoms, 10498 bonds, 2280 pseudobonds, 1563 residues, 13 models selected
> select subtract #2/B:3@C
10597 atoms, 10497 bonds, 2280 pseudobonds, 1563 residues, 13 models selected
> select subtract #2/B:3@C10
10596 atoms, 10496 bonds, 2280 pseudobonds, 1563 residues, 13 models selected
> select subtract #2/B:3@C15
10595 atoms, 10496 bonds, 2280 pseudobonds, 1563 residues, 13 models selected
> select subtract #2/B:3@C12
10594 atoms, 10496 bonds, 2280 pseudobonds, 1563 residues, 13 models selected
> select add #2/B:3@C12
10595 atoms, 10496 bonds, 2280 pseudobonds, 1563 residues, 13 models selected
> select subtract #2/B:3@C12
10594 atoms, 10496 bonds, 2280 pseudobonds, 1563 residues, 13 models selected
> select subtract #2/B:3@CL
10593 atoms, 10497 bonds, 2280 pseudobonds, 1563 residues, 13 models selected
> select add #2/B:3@C12
10594 atoms, 10500 bonds, 2280 pseudobonds, 1563 residues, 13 models selected
> select subtract #2/B:441
10586 atoms, 10493 bonds, 2280 pseudobonds, 1562 residues, 13 models selected
> select add #2/B:441
10594 atoms, 10500 bonds, 2280 pseudobonds, 1563 residues, 13 models selected
> select add #2/B:3@C11
10595 atoms, 10501 bonds, 2280 pseudobonds, 1563 residues, 13 models selected
> select add #2/B:3@C14
10596 atoms, 10503 bonds, 2280 pseudobonds, 1563 residues, 13 models selected
> select add #2/B:3@C15
10597 atoms, 10503 bonds, 2280 pseudobonds, 1563 residues, 13 models selected
> select subtract #2/B:3@C15
10596 atoms, 10503 bonds, 2280 pseudobonds, 1563 residues, 13 models selected
> select add #2/B:3@C15
10597 atoms, 10503 bonds, 2280 pseudobonds, 1563 residues, 13 models selected
> select subtract #2/B:3@O1
10596 atoms, 10504 bonds, 2280 pseudobonds, 1563 residues, 13 models selected
> select add #2/B:3@C8
10597 atoms, 10511 bonds, 2280 pseudobonds, 1563 residues, 13 models selected
> select add #2/B:3@C16
10598 atoms, 10514 bonds, 2280 pseudobonds, 1563 residues, 13 models selected
> select subtract #2/B:3@O3
10597 atoms, 10515 bonds, 2280 pseudobonds, 1563 residues, 13 models selected
> select add #2/B:3@C18
10598 atoms, 10515 bonds, 2280 pseudobonds, 1563 residues, 13 models selected
> select subtract #2/B:3@C18
10597 atoms, 10516 bonds, 2280 pseudobonds, 1563 residues, 13 models selected
> select add #2/B:3@C6
10598 atoms, 10515 bonds, 2280 pseudobonds, 1563 residues, 13 models selected
> select subtract #2/B:3@C6
10597 atoms, 10515 bonds, 2280 pseudobonds, 1563 residues, 13 models selected
> select add #2/B:3@C18
10598 atoms, 10516 bonds, 2280 pseudobonds, 1563 residues, 13 models selected
> select subtract #2/B:3@C18
10597 atoms, 10516 bonds, 2280 pseudobonds, 1563 residues, 13 models selected
> select add #2/B:3@C18
10598 atoms, 10516 bonds, 2280 pseudobonds, 1563 residues, 13 models selected
> select subtract #2/B:3@C18
10597 atoms, 10516 bonds, 2280 pseudobonds, 1563 residues, 13 models selected
> color (#!2 & sel) orange
> undo
> ui mousemode right select
> ui mousemode right rotate
> ui mousemode right select
> select #2/B:287
11 atoms, 11 bonds, 1 residue, 1 model selected
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> select add #1/B:4@CD2
1 atom, 2 bonds, 1 pseudobond, 1 residue, 2 models selected
> select add #1/B:4@CG
2 atoms, 3 bonds, 1 pseudobond, 1 residue, 2 models selected
> select add #1/B:4@CD1
3 atoms, 4 bonds, 1 pseudobond, 1 residue, 2 models selected
> select add #1/B:4@CE2
4 atoms, 6 bonds, 1 pseudobond, 1 residue, 2 models selected
> select add #1/B:4@CZ2
5 atoms, 7 bonds, 1 pseudobond, 1 residue, 2 models selected
> select add #1/B:4@CZ3
6 atoms, 9 bonds, 1 pseudobond, 1 residue, 2 models selected
> select add #1/B:4@CE3
7 atoms, 11 bonds, 1 pseudobond, 1 residue, 2 models selected
> select add #1/B:4@CB
8 atoms, 11 bonds, 1 pseudobond, 1 residue, 2 models selected
> select add #1/B:4@CA
9 atoms, 11 bonds, 1 pseudobond, 1 residue, 2 models selected
> color (#!1 & sel) yellow
> select add #1/B:4@CH2
10 atoms, 14 bonds, 1 pseudobond, 1 residue, 2 models selected
> color (#!1 & sel) forest green
> hbonds sel reveal true
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: agonist_2.pdb #2/A PRO 206 N; antagonist.pdb #3/A PRO 206 N;
antagonist.pdb #3/D ARG 357 NE
0 hydrogen bonds found
> select ligand
170 atoms, 185 bonds, 6 residues, 3 models selected
> hbonds sel & #!1 reveal true
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: agonist_2.pdb #2/A PRO 206 N; antagonist.pdb #3/A PRO 206 N;
antagonist.pdb #3/D ARG 357 NE
7 hydrogen bonds found
> coulombic sel & #!1
Using Amber 20 recommended default charges and atom types for standard
residues
Assigning partial charges to residue SRO (net charge +1) with am1-bcc method
Running ANTECHAMBER command:
/Applications/ChimeraX-1.3.app/Contents/bin/amber20/bin/antechamber -ek
qm_theory='AM1', -i
/var/folders/k9/52yp04c17k11ykf6bljvnrd40000gn/T/tmp7alnnijr/ante.in.mol2 -fi
mol2 -o
/var/folders/k9/52yp04c17k11ykf6bljvnrd40000gn/T/tmp7alnnijr/ante.out.mol2 -fo
mol2 -c bcc -nc 1 -j 5 -s 2 -dr n
(SRO) ``
(SRO) `Welcome to antechamber 20.0: molecular input file processor.`
(SRO) ``
(SRO) `Info: Finished reading file
(/var/folders/k9/52yp04c17k11ykf6bljvnrd40000gn/T/tmp7alnnijr/ante.in.mol2);
atoms read (26), bonds read (27).`
(SRO) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(SRO) `Running:
/Applications/ChimeraX-1.3.app/Contents/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`
(SRO) ``
(SRO) ``
(SRO) `Running:
/Applications/ChimeraX-1.3.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`
(SRO) `Info: Total number of electrons: 94; net charge: 1`
(SRO) ``
(SRO) `Running: /Applications/ChimeraX-1.3.app/Contents/bin/amber20/bin/sqm -O
-i sqm.in -o sqm.out`
(SRO) ``
(SRO) `Running: /Applications/ChimeraX-1.3.app/Contents/bin/amber20/bin/am1bcc
-i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p
/Applications/ChimeraX-1.3.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT
-s 2 -j 1`
(SRO) ``
(SRO) `Running:
/Applications/ChimeraX-1.3.app/Contents/bin/amber20/bin/atomtype -f ac -p bcc
-o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`
(SRO) ``
Charges for residue SRO determined
Coulombic values for agonist_1.pdb_B SES surface #1.2: minimum, 1.12, mean
3.76, maximum 7.69
To also show corresponding color key, enter the above coulombic command and
add key true
Drag select of agonist_1.pdb_B SES surface, 5 of 3174 triangles
> coulombic #!1
Coulombic values for agonist_1.pdb_B SES surface #1.4: minimum, -17.89, mean
-1.45, maximum 12.60
To also show corresponding color key, enter the above coulombic command and
add key true
> coulombic #!1
Coulombic values for agonist_1.pdb_B SES surface #1.4: minimum, -17.89, mean
-1.45, maximum 12.60
To also show corresponding color key, enter the above coulombic command and
add key true
> hide #1.4 models
> hide #1.2 models
No visible Surface models
> show (#!1 & sidechain) target ab
> hide #* target a
> show #!1 target ab
> hide #!1 models
> show #!1 models
> show #2.4 models
> hide #2.4 models
> show #2.4 models
> hide #2.4 models
> show #2.4 models
> hide #2.4 models
> show #!3 models
> show #2.5 models
> hide #2.5 models
> hide #!1 models
> hide #!2 models
> select clear
> show #!1 models
> hide #2.1 models
> hide #!3 models
> select clear
> select ligand
170 atoms, 185 bonds, 6 residues, 3 models selected
> undo
Drag select of 2 residues
> select #1/B:230
9 atoms, 8 bonds, 1 residue, 1 model selected
> ui tool show Contacts
> contacts select true color #992e1c reveal true
98337 contacts
> contacts select true color #992e1c reveal true
98337 contacts
> contacts select true color #992e1c reveal true
98337 contacts
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 INTEL-18.3.5
OpenGL renderer: Intel(R) HD Graphics 6000
OpenGL vendor: Intel Inc.Hardware:
Hardware Overview:
Model Name: MacBook Air
Model Identifier: MacBookAir7,2
Processor Name: Dual-Core Intel Core i5
Processor Speed: 1.8 GHz
Number of Processors: 1
Total Number of Cores: 2
L2 Cache (per Core): 256 KB
L3 Cache: 3 MB
Hyper-Threading Technology: Enabled
Memory: 8 GB
System Firmware Version: 428.60.3.0.0
OS Loader Version: 540.60.2~89
SMC Version (system): 2.27f2
Software:
System Software Overview:
System Version: macOS 12.1 (21C52)
Kernel Version: Darwin 21.2.0
Time since boot: 2 days 23:59
Graphics/Displays:
Intel HD Graphics 6000:
Chipset Model: Intel HD Graphics 6000
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x1626
Revision ID: 0x0009
Metal Family: Supported, Metal GPUFamily macOS 1
Displays:
Color LCD:
Display Type: LCD
Resolution: 1440 x 900 (Widescreen eXtended Graphics Array Plus)
UI Looks like: 1440 x 900
Framebuffer Depth: 24-Bit Color (ARGB8888)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.2
Babel: 2.9.1
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2021.5.30
cftime: 1.5.1.1
charset-normalizer: 2.0.9
ChimeraX-AddCharge: 1.2.2
ChimeraX-AddH: 2.1.11
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.2.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.31
ChimeraX-AtomicLibrary: 4.2
ChimeraX-AtomSearch: 2.0
ChimeraX-AtomSearchLibrary: 1.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.0
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.6.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.2
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.2
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5
ChimeraX-CommandLine: 1.1.5
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.3
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1.5
ChimeraX-DistUI: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.1
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.1.2
ChimeraX-Help: 1.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0
ChimeraX-Label: 1.1
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.4
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 2.0.4
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.4
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.2.6
ChimeraX-ModelPanel: 1.2.1
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.2
ChimeraX-OpenCommand: 1.7
ChimeraX-PDB: 2.6.5
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.4.6
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.1
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.6.1
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-Struts: 1.0
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1
ChimeraX-ToolshedUtils: 1.2
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.13.7
ChimeraX-uniprot: 2.2
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.0.1
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.0
ChimeraX-Zone: 1.0
colorama: 0.4.4
cxservices: 1.1
cycler: 0.11.0
Cython: 0.29.24
decorator: 5.1.0
docutils: 0.17.1
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 3.6.0
html2text: 2020.1.16
idna: 3.3
ihm: 0.21
imagecodecs: 2021.4.28
imagesize: 1.3.0
ipykernel: 5.5.5
ipython: 7.23.1
ipython-genutils: 0.2.0
jedi: 0.18.0
Jinja2: 3.0.1
jupyter-client: 6.1.12
jupyter-core: 4.9.1
kiwisolver: 1.3.2
lxml: 4.6.3
lz4: 3.1.3
MarkupSafe: 2.0.1
matplotlib: 3.4.3
matplotlib-inline: 0.1.3
msgpack: 1.0.2
netCDF4: 1.5.7
networkx: 2.6.3
numexpr: 2.8.0
numpy: 1.21.2
openvr: 1.16.801
packaging: 21.0
ParmEd: 3.2.0
parso: 0.8.3
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 8.3.2
pip: 21.2.4
pkginfo: 1.7.1
prompt-toolkit: 3.0.23
psutil: 5.8.0
ptyprocess: 0.7.0
pycollada: 0.7.1
pydicom: 2.1.2
Pygments: 2.10.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.6
PyQt5-commercial: 5.15.2
PyQt5-sip: 12.8.1
PyQtWebEngine-commercial: 5.15.2
python-dateutil: 2.8.2
pytz: 2021.3
pyzmq: 22.3.0
qtconsole: 5.1.1
QtPy: 1.11.3
RandomWords: 0.3.0
requests: 2.26.0
scipy: 1.7.1
setuptools: 57.5.0
sfftk-rw: 0.7.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 4.2.0
sphinx-autodoc-typehints: 1.12.0
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 2.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
suds-jurko: 0.6
tifffile: 2021.4.8
tinyarray: 1.2.3
tornado: 6.1
traitlets: 5.1.1
urllib3: 1.26.7
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.37.0
wheel-filename: 1.3.0
Change History (2)
comment:1 by , 4 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Window Toolkit |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash removing dock widget from main window |
comment:2 by , 4 years ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
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