![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 3 years ago
Last modified 3 years ago
#7196 feedback defect
Crash during drag/drop
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| 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: 1.4 (2022-06-03 23:39:42 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
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{
"uptime" : 350000,
"procLaunch" : "2022-06-27 14:37:48.4370 +0900",
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro16,1",
"procStartAbsTime" : 170487305809659,
"coalitionID" : 455,
"osVersion" : {
"train" : "macOS 12.4",
"build" : "21F79",
"releaseType" : "User"
},
"captureTime" : "2022-06-29 16:40:03.2353 +0900",
"incident" : "E0C4A5B0-61B6-4F71-BD33-5AAF0F60B2ED",
"bug_type" : "309",
"pid" : 98534,
"procExitAbsTime" : 350620017604281,
"cpuType" : "X86-64",
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.4.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.4.0","CFBundleVersion":"1.4.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"82B96F1A-5EC8-559C-91A7-3529C0A78208","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "41A65D72-BF6F-AB83-4222-DE724F7A2F41",
"wakeTime" : 198724,
"bridgeVersion" : {"build":"19P5071","train":"6.5"},
"sleepWakeUUID" : "7E945727-8458-440E-8F4B-2B2672C4A914",
"sip" : "enabled",
"isCorpse" : 1,
"exception" : {"codes":"0x0000000000000000, 0x0000000000000000","rawCodes":[0,0],"type":"EXC_CRASH","signal":"SIGABRT"},
"ktriageinfo" : "VM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\n",
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"faultingThread" : 0,
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"source" : "P",
"arch" : "x86_64",
"base" : 4637224960,
"size" : 63488000,
"uuid" : "10431d8f-5e3b-3bbc-abd5-81f6a73a5269",
"path" : "\/Applications\/ChimeraX-1.4.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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"sharedCache" : {
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"size" : 15220686848,
"uuid" : "398acfb4-57f6-31e0-bc82-e9959e5c92ce"
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"vmSummary" : "ReadOnly portion of Libraries: Total=1.5G resident=0K(0%) swapped_out_or_unallocated=1.5G(100%)\nWritable regions: Total=6.1G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=6.1G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 1152K 9 \nActivity Tracing 256K 1 \nCG backing stores 18.9M 11 \nCG image 1128K 101 \nColorSync 236K 28 \nCoreAnimation 3472K 208 \nCoreGraphics 16K 3 \nCoreImage 40K 10 \nCoreServices 624K 2 \nCoreUI image data 5360K 61 \nFoundation 40K 2 \nKernel Alloc Once 8K 1 \nMALLOC 5.1G 2284 \nMALLOC guard page 32K 8 \nMALLOC_LARGE (reserved) 256K 1 reserved VM address space (unallocated)\nMALLOC_NANO (reserved) 128.0M 1 reserved VM address space (unallocated)\nMach message 16K 3 \nObjC additional data 15K 1 \nOpenGL GLSL 384K 4 \nSTACK GUARD 200K 50 \nStack 485.9M 51 \nStack Guard 56.0M 1 \nVM_ALLOCATE 241.7M 278 \nVM_ALLOCATE (reserved) 128.0M 1 reserved VM address space (unallocated)\n__CTF 756 1 \n__DATA 57.5M 693 \n__DATA_CONST 33.1M 355 \n__DATA_DIRTY 1659K 217 \n__FONT_DATA 4K 1 \n__GLSLBUILTINS 5176K 1 \n__LINKEDIT 678.7M 150 \n__TEXT 825.9M 688 \n__UNICODE 592K 1 \ndyld private memory 1184K 3 \nmapped file 562.5M 94 \nshared memory 2996K 32 \n=========== ======= ======= \nTOTAL 8.3G 5356 \nTOTAL, minus reserved VM space 8.0G 5356 \n",
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"queue" : "com.apple.main-thread"
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"trialInfo" : {
"rollouts" : [
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"factorPackIds" : {
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===== Log before crash start =====
Startup Messages
---
warning | No presets found in custom preset folder
/Users/ich/Charisma/S-PRED/ep2_ab
UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/ich/Downloads/7cx2.pdb format pdb
No such file/path: /Users/ich/Downloads/7cx2.pdb
> open /Users/ich/Charisma/S-PRED/ep2_ab/ep2_alphafold.pdb
> /Users/ich/Charisma/S-PRED/ep2_ab/ep2_blast.pdb
> /Users/ich/Charisma/S-PRED/ep2_ab/ep2_7cx2.pdb format pdb
Chain information for ep2_alphafold.pdb #1
---
Chain | Description
A | No description available
Chain information for ep2_blast.pdb #2
---
Chain | Description
A | No description available
Chain information for ep2_7cx2.pdb #3
---
Chain | Description
R | No description available
> set bgColor white
> hide #!3 models
> hide #2 models
> color #1 ocean
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword
> color name
Missing or invalid "name" argument: Expected a text string
> name frozen af #1
> select af
5630 atoms, 5688 bonds, 358 residues, 1 model selected
> color sel #0066cc
> view
> color list
No custom colors.
248 builtin colors: alice blue
, aliceblue
, antique white
, antiquewhite
, aqua
, aquamarine
, azure
, beige
, bisque
, black
, blanched almond
, blanchedalmond
, blue
, blue violet
, blueviolet
, brown
, burly wood
, burlywood
, cadet blue
, cadetblue
, chartreuse
, chocolate
, coral
, cornflower blue
, cornflowerblue
, cornsilk
, crimson
, cyan
, dark blue
, dark cyan
, dark goldenrod
, dark gray
, dark green
, dark grey
, dark khaki
, dark magenta
, dark olive green
, dark orange
, dark orchid
, dark red
, dark salmon
, dark sea green
, dark seagreen
, dark slate blue
, dark slate gray
, dark slate grey
, dark turquoise
, dark violet
, darkblue
, darkcyan
, darkgoldenrod
, darkgray
, darkgreen
, darkgrey
, darkkhaki
, darkmagenta
, darkolivegreen
, darkorange
, darkorchid
, darkred
, darksalmon
, darkseagreen
, darkslateblue
, darkslategray
, darkslategrey
, darkturquoise
, darkviolet
, deep pink
, deep sky blue
, deep skyblue
, deeppink
, deepskyblue
, dim gray
, dim grey
, dimgray
, dimgrey
, dodger blue
, dodgerblue
, fire brick
, firebrick
, floral white
, floralwhite
, forest green
, forestgreen
, fuchsia
, gainsboro
, ghost white
, ghostwhite
, gold
, goldenrod
, gray
, green
, green yellow
, greenyellow
, grey
, honeydew
, hot pink
, hotpink
, indian red
, indianred
, indigo
, ivory
, khaki
, lavender
, lavender blush
, lavenderblush
, lawn green
, lawngreen
, lemon chiffon
, lemonchiffon
, light blue
, light coral
, light cyan
, light goldenrod yellow
, light gray
, light green
, light grey
, light pink
, light salmon
, light sea green
, light seagreen
, light sky blue
, light skyblue
, light slate gray
, light slate grey
, light steel blue
, light yellow
, lightblue
, lightcoral
, lightcyan
, lightgoldenrodyellow
, lightgray
, lightgreen
, lightgrey
, lightpink
, lightsalmon
, lightseagreen
, lightskyblue
, lightslategray
, lightslategrey
, lightsteelblue
, lightyellow
, lime
, lime green
, limegreen
, linen
, magenta
, maroon
, medium aquamarine
, medium blue
, medium orchid
, medium purple
, medium sea green
, medium seagreen
, medium slate blue
, medium spring green
, medium turquoise
, medium violet red
, mediumaquamarine
, mediumblue
, mediumorchid
, mediumpurple
, mediumseagreen
, mediumslateblue
, mediumspringgreen
, mediumturquoise
, mediumvioletred
, midnight blue
, midnightblue
, mint cream
, mintcream
, misty rose
, mistyrose
, moccasin
, navajo white
, navajowhite
, navy
, old lace
, oldlace
, olive
, olive drab
, olivedrab
, orange
, orange red
, orangered
, orchid
, pale goldenrod
, pale green
, pale turquoise
, pale violet red
, palegoldenrod
, palegreen
, paleturquoise
, palevioletred
, papaya whip
, papayawhip
, peach puff
, peachpuff
, peru
, pink
, plum
, powder blue
, powderblue
, purple
, rebecca purple
, rebeccapurple
, red
, rosy brown
, rosybrown
, royal blue
, royalblue
, saddle brown
, saddlebrown
, salmon
, sandy brown
, sandybrown
, sea green
, seagreen
, seashell
, sienna
, silver
, sky blue
, skyblue
, slate blue
, slate gray
, slate grey
, slateblue
, slategray
, slategrey
, snow
, spring green
, springgreen
, steel blue
, steelblue
, tan
, teal
, thistle
, tomato
, transparent
, turquoise
, violet
, wheat
, white
, white smoke
, whitesmoke
, yellow
, yellow green
, and yellowgreen
.
> color sel cornflowerblue
> ligth soft
Unknown command: ligth soft
> lighting soft
> select clear
> graphics silhouettes true
> lighting soft
> graphics silhouettes true width 1
> surface af
> color af cornflowerblue
> transparency 95 target s
> show ions : graphics silhouettes grey true width 1
Expected true or false or a keyword
> graphics silhouettes true width 1 color grey
> open
> /Users/ich/Charisma/S-PRED/ep2_ab/7cx2_rabgn_ab0_method3/7cx2_rabgn_ab0_55e8a_unrelaxed_rank_1_model_4.pdb
Chain information for 7cx2_rabgn_ab0_55e8a_unrelaxed_rank_1_model_4.pdb #4
---
Chain | Description
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
> hide #!1 models
> view
> select #4/F:1-128
973 atoms, 993 bonds, 128 residues, 1 model selected
> select #4/F:1-128
973 atoms, 993 bonds, 128 residues, 1 model selected
> select #4/E:1-71
547 atoms, 555 bonds, 71 residues, 1 model selected
> select #4/D:1-358
2762 atoms, 2817 bonds, 358 residues, 1 model selected
> select #4/C:1-394
3210 atoms, 3272 bonds, 394 residues, 1 model selected
> select #4/B:1-505
3806 atoms, 3885 bonds, 505 residues, 1 model selected
> delete #4 /c/d/e/f
> view
> show sel target c
> hide sel target a
> color sel maroon
> view
Alignment identifier is 4/B
> select #4/B:1
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #4/B:1-117
900 atoms, 920 bonds, 117 residues, 1 model selected
> select ~sel
13350 atoms, 13573 bonds, 2 pseudobonds, 1370 residues, 5 models selected
> delete sel
> select clear
Drag select of 117 residues
> view
> rename #4 ab0
> open
> /Users/ich/Charisma/S-PRED/ep2_ab/7cx2_rabgn_ab1_method3/7cx2_rabgn_ab1_fe4cf_unrelaxed_rank_1_model_2.pdb
Chain information for 7cx2_rabgn_ab1_fe4cf_unrelaxed_rank_1_model_2.pdb #1
---
Chain | Description
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
> rename #1 ab1
> rename #1 #2
No name or id option specified for renaming
> rename #1 id #2
> rename #4 id #1
> hide #1 models
> select add #1
900 atoms, 920 bonds, 117 residues, 1 model selected
> select subtract #1
Nothing selected
> delete #2 /c/d/e/f
Alignment identifier is 2/B
Alignment identifier is 1/B
> select #2/B:115
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #2/B:115-502
2906 atoms, 2964 bonds, 388 residues, 1 model selected
> delete sel
Drag select of 846 atoms
> view
> show sel target c
> hide sel target a
> color #2 #005493 transparency 0
> show #1 models
> open
> /Users/ich/Charisma/S-PRED/ep2_ab/7cx2_rabgn_ab2_method3/7cx2_rabgn_ab2_0feb1_unrelaxed_rank_1_model_4.pdb
Chain information for 7cx2_rabgn_ab2_0feb1_unrelaxed_rank_1_model_4.pdb #3
---
Chain | Description
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
> color #3 #941751 transparency 0
> rename #3 ab3
> delete #3 /c/d/e/f
Alignment identifier is 2/B
> select add #3
4697 atoms, 3936 bonds, 626 residues, 2 models selected
> select add #2
4697 atoms, 4800 bonds, 626 residues, 2 models selected
> select subtract #2
3851 atoms, 3936 bonds, 512 residues, 1 model selected
Alignment identifier is 3/B
> select #3/B:125
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #3/B:125-512
2906 atoms, 2964 bonds, 388 residues, 1 model selected
> delete sel
Drag select of 945 atoms
> show sel target c
> hide sel target a
> select add #3
945 atoms, 971 bonds, 124 residues, 1 model selected
> select subtract #3
Nothing selected
> open
> /Users/ich/Charisma/S-PRED/ep2_ab/7cx2_rabgn_ab3_method3/7cx2_rabgn_ab3_5df0d_unrelaxed_rank_1_model_2.pdb
Chain information for 7cx2_rabgn_ab3_5df0d_unrelaxed_rank_1_model_2.pdb #4
---
Chain | Description
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
> hide #3 models
> hide #2 models
> hide #1 models
> delete #4 /c/d/e/f
> color #4 #008f00 transparency 0
> color #4 #009051 transparency 0
Alignment identifier is 2/B
Alignment identifier is 1/B
Alignment identifier is 3/B
Alignment identifier is 4/B
> select #4/B:128
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #4/B:128-270
963 atoms, 978 bonds, 143 residues, 1 model selected
> select #4/B:128-515
2906 atoms, 2964 bonds, 388 residues, 1 model selected
> delete sel
Drag select of 963 atoms
> view
> show sel target c
> hide sel target a
> rename #4 ab4
> open
> /Users/ich/Charisma/S-PRED/ep2_ab/7cx2_rabgn_ab4_method3/7cx2_rabgn_ab3_c9300_unrelaxed_rank_1_model_4.pdb
Chain information for 7cx2_rabgn_ab3_c9300_unrelaxed_rank_1_model_4.pdb #5
---
Chain | Description
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
> select add #4
963 atoms, 985 bonds, 127 residues, 1 model selected
> select subtract #4
Nothing selected
> hide #4 models
> color #5 #945200 transparency 0
> delete #5 /c/d/e/f
> select add #5
3786 atoms, 3866 bonds, 505 residues, 1 model selected
Alignment identifier is 5/B
> select #5/B:118
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #5/B:118-505
2906 atoms, 2964 bonds, 388 residues, 1 model selected
> delete sel
> select add #5
880 atoms, 901 bonds, 117 residues, 1 model selected
> view
> show sel target c
> hide sel target a
> mmaker #2-5 to 1
> matchmaker #2-5 to 1
Invalid "to" argument: invalid atoms specifier
> mmaker #2-5 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker ab0, chain B (#1) with ab1, chain B (#2), sequence alignment score
= 1881.4
RMSD between 104 pruned atom pairs is 0.429 angstroms; (across all 113 pairs:
2.078)
Matchmaker ab0, chain B (#1) with ab3, chain B (#3), sequence alignment score
= 1911.2
RMSD between 109 pruned atom pairs is 0.429 angstroms; (across all 117 pairs:
1.746)
Matchmaker ab0, chain B (#1) with ab4, chain B (#4), sequence alignment score
= 1913.2
RMSD between 113 pruned atom pairs is 0.325 angstroms; (across all 117 pairs:
1.541)
Matchmaker ab0, chain B (#1) with
7cx2_rabgn_ab3_c9300_unrelaxed_rank_1_model_4.pdb, chain B (#5), sequence
alignment score = 1930
RMSD between 111 pruned atom pairs is 0.454 angstroms; (across all 117 pairs:
1.369)
> view
> show #4 models
> show #3 models
> show #2 models
> show #1 models
> select clear
> pwd
Current working directory is: /Users/ich/Desktop
> chdir ~/Charisma/S-PRED/ep2_ab/
Unknown command: chdir ~/Charisma/S-PRED/ep2_ab/
> cd /Users/ich/Charisma/S-PRED/ep2_ab/
Current working directory is: /Users/ich/Charisma/S-PRED/ep2_ab
> save ab_af.cxs
> save ab_af.png
> rename #5 ab5
> save ab_af.cxs
> hide #5 models
> hide #3 models
> hide #2 models
> hide #1 models
> surface #4
> color #4 #009051 transparency 0
> transparency 95 target s
> lighting soft
> graphics sillhouettes true color gre width 1
Expected a keyword
> graphics silhouettes true color grey width 1
> save ab_af.cxs
> rename #3 ab2
> rename #4 ab3
> rename #5 ab4
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> show #3 models
> show #5 models
> show #2 models
> show #1 models
Populating font family aliases took 373 ms. Replace uses of missing font
family ".AppleSystemUIFont" with one that exists to avoid this cost.
> save /Users/ich/Charisma/S-PRED/ep2_ab/ab0.pdb models #1
> save ab1.pdb models #2
> save ab2.pdb models #3
> save ab3.pdb models #4
> save ab4.pdb models #5
> mmaker
> matchmaker
Missing or invalid "matchAtoms" argument: empty atom specifier
> save ab_af.cxs
> close #1-3,5#4
> set silhouettes true
> open ltag
'ltag' has no suffix
> open 1tag
Summary of feedback from opening 1tag fetched from pdb
---
warnings | Unknown polymer entity '3' near line 3513
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
1tag title:
Structural determinants for activation of the α-subunit of A heterotrimeric G
protein [more info...]
Chain information for 1tag #1
---
Chain | Description | UniProt
A | transducin-α | GNAT1_BOVIN
Non-standard residues in 1tag #1
---
MG — magnesium ion
> open 1tnd
Summary of feedback from opening 1tnd fetched from pdb
---
notes | Fetching compressed mmCIF 1tnd from
http://files.rcsb.org/download/1tnd.cif
Fetching CCD CAC from http://ligand-expo.rcsb.org/reports/C/CAC/CAC.cif
Fetching CCD GSP from http://ligand-expo.rcsb.org/reports/G/GSP/GSP.cif
1tnd title:
The 2.2 angstroms crystal structure of transducin-α complexed with GTP γ S
[more info...]
Chain information for 1tnd #2
---
Chain | Description | UniProt
A B C | transducin | GNAT1_BOVIN
Non-standard residues in 1tnd #2
---
CAC — cacodylate ion (dimethylarsinate)
GSP — 5'-guanosine-diphosphate-monothiophosphate
MG — magnesium ion
1tnd mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
3| author_defined_assembly
> delete ~/a
> hide
> show
> hide
> mmaker #2 to #1 compute f
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 1tag, chain A (#1) with 1tnd, chain A (#2), sequence alignment
score = 1667.6
RMSD between 290 pruned atom pairs is 0.544 angstroms; (across all 314 pairs:
1.253)
> view
> cartoon style model tube side 24
Expected an atoms specifier or a keyword
> cartoon style modeHelix tube sides 24
> transparency (protein & ~:173-182,196-211,228-237) 100 target c
> hide (#1 & protein & ~:173-182,196-211,228-237) cartoons
> show #2 & ligand
> style ligand sphere
Changed 60 atom styles
> 2dlabels text "Switch 1" xpos .05 ypos .38
> 2dlabels text "Switch 2" xpos .22 ypos .07
> 2dlabels text "Switch 3" xpos .65 ypos .48
> 2dlabels text GDP-bound color tan xpos .73 ypos .08
> 2dlabels text GTP-bound color deepskyblue xpos .73 ypos .04
> 2dlabels text "Transducin α-Subunit" xpos .04 ypos .93 size 30
> windowsize 600 800
> ui mousemode right "move label"
> 2dlabels #3.1 xpos 0.238 ypos 0.339
> 2dlabels #3.2 xpos 0.327 ypos 0.052
> 2dlabels #3.3 xpos 0.574 ypos 0.458
> 2dlabels #3.6 xpos 0.237 ypos 0.943
> 2dlabels #3.4 xpos 0.668 ypos 0.110
> 2dlabels #3.5 xpos 0.670 ypos 0.068
> close #1-3
> open 5vms
Summary of feedback from opening 5vms fetched from pdb
---
notes | Fetching compressed mmCIF 5vms from
http://files.rcsb.org/download/5vms.cif
Fetching CCD CA from http://ligand-expo.rcsb.org/reports/C/CA/CA.cif
5vms title:
CryoEM structure of Xenopus KCNQ1 channel [more info...]
Chain information for 5vms #1
---
Chain | Description | UniProt
A | Potassium voltage-gated channel subfamily KQT member 1 | KCNQ1_XENLA
B | Calmodulin | CALM_HUMAN
Non-standard residues in 5vms #1
---
CA — calcium ion
5vms mmCIF Assemblies
---
1| complete point assembly
2| point asymmetric unit
3| point asymmetric unit, std point frame
> view
> sym #1 assembly 1 copies true
> close #1
> view
> zomm 1.1; turn x180
Unknown command: zomm 1.1; turn x180
> zoom 1.1
> turn x180
Expected an axis vector or a keyword
> zoom 1.1
> turn x 180
Fetching compressed palette paste12-4 from
http://www.colourlovers.com/api/palettes?keywords=paste12-4&format=json&numResults=100
Could not find palette paste12-4 at COLOURlovers.com using keyword search
> rainbow #2 structures palette pastel2-4
> surface /a
> color fromatoms target s
> hide /a target ac
> hide /b
> show Ca
> color modify /b whiteness -50
> color modify /b blackness -50
> color modify /b whiteness -50
> cartoon style modeHelix tube sides 20
> lighting gentle
> set silhouettes true
> set silhouettes depth 0.02
Invalid "silhouettes" argument: Expected true or false (or 1 or 0)
> set sildepth 0.02
Expected a keyword
> set silhouetteDepthJump 0.02
> size ions atomRadius 1.6
Changed 12 atom radii
> color modify ions hue +45
> close
> open 1eys
Summary of feedback from opening 1eys fetched from pdb
---
notes | Fetching compressed mmCIF 1eys from
http://files.rcsb.org/download/1eys.cif
Fetching CCD HEM from http://ligand-expo.rcsb.org/reports/H/HEM/HEM.cif
Fetching CCD BGL from http://ligand-expo.rcsb.org/reports/B/BGL/BGL.cif
Fetching CCD BCL from http://ligand-expo.rcsb.org/reports/B/BCL/BCL.cif
Fetching CCD BPH from http://ligand-expo.rcsb.org/reports/B/BPH/BPH.cif
Fetching CCD LDA from http://ligand-expo.rcsb.org/reports/L/LDA/LDA.cif
Fetching CCD FE from http://ligand-expo.rcsb.org/reports/F/FE/FE.cif
Fetching CCD MQ8 from http://ligand-expo.rcsb.org/reports/M/MQ8/MQ8.cif
Fetching CCD CRT from http://ligand-expo.rcsb.org/reports/C/CRT/CRT.cif
Fetching CCD PEF from http://ligand-expo.rcsb.org/reports/P/PEF/PEF.cif
1eys title:
Crystal structure of photosynthetic reaction center from A thermophilic
bacterium, thermochromatium tepidum [more info...]
Chain information for 1eys #1
---
Chain | Description | UniProt
C | photosynthetic reaction center |
H | photosynthetic reaction center | Q93RD8_THETI
L | photosynthetic reaction center |
M | photosynthetic reaction center |
Non-standard residues in 1eys #1
---
BCL — bacteriochlorophyll A
BGL — 2-O-octyl-beta-D-glucopyranose
BPH — bacteriopheophytin A
CRT — spirilloxanthin (rhodoviolascin)
FE — Fe (III) ion
HEM — protoporphyrin IX containing Fe (HEME)
LDA — lauryl dimethylamine-N-oxide
MQ8 — menaquinone 8 (2-methyl-3-(3,7,11,15,19,23,27,31-octamethyl-
dotriaconta-2,6,10,14,18,22,26,30-octaenyl)-[1,4]napthoquinone)
PEF — di-palmitoyl-3-Sn-phosphatidylethanolamine
(3-[aminoethylphosphoryl]-[1,2-di-palmitoyl]-Sn-glycerol)
> view
> zoom 1.1
> turn x180
Expected an axis vector or a keyword
> turn x 180
> ui mousemode right zoom
> hide
> cartoon style #1 modeHelix tube sides 24
> rainbow #1 structures palette pastel2-4
> rainbow #1 chains palette pastel2-4
> close
> open /Users/ich/Downloads/prc.cxs
restore_snapshot for "Labels" returned None
opened ChimeraX session
> view
> select ligand
835 atoms, 879 bonds, 20 residues, 1 model selected
> select clear
> select /?:4567@O
1 atom, 1 residue, 1 model selected
> select /?:4320@O
1 atom, 1 residue, 1 model selected
> select /M:82
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /?:4650@O
1 atom, 1 residue, 1 model selected
> select clear
> clip
> clip off
> close #1
> clsoe
Unknown command: clsoe
> close
> open 6 ddf
'6' has no suffix
> open 6ddf
Summary of feedback from opening 6ddf fetched from pdb
---
notes | Fetching compressed mmCIF 6ddf from
http://files.rcsb.org/download/6ddf.cif
Fetching CCD DAL from http://ligand-expo.rcsb.org/reports/D/DAL/DAL.cif
Fetching CCD MEA from http://ligand-expo.rcsb.org/reports/M/MEA/MEA.cif
Fetching CCD ETA from http://ligand-expo.rcsb.org/reports/E/ETA/ETA.cif
6ddf title:
μ Opioid Receptor-Gi Protein Complex [more info...]
Chain information for 6ddf #1
---
Chain | Description | UniProt
A | Guanine nucleotide-binding protein G(i) subunit alpha-1 | GNAI1_HUMAN
B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 |
GBB1_HUMAN
C | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 |
GBG2_HUMAN
D | DAMGO |
R | Mu-type opioid receptor | OPRM_MOUSE
Non-standard residues in 6ddf #1
---
ETA — ethanolamine
> set bgColor white
> close
> open 4n6h
Summary of feedback from opening 4n6h fetched from pdb
---
notes | Fetching compressed mmCIF 4n6h from
http://files.rcsb.org/download/4n6h.cif
Fetching CCD OLA from http://ligand-expo.rcsb.org/reports/O/OLA/OLA.cif
Fetching CCD OLC from http://ligand-expo.rcsb.org/reports/O/OLC/OLC.cif
Fetching CCD PGE from http://ligand-expo.rcsb.org/reports/P/PGE/PGE.cif
Fetching CCD TLA from http://ligand-expo.rcsb.org/reports/T/TLA/TLA.cif
Fetching CCD EJ4 from http://ligand-expo.rcsb.org/reports/E/EJ4/EJ4.cif
4n6h title:
1.8 A Structure of the human δ opioid 7TM receptor (PSI Community Target)
[more info...]
Chain information for 4n6h #1
---
Chain | Description | UniProt
A | Soluble cytochrome b562, Delta-type opioid receptor chimeric protein |
OPRD_HUMAN
Non-standard residues in 4n6h #1
---
EJ4 —
(4bS,8R,8aS,14bR)-7-(cyclopropylmethyl)-5,6,7,8,14,14b-hexahydro-4,8-methano[1]benzofuro[2,3-a]pyrido[4,3-b]carbazole-1,8a(9H)-diol
(Naltrindole)
NA — sodium ion
OLA — oleic acid
OLC — (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate (1-Oleoyl-R-glycerol)
PGE — triethylene glycol
TLA — L(+)-tartaric acid
> surface
> mlp
Map values for surface "4n6h_A SES surface": minimum -26.77, mean -0.8566,
maximum 23.81
> lighting soft
> lighting simple
> hide surfaces
> delete :1002-1106
> hbonds
582 hydrogen bonds found
> hbonds :ej4
10 hydrogen bonds found
> :ej4
Unknown command: :ej4
> view:ej4
Unknown command: view:ej4
> view :ej4
> clip
> color :ej4 orange
> color byhetero
> hide cartoons
> clip off
> hide cartoons
> hide atoms
> show :ej4 : view
> addh
Summary of feedback from adding hydrogens to 4n6h #1
---
warnings | Not adding hydrogens to /A ARG 41 CD because it is missing heavy-
atom bond partners
Not adding hydrogens to /A VAL 154 CB because it is missing heavy-atom bond
partners
Not adding hydrogens to /A LEU 157 CG because it is missing heavy-atom bond
partners
Not adding hydrogens to /A LYS 166 CE because it is missing heavy-atom bond
partners
Not adding hydrogens to /A ARG 192 CD because it is missing heavy-atom bond
partners
10 messages similar to the above omitted
notes | Termini for 4n6h (#1) chain A determined from SEQRES records
Chain-initial residues that are actual N termini:
Chain-initial residues that are not actual N termini: /A GLY 36
Chain-final residues that are actual C termini: /A GLY 338
Chain-final residues that are not actual C termini:
Missing OXT added to C-terminal residue /A GLY 338
581 hydrogen bonds
Adding 'H' to /A GLY 36
3076 hydrogens added
> open 4n6h fromDatabase eds
Summary of feedback from opening 4n6h fetched from eds
---
note | Fetching map 4n6h from
http://www.ebi.ac.uk/pdbe/coordinates/files/4n6h.ccp4
Opened eds 4n6h as #2, grid size 114,100,190, pixel 0.599,0.607,0.603, shown
at level 0.799, step 1, values float32
> hide #!1 models
> show #!1 models
> set bgColor black
> clip
> clip off
> volume zone #2 nearAtoms :ej4 range 6 newMap false
> delete H
> volume #2 style image region all imageMode "tilted slab" tiltedSlabAxis
> 0,0,1 tiltedSlabOffset 67.28 tiltedSlabSpacing 0.5988 tiltedSlabPlaneCount
> 10
> mousemode rightMode "rotate slab"
> volume planes z style image imageMode "full region"
> mousemode rightMode "move planes"
> volume #2 orthoplanes xyz positionPlanes 57,50,95 style image region all
> mousemode rightMode "move planes"
> volume #2 orthoplanes xyz positionPlanes 57,50,95 style image region all
> mousemode rightMode "move planes"
> volume showOutlineBox false
> volume showOutlineBox true
> volume showOutlineBox false
> volume showOutlineBox true
> undo
> close
> open 4n6h
4n6h title:
1.8 A Structure of the human δ opioid 7TM receptor (PSI Community Target)
[more info...]
Chain information for 4n6h #1
---
Chain | Description | UniProt
A | Soluble cytochrome b562, Delta-type opioid receptor chimeric protein |
OPRD_HUMAN
Non-standard residues in 4n6h #1
---
EJ4 —
(4bS,8R,8aS,14bR)-7-(cyclopropylmethyl)-5,6,7,8,14,14b-hexahydro-4,8-methano[1]benzofuro[2,3-a]pyrido[4,3-b]carbazole-1,8a(9H)-diol
(Naltrindole)
NA — sodium ion
OLA — oleic acid
OLC — (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate (1-Oleoyl-R-glycerol)
PGE — triethylene glycol
TLA — L(+)-tartaric acid
> surface
> mlp
Map values for surface "4n6h_A SES surface": minimum -26.77, mean -0.8566,
maximum 23.81
> hide surfaces
> hide
> delete :1002-1106
> hbonds :ej4
10 hydrogen bonds found
> show
> close
> open 4n6h
4n6h title:
1.8 A Structure of the human δ opioid 7TM receptor (PSI Community Target)
[more info...]
Chain information for 4n6h #1
---
Chain | Description | UniProt
A | Soluble cytochrome b562, Delta-type opioid receptor chimeric protein |
OPRD_HUMAN
Non-standard residues in 4n6h #1
---
EJ4 —
(4bS,8R,8aS,14bR)-7-(cyclopropylmethyl)-5,6,7,8,14,14b-hexahydro-4,8-methano[1]benzofuro[2,3-a]pyrido[4,3-b]carbazole-1,8a(9H)-diol
(Naltrindole)
NA — sodium ion
OLA — oleic acid
OLC — (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate (1-Oleoyl-R-glycerol)
PGE — triethylene glycol
TLA — L(+)-tartaric acid
> surface
> mlp
Map values for surface "4n6h_A SES surface": minimum -26.77, mean -0.8566,
maximum 23.81
> hide surfaces
> lighting gentle
> show surfaces
> hide surfaces
> lighting simple
> delete :1002-1106
> hbonds
582 hydrogen bonds found
> hbonds :ej4
10 hydrogen bonds found
> view side
Expected an objects specifier or a view name or a keyword
> ui tool show "Side View"
> sideview
Unknown command: sideview
> view :ej4
> clip
> clip front 0 position :ej4
> ui mousemode right clip
> view ligand
> ui mousemode right zoom
> color :ej4 orange
> color byhetero
> hide cartoons
> clip off
> hide atoms
> show :ej4 : addh sel
Summary of feedback from adding hydrogens to 4n6h #1
---
warnings | Not adding hydrogens to /A ARG 41 CD because it is missing heavy-
atom bond partners
Not adding hydrogens to /A VAL 154 CB because it is missing heavy-atom bond
partners
Not adding hydrogens to /A LEU 157 CG because it is missing heavy-atom bond
partners
Not adding hydrogens to /A LYS 166 CE because it is missing heavy-atom bond
partners
Not adding hydrogens to /A ARG 192 CD because it is missing heavy-atom bond
partners
10 messages similar to the above omitted
notes | Termini for 4n6h (#1) chain A determined from SEQRES records
Chain-initial residues that are actual N termini:
Chain-initial residues that are not actual N termini: /A GLY 36
Chain-final residues that are actual C termini: /A GLY 338
Chain-final residues that are not actual C termini:
Missing OXT added to C-terminal residue /A GLY 338
581 hydrogen bonds
Adding 'H' to /A GLY 36
3076 hydrogens added
> select clear
> open 4n6h fromDatabase eds
Opened eds 4n6h as #2, grid size 114,100,190, pixel 0.599,0.607,0.603, shown
at level 0.799, step 1, values float32
> volume none #2 near :ej4 range 6 newmap false
Expected a density maps specifier or a keyword
> volume zone #2 nearAtoms :ej4 range 6 newMap false
> delete h
Missing or invalid "atoms" argument: invalid atoms specifier
> delete H
> view
> ui tool show "Side View"
> clip off
> volume level .5
> ui mousemode right select
> ui mousemode right zoom
> select /A:132@CA
1 atom, 1 residue, 1 model selected
> select /A:132@CA
1 atom, 1 residue, 1 model selected
> select clear
> select /A:132@C
1 atom, 1 residue, 1 model selected
> select /A:132@CA
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 2 models selected
> select /A:129@CB
1 atom, 1 residue, 1 model selected
> close #2
Window position QRect(0,1145 575x178) outside any known screen, using primary
screen
> style :ej4 sphere
Changed 31 atom styles
> surface :ej4 : transparency 50
===== Log before crash end =====
Log:
Startup Messages
---
warning | No presets found in custom preset folder
/Users/ich/Charisma/S-PRED/ep2_ab
UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/ich/Downloads/7cx2_rabgn_ab0_8d82b.result/7cx2_rabgn_ab0_8d82b_unrelaxed_rank_3_model_1.pdb
> format pdb
No such file/path:
/Users/ich/Downloads/7cx2_rabgn_ab0_8d82b.result/7cx2_rabgn_ab0_8d82b_unrelaxed_rank_3_model_1.pdb
OpenGL version: 4.1 ATI-4.8.54
OpenGL renderer: AMD Radeon Pro 5500M OpenGL Engine
OpenGL vendor: ATI Technologies Inc.
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro16,1
Processor Name: 8-Core Intel Core i9
Processor Speed: 2.3 GHz
Number of Processors: 1
Total Number of Cores: 8
L2 Cache (per Core): 256 KB
L3 Cache: 16 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
System Firmware Version: 1731.120.10.0.0 (iBridge: 19.16.15071.0.0,0)
OS Loader Version: 540.120.3~6
Software:
System Software Overview:
System Version: macOS 12.4 (21F79)
Kernel Version: Darwin 21.5.0
Time since boot: 1 minute
Graphics/Displays:
Intel UHD Graphics 630:
Chipset Model: Intel UHD Graphics 630
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x3e9b
Revision ID: 0x0002
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Family: Supported, Metal GPUFamily macOS 2
AMD Radeon Pro 5500M:
Chipset Model: AMD Radeon Pro 5500M
Type: GPU
Bus: PCIe
PCIe Lane Width: x16
VRAM (Total): 4 GB
Vendor: AMD (0x1002)
Device ID: 0x7340
Revision ID: 0x0040
ROM Revision: 113-D3220E-190
VBIOS Version: 113-D32206U1-020
Option ROM Version: 113-D32206U1-020
EFI Driver Version: 01.A1.190
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Family: Supported, Metal GPUFamily macOS 2
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 3072 x 1920 Retina
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
LG HDR WQHD:
Resolution: 3440 x 1440 (UWQHD - Ultra-Wide Quad HD)
UI Looks like: 3440 x 1440 @ 100.00Hz
Framebuffer Depth: 24-Bit Color (ARGB8888)
Display Serial Number: 111NTJJ17772
Mirror: Off
Online: Yes
Rotation: Supported
Connection Type: Thunderbolt/DisplayPort
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.3
Babel: 2.10.1
backcall: 0.2.0
blockdiag: 3.0.0
certifi: 2021.10.8
cftime: 1.6.0
charset-normalizer: 2.0.12
ChimeraX-AddCharge: 1.2.3
ChimeraX-AddH: 2.1.3
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2.1
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.4.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.39.1
ChimeraX-AtomicLibrary: 7.0
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.1
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.1
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.7
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.2
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.1
ChimeraX-CommandLine: 1.2.3
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.4
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.1
ChimeraX-DistMonitor: 1.1.5
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.2
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.1.2
ChimeraX-Help: 1.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0
ChimeraX-Label: 1.1.1
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 2.0.6
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.7
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.5.5
ChimeraX-ModelPanel: 1.3.2
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.2
ChimeraX-OpenCommand: 1.9
ChimeraX-PDB: 2.6.6
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.6
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.1
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.8
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.0.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.1
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.2.1
ChimeraX-uniprot: 2.2
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.1.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.1.0
ChimeraX-Zone: 1.0
colorama: 0.4.4
cxservices: 1.2
cycler: 0.11.0
Cython: 0.29.26
debugpy: 1.6.0
decorator: 5.1.1
docutils: 0.17.1
entrypoints: 0.4
filelock: 3.4.2
fonttools: 4.33.3
funcparserlib: 1.0.0
grako: 3.16.5
h5py: 3.7.0
html2text: 2020.1.16
idna: 3.3
ihm: 0.27
imagecodecs: 2021.11.20
imagesize: 1.3.0
ipykernel: 6.6.1
ipython: 7.31.1
ipython-genutils: 0.2.0
jedi: 0.18.1
Jinja2: 3.0.3
jupyter-client: 7.1.0
jupyter-core: 4.10.0
kiwisolver: 1.4.2
line-profiler: 3.4.0
lxml: 4.7.1
lz4: 3.1.10
MarkupSafe: 2.1.1
matplotlib: 3.5.1
matplotlib-inline: 0.1.3
MolecularDynamicsViewer: 1.4
msgpack: 1.0.3
nest-asyncio: 1.5.5
netCDF4: 1.5.8
networkx: 2.6.3
numexpr: 2.8.1
numpy: 1.22.1
openvr: 1.16.802
packaging: 21.0
ParmEd: 3.4.3
parso: 0.8.3
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.0.1
pip: 21.3.1
pkginfo: 1.8.2
prompt-toolkit: 3.0.29
psutil: 5.9.0
ptyprocess: 0.7.0
pycollada: 0.7.2
pydicom: 2.2.2
Pygments: 2.11.2
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
PyQt6-commercial: 6.3.0
PyQt6-Qt6: 6.3.0
PyQt6-sip: 13.3.1
PyQt6-WebEngine-commercial: 6.3.0
PyQt6-WebEngine-Qt6: 6.3.0
python-dateutil: 2.8.2
pytz: 2022.1
pyzmq: 23.1.0
qtconsole: 5.3.0
QtPy: 2.1.0
RandomWords: 0.3.0
requests: 2.27.1
scipy: 1.7.3
setuptools: 59.8.0
sfftk-rw: 0.7.2
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 4.3.2
sphinx-autodoc-typehints: 1.15.2
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
suds-community: 1.0.0
tables: 3.7.0
tifffile: 2021.11.2
tinyarray: 1.2.4
tornado: 6.1
traitlets: 5.1.1
urllib3: 1.26.9
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.37.1
wheel-filename: 1.3.0
Change History (2)
comment:1 by , 3 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Window Toolkit |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash during drag/drop |
comment:2 by , 3 years ago
| Status: | accepted → feedback |
|---|
Note:
See TracTickets
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Hi Charisma,
--Eric