![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 20 months ago
Closed 20 months ago
#14726 closed defect (can't reproduce)
Crash running file-save dialog
| 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-14.2.1-arm64-arm-64bit
ChimeraX Version: 1.7rc202312020245 (2023-12-02 02:45:06 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
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{
"uptime" : 1200000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "Mac15,8",
"coalitionID" : 84273,
"osVersion" : {
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"build" : "23C71",
"releaseType" : "User"
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"captureTime" : "2024-03-07 22:59:13.3321 -0500",
"codeSigningMonitor" : 1,
"incident" : "5F3150F1-F04E-46B5-B875-4BB0BB11C850",
"pid" : 17464,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-03-07 22:42:54.5659 -0500",
"procStartAbsTime" : 29955693263821,
"procExitAbsTime" : 29979182764018,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.7-rc2023.12.02.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.7.0","CFBundleVersion":"1.7.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"10EB890B-A5D3-5CB4-AD3F-514DEEFAB0A8","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "D458AC9B-AD4E-F257-B057-B307F6A2ACE0",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"instructionByteStream" : {"beforePC":"ARAA1MADX9aQBYCSARAA1MADX9awBYCSARAA1MADX9bQBYCSARAA1A==","atPC":"wANf1vAFgJIBEADUwANf1hAGgJIBEADUwANf1jAGgJIBEADUwANf1g=="},
"wakeTime" : 46809,
"sleepWakeUUID" : "1E2ECB8F-6335-47BA-8B8A-9BC63797214B",
"sip" : "enabled",
"sroute_id" : 12,
"exception" : {"port":0,"signal":"SIGKILL","guardId":0,"codes":"0x0000000000000000, 0x0000000000000000","violations":["INVALID_OPTIONS"],"message":" INVALID_OPTIONS on mach port 0 (guarded with 0x0000000000000000)","subtype":"GUARD_TYPE_MACH_PORT","type":"EXC_GUARD","rawCodes":[0,0]},
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"path" : "\/Applications\/ChimeraX-1.7-rc2023.12.02.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/_datetime.cpython-311-darwin.so",
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===== Log before crash start =====
UCSF ChimeraX version: 1.7rc202312020245 (2023-12-02)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/liyiyuian/Library/CloudStorage/GoogleDrive-
> liyiyuian@gmail.com/My Drive/2024/hbppi_manuscript/P80188.cxs"
Log from Wed Mar 6 14:38:32 2024 Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
UCSF ChimeraX version: 1.7rc202312020245 (2023-12-02)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/liyiyuian/Downloads/AF-P80188-F1-model_v4.pdb
AF-P80188-F1-model_v4.pdb title:
Alphafold monomer V2.0 prediction for neutrophil gelatinase- associated
lipocalin (P80188) [more info...]
Chain information for AF-P80188-F1-model_v4.pdb #1
---
Chain | Description | UniProt
A | neutrophil gelatinase-associated lipocalin | NGAL_HUMAN 1-198
> select
> :15,16,19,26,27,28,29,30,31,32,33,69,72,73,76,77,79,80,81,84,89,91,92,93,96,97,98,100,101,102,103,104,106,107,153,156,157,159,160,161,162,163,164,165,166,217,218,219,220,356,357,365,367,368,374,375,376,377,378,379,380,381,382,383,418,640,641,643,644,645,646,647,648,649,650,651,652,653,654,655,656,657,658,659,678,682,685
370 atoms, 364 bonds, 45 residues, 1 model selected
> color #1 #c2d79aff
> select
> :15,16,19,26,27,28,29,30,31,32,33,69,72,73,76,77,79,80,81,84,89,91,92,93,96,97,98,100,101,102,103,104,106,107,153,156,157,159,160,161,162,163,164,165,166,217,218,219,220,356,357,365,367,368,374,375,376,377,378,379,380,381,382,383,418,640,641,643,644,645,646,647,648,649,650,651,652,653,654,655,656,657,658,659,678,682,685
370 atoms, 364 bonds, 45 residues, 1 model selected
> color #98971a sel
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> select :A
Nothing selected
> select A
Expected an objects specifier or a keyword
> select A
Expected an objects specifier or a keyword
> select :.A
Expected an objects specifier or a keyword
> select .A
Expected an objects specifier or a keyword
> select all
1596 atoms, 1637 bonds, 198 residues, 1 model selected
> color #a89984 sel
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color #a89984 ribbonssel
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color #a89984 ribbonssel
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color #a89984 ribbons sel
Expected ',' or a keyword
> color #a89984 ribbons sel
Expected ',' or a keyword
> color #a89984 ribbons, sel
Missing or invalid "what" argument: Should be one of 'All', 'atoms', 'bonds',
'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or
'surfaces'
> color ribbons #a89984 sel
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> preset "molecular surfaces" "atomic coloring (transparent)"
Using preset: Molecular Surfaces / Atomic Coloring (Transparent)
Changed 0 atom styles
Preset expands to these ChimeraX commands:
style (protein|nucleic|solvent) & @@draw_mode=0 stick
surface
color fromatoms targ s trans 70
> preset "molecular surfaces" "ghostly white"
Using preset: Molecular Surfaces / Ghostly White
Changed 0 atom styles
Preset expands to these ChimeraX commands:
style (protein|nucleic|solvent) & @@draw_mode=0 stick
surface
color white targ s trans 80
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> color bfactor sel
1596 atoms, 198 residues, 1 surfaces, atom bfactor range 41.1 to 98.9
> preset "molecular surfaces" "ghostly white"
Using preset: Molecular Surfaces / Ghostly White
Changed 0 atom styles
Preset expands to these ChimeraX commands:
style (protein|nucleic|solvent) & @@draw_mode=0 stick
surface
color white targ s trans 80
> select subtract #1
1 model selected
> select
> :15,16,19,26,27,28,29,30,31,32,33,69,72,73,76,77,79,80,81,84,89,91,92,93,96,97,98,100,101,102,103,104,106,107,153,156,157,159,160,161,162,163,164,165,166,217,218,219,220,356,357,365,367,368,374,375,376,377,378,379,380,381,382,383,418,640,641,643,644,645,646,647,648,649,650,651,652,653,654,655,656,657,658,659,678,682,685
370 atoms, 364 bonds, 45 residues, 1 model selected
> open
> /Users/liyiyuian/Downloads/Q96EP0_UniRef90_Q57KZ6_unrelaxed_rank_001_alphafold2_multimer_v3_model_3_seed_000.pdb
Chain information for
Q96EP0_UniRef90_Q57KZ6_unrelaxed_rank_001_alphafold2_multimer_v3_model_3_seed_000.pdb
#2
---
Chain | Description
A | No description available
B | No description available
> hide #!1 models
> color #2 bychain
> select add #1
1596 atoms, 1637 bonds, 198 residues, 2 models selected
> select subtract #1
1 model selected
> select add #2
10976 atoms, 11211 bonds, 1422 residues, 1 model selected
> close #1
> close
> open /Users/liyiyuian/Downloads/AF-P80188-F1-model_v4.pdb
AF-P80188-F1-model_v4.pdb title:
Alphafold monomer V2.0 prediction for neutrophil gelatinase- associated
lipocalin (P80188) [more info...]
Chain information for AF-P80188-F1-model_v4.pdb #1
---
Chain | Description | UniProt
A | neutrophil gelatinase-associated lipocalin | NGAL_HUMAN 1-198
> open
> /Users/liyiyuian/Downloads/P80188_UniRef90_A0A174QTT2_unrelaxed_rank_001_alphafold2_multimer_v3_model_3_seed_000.pdb
Chain information for
P80188_UniRef90_A0A174QTT2_unrelaxed_rank_001_alphafold2_multimer_v3_model_3_seed_000.pdb
#2
---
Chain | Description
A | No description available
B | No description available
> hide #1 models
> color #2 bychain
> ui tool show Matchmaker
> matchmaker #2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker AF-P80188-F1-model_v4.pdb, chain A (#1) with
P80188_UniRef90_A0A174QTT2_unrelaxed_rank_001_alphafold2_multimer_v3_model_3_seed_000.pdb,
chain A (#2), sequence alignment score = 1019.9
RMSD between 173 pruned atom pairs is 0.244 angstroms; (across all 198 pairs:
10.243)
> show #1 models
> preset "molecular surfaces" "ghostly white"
Using preset: Molecular Surfaces / Ghostly White
Changed 0 atom styles
Preset expands to these ChimeraX commands:
style (protein|nucleic|solvent) & @@draw_mode=0 stick
surface
color white targ s trans 80
> preset "molecular surfaces" "atomic coloring (transparent)"
Using preset: Molecular Surfaces / Atomic Coloring (Transparent)
Changed 0 atom styles
Preset expands to these ChimeraX commands:
style (protein|nucleic|solvent) & @@draw_mode=0 stick
surface
color fromatoms targ s trans 70
> preset "molecular surfaces" "ghostly white"
Using preset: Molecular Surfaces / Ghostly White
Changed 0 atom styles
Preset expands to these ChimeraX commands:
style (protein|nucleic|solvent) & @@draw_mode=0 stick
surface
color white targ s trans 80
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> preset "molecular surfaces" "ghostly white"
Using preset: Molecular Surfaces / Ghostly White
Changed 0 atom styles
Preset expands to these ChimeraX commands:
style (protein|nucleic|solvent) & @@draw_mode=0 stick
surface
color white targ s trans 80
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> save /Users/liyiyuian/Downloads/P80188_UniRef90_A0A174QTT2.png width 2000
> height 2000 supersample 3 transparentBackground true
> hide #!2 models
> select all
4051 atoms, 4144 bonds, 504 residues, 2 models selected
> color #a89984 surfaces
> color #928374 surfaces
> preset "molecular surfaces" "ghostly white"
Using preset: Molecular Surfaces / Ghostly White
Changed 0 atom styles
Preset expands to these ChimeraX commands:
style (protein|nucleic|solvent) & @@draw_mode=0 stick
surface
color white targ s trans 80
> color #928374 ribbons
> select subtract #1
2455 atoms, 2507 bonds, 306 residues, 4 models selected
> 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 name mygreen 184, 187, 38,30
Missing or invalid "color" argument: Color must be 3 or 4 comma-separated
numbers 0-100
> color name mygreen 72.2, 1873.37, 14.9,30
Missing or invalid "color" argument: Color must be 3 or 4 comma-separated
numbers 0-100
> color name mygreen 72.2, 1873.37, 14.9,0.3
Missing or invalid "color" argument: Color must be 3 or 4 comma-separated
numbers 0-100
> color name mygreen 72.2, 1873.37, 14.9,30
Missing or invalid "color" argument: Color must be 3 or 4 comma-separated
numbers 0-100
> color name mygreen 72.2, 73.37, 14.9,30
Missing or invalid "color" argument: Color must be 3 or 4 comma-separated
numbers 0-100
> color name mygreen 72, 73,15,30
Missing or invalid "color" argument: Color must be 3 or 4 comma-separated
numbers 0-100
> color name mygreen 72,73,15,30
Color 'mygreen' is 70% transparent: rgba(72%, 73%, 15%, 30%) hex: #b8ba264d
> select
> :1,4,5,7,8,9,11,12,14,15,18,19,21,22,24,52,54,55,56,57,58,59,60,61,62,63,65,66,67,68,69,71,73,87,88,89,91,92,96,97,98,99,100,113,115,118,119,120,121,122,125,142,144,146,151,152,153,155,186,188
1270 atoms, 1232 bonds, 163 residues, 2 models selected
> color mygreen sel
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color mygreen ribbons sel
Expected ',' or a keyword
> color sel mygreen
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> close #2
> select
> :1,4,5,7,8,9,11,12,14,15,18,19,21,22,24,52,54,55,56,57,58,59,60,61,62,63,65,66,67,68,69,71,73,87,88,89,91,92,96,97,98,99,100,113,115,118,119,120,121,122,125,142,144,146,151,152,153,155,186,188
471 atoms, 458 bonds, 60 residues, 1 model selected
> color sel mygreen
> select add #1
1596 atoms, 1637 bonds, 198 residues, 2 models selected
> color name mygreen 72,73,15,50
Color 'mygreen' is 50% transparent: rgba(72%, 73%, 15%, 50%) hex: #b8ba2680
> select
> :1,4,5,7,8,9,11,12,14,15,18,19,21,22,24,52,54,55,56,57,58,59,60,61,62,63,65,66,67,68,69,71,73,87,88,89,91,92,96,97,98,99,100,113,115,118,119,120,121,122,125,142,144,146,151,152,153,155,186,188
471 atoms, 458 bonds, 60 residues, 1 model selected
> color sel mygreen
> color name mygreen 72,73,15,100
Color 'mygreen' is opaque: rgb(72%, 73%, 15%) hex: #b8ba26
> select
> :1,4,5,7,8,9,11,12,14,15,18,19,21,22,24,52,54,55,56,57,58,59,60,61,62,63,65,66,67,68,69,71,73,87,88,89,91,92,96,97,98,99,100,113,115,118,119,120,121,122,125,142,144,146,151,152,153,155,186,188
471 atoms, 458 bonds, 60 residues, 1 model selected
> color sel mygreen
> select up
1081 atoms, 1106 bonds, 135 residues, 2 models selected
> select down
471 atoms, 458 bonds, 60 residues, 2 models selected
> color sel mygreen 27,52,53,50
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color name myblue 27,52,53,50
Color 'myblue' is 50% transparent: rgba(27%, 52%, 53%, 50%) hex: #45858780
> select
> :1,4,5,7,8,9,11,12,14,15,18,19,21,22,24,52,54,55,56,57,58,59,60,61,62,63,65,66,67,68,69,71,73,87,88,89,91,92,96,97,98,99,100,113,115,118,119,120,121,122,125,142,144,146,151,152,153,155,186,188
471 atoms, 458 bonds, 60 residues, 1 model selected
> color sel myblue
> select add #1
1596 atoms, 1637 bonds, 198 residues, 2 models selected
> select
> :1,4,10,18,20,22,25,27,29,31,34,36,37,38,45,47,49,51,54,56,63,65,74,91,104
190 atoms, 174 bonds, 25 residues, 1 model selected
> color sel mygreen
> color sel red
> preset "molecular surfaces" "ghostly white"
Using preset: Molecular Surfaces / Ghostly White
Changed 0 atom styles
Preset expands to these ChimeraX commands:
style (protein|nucleic|solvent) & @@draw_mode=0 stick
surface
color white targ s trans 80
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> select add #1
1596 atoms, 1637 bonds, 198 residues, 2 models selected
> color name mygrey 89,89,90,50
Color 'mygrey' is 50% transparent: rgba(89%, 89%, 90%, 50%) hex: #e3e3e680
> color all mygrey
> preset "molecular surfaces" "ghostly white"
Using preset: Molecular Surfaces / Ghostly White
Changed 0 atom styles
Preset expands to these ChimeraX commands:
style (protein|nucleic|solvent) & @@draw_mode=0 stick
surface
color white targ s trans 80
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> color all ribbons mygrey
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color all ribbons mygrey
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color ribbons all mygrey
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color ribbons mygrey
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color sel byhetero
> color sel bychain
> color sel bypolymer
> hide sel surfaces
> color mygrey
> select
> :1,4,5,7,8,9,11,12,14,15,18,19,21,22,24,52,54,55,56,57,58,59,60,61,62,63,65,66,67,68,69,71,73,87,88,89,91,92,96,97,98,99,100,113,115,118,119,120,121,122,125,142,144,146,151,152,153,155,186,188
471 atoms, 458 bonds, 60 residues, 1 model selected
> color sel myblue
> select
> :1,4,10,18,20,22,25,27,29,31,34,36,37,38,45,47,49,51,54,56,63,65,74,91,104
190 atoms, 174 bonds, 25 residues, 1 model selected
> color sel mygreen
> show sel surfaces
> hide sel surfaces
> select add #1
1596 atoms, 1637 bonds, 198 residues, 2 models selected
> select subtract #1
1 model selected
> select add #1
1596 atoms, 1637 bonds, 198 residues, 1 model selected
> show sel surfaces
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> preset "molecular surfaces" "atomic coloring (transparent)"
Using preset: Molecular Surfaces / Atomic Coloring (Transparent)
Changed 0 atom styles
Preset expands to these ChimeraX commands:
style (protein|nucleic|solvent) & @@draw_mode=0 stick
surface
color fromatoms targ s trans 70
> preset "molecular surfaces" "ghostly white"
Using preset: Molecular Surfaces / Ghostly White
Changed 0 atom styles
Preset expands to these ChimeraX commands:
style (protein|nucleic|solvent) & @@draw_mode=0 stick
surface
color white targ s trans 80
> preset "initial styles" "original look"
Using preset: Initial Styles / Original Look
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset "molecular surfaces" "ghostly white"
Using preset: Molecular Surfaces / Ghostly White
Changed 0 atom styles
Preset expands to these ChimeraX commands:
style (protein|nucleic|solvent) & @@draw_mode=0 stick
surface
color white targ s trans 80
> color mygrey
> hide sel surfaces
> color mygrey
> preset "molecular surfaces" "ghostly white"
Using preset: Molecular Surfaces / Ghostly White
Changed 0 atom styles
Preset expands to these ChimeraX commands:
style (protein|nucleic|solvent) & @@draw_mode=0 stick
surface
color white targ s trans 80
> preset "molecular surfaces" "atomic coloring (transparent)"
Using preset: Molecular Surfaces / Atomic Coloring (Transparent)
Changed 0 atom styles
Preset expands to these ChimeraX commands:
style (protein|nucleic|solvent) & @@draw_mode=0 stick
surface
color fromatoms targ s trans 70
> preset "molecular surfaces" "chain id coloring (opaque)"
Using 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
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> preset "overall look" interactive
Using preset: Overall Look / Interactive
Preset expands to these ChimeraX commands:
~set bg
graphics silhouettes f
lighting depthCue t
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> preset cartoons/nucleotides cylinders/stubs
Using preset: Cartoons/Nucleotides / Cylinders/Stubs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh tube rad 2 sides 24 thick 0.6
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides stubs
> preset "initial styles" "space-filling (chain colors)"
Using preset: Initial Styles / Space-Filling (Chain Colors)
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset "initial styles" "space-filling (single color)"
Using preset: Initial Styles / Space-Filling (Single Color)
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset "molecular surfaces" "ghostly white"
Using preset: Molecular Surfaces / Ghostly White
Changed 1596 atom styles
Preset expands to these ChimeraX commands:
style (protein|nucleic|solvent) & @@draw_mode=0 stick
surface
color white targ s trans 80
> preset "molecular surfaces" "atomic coloring (transparent)"
Using preset: Molecular Surfaces / Atomic Coloring (Transparent)
Changed 0 atom styles
Preset expands to these ChimeraX commands:
style (protein|nucleic|solvent) & @@draw_mode=0 stick
surface
color fromatoms targ s trans 70
> preset "initial styles" "original look"
Using preset: Initial Styles / Original Look
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> preset "molecular surfaces" "atomic coloring (transparent)"
Using preset: Molecular Surfaces / Atomic Coloring (Transparent)
Changed 0 atom styles
Preset expands to these ChimeraX commands:
style (protein|nucleic|solvent) & @@draw_mode=0 stick
surface
color fromatoms targ s trans 70
> rainbow sel
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for AF-P80188-F1-model_v4.pdb_A SES surface #1.1: minimum,
-11.77, mean 0.67, maximum 13.17
To also show corresponding color key, enter the above coulombic command and
add key true
> mlp sel
Map values for surface "AF-P80188-F1-model_v4.pdb_A SES surface": minimum
-28.05, mean -3.877, maximum 22.78
To also show corresponding color key, enter the above mlp command and add key
true
> rainbow sel
> coulombic sel
Coulombic values for AF-P80188-F1-model_v4.pdb_A SES surface #1.1: minimum,
-11.77, mean 0.67, maximum 13.17
To also show corresponding color key, enter the above coulombic command and
add key true
> color bfactor sel
1596 atoms, 198 residues, 1 surfaces, atom bfactor range 41.1 to 98.9
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> style sel stick
Changed 1596 atom styles
> style sel sphere
Changed 1596 atom styles
> style sel ball
Changed 1596 atom styles
> style sel sphere
Changed 1596 atom styles
> hide sel atoms
> show sel cartoons
> hide sel surfaces
> show sel surfaces
> preset "molecular surfaces" "atomic coloring (transparent)"
Using preset: Molecular Surfaces / Atomic Coloring (Transparent)
Changed 1596 atom styles
Preset expands to these ChimeraX commands:
style (protein|nucleic|solvent) & @@draw_mode=0 stick
surface
color fromatoms targ s trans 70
> select
> :1,4,5,7,8,9,11,12,14,15,18,19,21,22,24,52,54,55,56,57,58,59,60,61,62,63,65,66,67,68,69,71,73,87,88,89,91,92,96,97,98,99,100,113,115,118,119,120,121,122,125,142,144,146,151,152,153,155,186,188
471 atoms, 458 bonds, 60 residues, 1 model selected
> color sel myblue
> select
> :1,4,10,18,20,22,25,27,29,31,34,36,37,38,45,47,49,51,54,56,63,65,74,91,104
190 atoms, 174 bonds, 25 residues, 1 model selected
> color sel mygreen
> select add #1
1596 atoms, 1637 bonds, 198 residues, 2 models selected
> select subtract #1
1 model selected
> lighting soft
> lighting full
> lighting flat
> lighting shadows true intensity 0.5
> graphics silhouettes false
> lighting full
> lighting soft
> lighting simple
[Repeated 5 time(s)]
> volume style surface
No volumes specified
> volume style mesh
No volumes specified
> volume style mesh
No volumes specified
> volume style image
No volumes specified
> ui tool show "Surface Color"
> color #1 #45858736
> select
> :1,4,5,7,8,9,11,12,14,15,18,19,21,22,24,52,54,55,56,57,58,59,60,61,62,63,65,66,67,68,69,71,73,87,88,89,91,92,96,97,98,99,100,113,115,118,119,120,121,122,125,142,144,146,151,152,153,155,186,188
471 atoms, 458 bonds, 60 residues, 1 model selected
> color sel myblue
> select
> :1,4,10,18,20,22,25,27,29,31,34,36,37,38,45,47,49,51,54,56,63,65,74,91,104
190 atoms, 174 bonds, 25 residues, 1 model selected
> color sel mygreen
> color #1 #95919836
> select
> :1,4,5,7,8,9,11,12,14,15,18,19,21,22,24,52,54,55,56,57,58,59,60,61,62,63,65,66,67,68,69,71,73,87,88,89,91,92,96,97,98,99,100,113,115,118,119,120,121,122,125,142,144,146,151,152,153,155,186,188
471 atoms, 458 bonds, 60 residues, 1 model selected
> color sel myblue
> select
> :1,4,10,18,20,22,25,27,29,31,34,36,37,38,45,47,49,51,54,56,63,65,74,91,104
190 atoms, 174 bonds, 25 residues, 1 model selected
> color sel mygreen
> select add #1
1596 atoms, 1637 bonds, 198 residues, 2 models selected
> color #1 #95919880
> select
> :1,4,5,7,8,9,11,12,14,15,18,19,21,22,24,52,54,55,56,57,58,59,60,61,62,63,65,66,67,68,69,71,73,87,88,89,91,92,96,97,98,99,100,113,115,118,119,120,121,122,125,142,144,146,151,152,153,155,186,188
471 atoms, 458 bonds, 60 residues, 1 model selected
> color sel myblue
> select
> :1,4,10,18,20,22,25,27,29,31,34,36,37,38,45,47,49,51,54,56,63,65,74,91,104
190 atoms, 174 bonds, 25 residues, 1 model selected
> color sel mygreen
> select add #1
1596 atoms, 1637 bonds, 198 residues, 2 models selected
> color name mygreen 72,73,15,50
Color 'mygreen' is 50% transparent: rgba(72%, 73%, 15%, 50%) hex: #b8ba2680
> color name myblue 27,52,53,50
Color 'myblue' is 50% transparent: rgba(27%, 52%, 53%, 50%) hex: #45858780
> color name mygrey 89,89,90,50
Color 'mygrey' is 50% transparent: rgba(89%, 89%, 90%, 50%) hex: #e3e3e680
> color name mygrey 89,89,90,50
Color 'mygrey' is 50% transparent: rgba(89%, 89%, 90%, 50%) hex: #e3e3e680
> select
> :1,4,5,7,8,9,11,12,14,15,18,19,21,22,24,52,54,55,56,57,58,59,60,61,62,63,65,66,67,68,69,71,73,87,88,89,91,92,96,97,98,99,100,113,115,118,119,120,121,122,125,142,144,146,151,152,153,155,186,188
471 atoms, 458 bonds, 60 residues, 1 model selected
> color sel myblue
> select
> :1,4,10,18,20,22,25,27,29,31,34,36,37,38,45,47,49,51,54,56,63,65,74,91,104
190 atoms, 174 bonds, 25 residues, 1 model selected
> color sel mygreen
> select add #1
1596 atoms, 1637 bonds, 198 residues, 2 models selected
> select subtract #1
1 model selected
> show cartoons
> hide cartoons
> hide surfaces
> show surfaces
> hide surfaces
> show cartoons
> show surfaces
> hide surfaces
> show surfaces
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> preset "overall look" "publication 2 (depth-cued)"
Using preset: Overall Look / Publication 2 (Depth-Cued)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes f
lighting depthCue t
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> save /Users/liyiyuian/Downloads/P80188.cxs
> transparency 50,s
Missing or invalid "percent" argument: Expected a number
> transparency 50 surfaces
> transparency 80 surfaces
> transparency 30 surfaces
> transparency 40 surfaces
> transparency 50 surfaces
> color grey cartoons
> hide surfaces
> show surfaces
> transparency 90 surfaces
> transparency 50 surfaces
> show cartoons
[Repeated 2 time(s)]
> show surfaces
> show ribbons
> view
> transparency 90 surfaces
> transparency 40 surfaces
> nucleotides atoms
> style nucleic stick
Changed 0 atom styles
> hide surfaces
> hide cartoons
> show cartoons
> show surfaces
> presents
Unknown command: presents
> preset
Missing or invalid "text1" argument: Expected a text string
> silhouettes true
Unknown command: silhouettes true
> silhouettes on
Unknown command: silhouettes on
> graphics silhouettes true
> set depthCueing false
Expected a keyword
> preset "molecular surfaces" "atomic coloring (transparent)"
Using preset: Molecular Surfaces / Atomic Coloring (Transparent)
Changed 0 atom styles
Preset expands to these ChimeraX commands:
style (protein|nucleic|solvent) & @@draw_mode=0 stick
surface
color fromatoms targ s trans 70
> preset "molecular surfaces" "chain id coloring (opaque)"
Using 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
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> hide surfaces
> preset "initial styles" "original look"
Using preset: Initial Styles / Original Look
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset "molecular surfaces" "ghostly white"
Using preset: Molecular Surfaces / Ghostly White
Changed 0 atom styles
Preset expands to these ChimeraX commands:
style (protein|nucleic|solvent) & @@draw_mode=0 stick
surface
color white targ s trans 80
> select add #1
1596 atoms, 1637 bonds, 198 residues, 1 model selected
> color grey
> color mygrey
No help found for 'help:user/commands/presets.html'
> help help:user/preferences.html#startup
> select
> :1,4,5,7,8,9,11,12,14,15,18,19,21,22,24,52,54,55,56,57,58,59,60,61,62,63,65,66,67,68,69,71,73,87,88,89,91,92,96,97,98,99,100,113,115,118,119,120,121,122,125,142,144,146,151,152,153,155,186,188
471 atoms, 458 bonds, 60 residues, 1 model selected
> color sel myblue
> select
> :1,4,10,18,20,22,25,27,29,31,34,36,37,38,45,47,49,51,54,56,63,65,74,91,104
190 atoms, 174 bonds, 25 residues, 1 model selected
> color sel mygreen
> undo
[Repeated 2 time(s)]
> transparency 50 surfaces
> transparency 90 surfaces
> color name mygrey 89,89,90,10
Color 'mygrey' is 90% transparent: rgba(89%, 89%, 90%, 10%) hex: #e3e3e61a
> color mygrey surfaces
> color mygrey cartoons
> color grey cartoons
> select
> :1,4,5,7,8,9,11,12,14,15,18,19,21,22,24,52,54,55,56,57,58,59,60,61,62,63,65,66,67,68,69,71,73,87,88,89,91,92,96,97,98,99,100,113,115,118,119,120,121,122,125,142,144,146,151,152,153,155,186,188
471 atoms, 458 bonds, 60 residues, 1 model selected
> color sel myblue surfaces
> color name mygreen 72,73,15,50
Color 'mygreen' is 50% transparent: rgba(72%, 73%, 15%, 50%) hex: #b8ba2680
> color name myblue 27,52,53,50
Color 'myblue' is 50% transparent: rgba(27%, 52%, 53%, 50%) hex: #45858780
> color name mygrey 89,89,90,10
Color 'mygrey' is 90% transparent: rgba(89%, 89%, 90%, 10%) hex: #e3e3e61a
> color mygrey surfaces
> color grey cartoons
> select
> :1,4,5,7,8,9,11,12,14,15,18,19,21,22,24,52,54,55,56,57,58,59,60,61,62,63,65,66,67,68,69,71,73,87,88,89,91,92,96,97,98,99,100,113,115,118,119,120,121,122,125,142,144,146,151,152,153,155,186,188
471 atoms, 458 bonds, 60 residues, 1 model selected
> color sel myblue
> select
> :1,4,10,18,20,22,25,27,29,31,34,36,37,38,45,47,49,51,54,56,63,65,74,91,104
190 atoms, 174 bonds, 25 residues, 1 model selected
> color sel mygreen
> transparency 50 surfaces
> graphics silhouettes true
> color name mygreen 72,73,15,10
Color 'mygreen' is 90% transparent: rgba(72%, 73%, 15%, 10%) hex: #b8ba261a
> color name myblue 27,52,53,10
Color 'myblue' is 90% transparent: rgba(27%, 52%, 53%, 10%) hex: #4585871a
> color name mygrey 89,89,90,10
Color 'mygrey' is 90% transparent: rgba(89%, 89%, 90%, 10%) hex: #e3e3e61a
> color mygrey surfaces
> color grey cartoons
> select
> :1,4,5,7,8,9,11,12,14,15,18,19,21,22,24,52,54,55,56,57,58,59,60,61,62,63,65,66,67,68,69,71,73,87,88,89,91,92,96,97,98,99,100,113,115,118,119,120,121,122,125,142,144,146,151,152,153,155,186,188
471 atoms, 458 bonds, 60 residues, 1 model selected
> color sel myblue
> select
> :1,4,10,18,20,22,25,27,29,31,34,36,37,38,45,47,49,51,54,56,63,65,74,91,104
190 atoms, 174 bonds, 25 residues, 1 model selected
> color sel mygreen
> transparency 50 surfaces
> graphics silhouettes true
> select add #1
1596 atoms, 1637 bonds, 198 residues, 2 models selected
> select subtract #1
1 model selected
> color black cartoons
> color all black cartoons
> graphics silhouettes false
> color name mygreen 72,73,15,10
Color 'mygreen' is 90% transparent: rgba(72%, 73%, 15%, 10%) hex: #b8ba261a
> color name myblue 27,52,53,10
Color 'myblue' is 90% transparent: rgba(27%, 52%, 53%, 10%) hex: #4585871a
> color name mygrey 89,89,90,10
Color 'mygrey' is 90% transparent: rgba(89%, 89%, 90%, 10%) hex: #e3e3e61a
> color mygrey surfaces
> color grey cartoons
> select add #1
1596 atoms, 1637 bonds, 198 residues, 1 model selected
> color #1 #282828ff
> color #1 #1a1b1bff
> hide sel surfaces
> color name mygreen 72,73,15,10
Color 'mygreen' is 90% transparent: rgba(72%, 73%, 15%, 10%) hex: #b8ba261a
> color name myblue 27,52,53,10
Color 'myblue' is 90% transparent: rgba(27%, 52%, 53%, 10%) hex: #4585871a
> color name mygrey 89,89,90,10
Color 'mygrey' is 90% transparent: rgba(89%, 89%, 90%, 10%) hex: #e3e3e61a
> color mygrey surfaces
> color grey cartoons
> show sel surfaces
> select
> :1,4,5,7,8,9,11,12,14,15,18,19,21,22,24,52,54,55,56,57,58,59,60,61,62,63,65,66,67,68,69,71,73,87,88,89,91,92,96,97,98,99,100,113,115,118,119,120,121,122,125,142,144,146,151,152,153,155,186,188
471 atoms, 458 bonds, 60 residues, 1 model selected
> color sel myblue surfaces
> select
> :1,4,10,18,20,22,25,27,29,31,34,36,37,38,45,47,49,51,54,56,63,65,74,91,104
190 atoms, 174 bonds, 25 residues, 1 model selected
> color sel mygreen surfaces
> transparency 50 surfaces
> select add #1
1596 atoms, 1637 bonds, 198 residues, 2 models selected
> graphics silhouettes true
> save /Users/liyiyuian/Downloads/P80188_UniRef90_A0A174QTT2.png width 2000
> height 2000 supersample 3 transparentBackground true
> select subtract #1
1 model selected
> save /Users/liyiyuian/Downloads/P80188_UniRef90_A0A174QTT2.png width 2000
> height 2000 supersample 3 transparentBackground true
> save /Users/liyiyuian/Downloads/P80188_UniRef90_A0A174QTT2.png width 5000
> height 5000 supersample 3 transparentBackground true
> hide target m
> open /Users/liyiyuian/Downloads/P80188_UniRef90_A0A174QTT2.png
Image mode RGBA is not supported (L, P, I;16, I;16B, I;16L, I;16S, F, F;32BF,
I, RGB)
> open
> /Users/liyiyuian/Downloads/P80188_UniRef90_A0A174QTT2_unrelaxed_rank_001_alphafold2_multimer_v3_model_3_seed_000.pdb
Chain information for
P80188_UniRef90_A0A174QTT2_unrelaxed_rank_001_alphafold2_multimer_v3_model_3_seed_000.pdb
#2
---
Chain | Description
A | No description available
B | No description available
> color #2 bychain
> color mygrey surfaces
> surface showPatches
> show surfaces
> color mygrey surfaces
> transparency 50 surfaces
> select
> :1,4,5,7,8,9,11,12,14,15,18,19,21,22,24,52,54,55,56,57,58,59,60,61,62,63,65,66,67,68,69,71,73,87,88,89,91,92,96,97,98,99,100,113,115,118,119,120,121,122,125,142,144,146,151,152,153,155,186,188.A
Expected an objects specifier or a keyword
> select
> /A:1,4,5,7,8,9,11,12,14,15,18,19,21,22,24,52,54,55,56,57,58,59,60,61,62,63,65,66,67,68,69,71,73,87,88,89,91,92,96,97,98,99,100,113,115,118,119,120,121,122,125,142,144,146,151,152,153,155,186,188
942 atoms, 916 bonds, 120 residues, 2 models selected
> color sel myblue surfaces
> select
> /A:1,4,10,18,20,22,25,27,29,31,34,36,37,38,45,47,49,51,54,56,63,65,74,91,104
380 atoms, 348 bonds, 50 residues, 2 models selected
> color sel mygreen surfaces
> select /A
3191 atoms, 3273 bonds, 396 residues, 2 models selected
> color sel mygrey ribbons
> color list
3 custom colors: myblue
, mygreen
, and mygrey
.
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
.
> select /A
3191 atoms, 3273 bonds, 396 residues, 2 models selected
> color sel gray ribbons
> select /B
860 atoms, 871 bonds, 108 residues, 1 model selected
> color sel grey ribbons
> select add #2
2455 atoms, 2507 bonds, 306 residues, 2 models selected
> hide #!2 models
> show #!1 models
> select subtract #2
2 models selected
> color name mygreen 72,73,15,20
Color 'mygreen' is 80% transparent: rgba(72%, 73%, 15%, 20%) hex: #b8ba2633
> color name myblue 27,52,53,20
Color 'myblue' is 80% transparent: rgba(27%, 52%, 53%, 20%) hex: #45858733
> color name mygrey 89,89,90,20
Color 'mygrey' is 80% transparent: rgba(89%, 89%, 90%, 20%) hex: #e3e3e633
> color mygrey surfaces
> color grey cartoons
> select
> :1,4,5,7,8,9,11,12,14,15,18,19,21,22,24,52,54,55,56,57,58,59,60,61,62,63,65,66,67,68,69,71,73,87,88,89,91,92,96,97,98,99,100,113,115,118,119,120,121,122,125,142,144,146,151,152,153,155,186,188
1270 atoms, 1232 bonds, 163 residues, 2 models selected
> color sel myblue surfaces
> select
> :1,4,10,18,20,22,25,27,29,31,34,36,37,38,45,47,49,51,54,56,63,65,74,91,104
580 atoms, 526 bonds, 75 residues, 2 models selected
> color sel mygreen surfaces
> transparency 50 surfaces
> graphics silhouettes true
> ui tool show Matchmaker
> matchmaker #!2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker AF-P80188-F1-model_v4.pdb, chain A (#1) with
P80188_UniRef90_A0A174QTT2_unrelaxed_rank_001_alphafold2_multimer_v3_model_3_seed_000.pdb,
chain A (#2), sequence alignment score = 1019.9
RMSD between 173 pruned atom pairs is 0.244 angstroms; (across all 198 pairs:
10.243)
> hide #!1 models
> show #!1 models
> select add #1
1986 atoms, 1989 bonds, 248 residues, 5 models selected
> select add #2
4051 atoms, 4144 bonds, 504 residues, 5 models selected
> select subtract #2
1596 atoms, 1637 bonds, 198 residues, 4 models selected
> select subtract #1
1 model selected
> save /Users/liyiyuian/Downloads/P80188_UniRef90_A0A174QTT2.jpeg width 5000
> height 5000 supersample 3 transparentBackground true
The JPEG file format does not support transparency, use PNG or TIFF instead.
> save /Users/liyiyuian/Downloads/P80188_UniRef90_A0A174QTT2.tiff width 5000
> height 5000 supersample 3 transparentBackground true
> hide #!1 models
> show #!2 models
> show #!1 models
> hide #!1 models
> show surfaces
> color mygrey surfaces
> transparency 50 surfaces
> select
> /A:1,4,5,7,8,9,11,12,14,15,18,19,21,22,24,52,54,55,56,57,58,59,60,61,62,63,65,66,67,68,69,71,73,87,88,89,91,92,96,97,98,99,100,113,115,118,119,120,121,122,125,142,144,146,151,152,153,155,186,188
942 atoms, 916 bonds, 120 residues, 2 models selected
> select
> /A:1,4,10,18,20,22,25,27,29,31,34,36,37,38,45,47,49,51,54,56,63,65,74,91,104
380 atoms, 348 bonds, 50 residues, 2 models selected
> color sel mygreen surfaces
> select /A
3191 atoms, 3273 bonds, 396 residues, 2 models selected
> color sel gray ribbons
> select /B
860 atoms, 871 bonds, 108 residues, 1 model selected
> color sel grey ribbons
> select add #2
2455 atoms, 2507 bonds, 306 residues, 2 models selected
> select subtract #2
2 models selected
> show surfaces
> color mygrey surfaces
> transparency 50 surfaces
> select
> /A:1,4,5,7,8,9,11,12,14,15,18,19,21,22,24,52,54,55,56,57,58,59,60,61,62,63,65,66,67,68,69,71,73,87,88,89,91,92,96,97,98,99,100,113,115,118,119,120,121,122,125,142,144,146,151,152,153,155,186,188
942 atoms, 916 bonds, 120 residues, 2 models selected
> color sel myblue surfaces
> select
> /A:1,4,10,18,20,22,25,27,29,31,34,36,37,38,45,47,49,51,54,56,63,65,74,91,104
380 atoms, 348 bonds, 50 residues, 2 models selected
> color sel mygreen surfaces
> select /A
3191 atoms, 3273 bonds, 396 residues, 2 models selected
> color sel gray ribbons
> select /B
860 atoms, 871 bonds, 108 residues, 1 model selected
> color sel grey ribbons
> save /Users/liyiyuian/Downloads/P80188.cxs
> hide #!2 models
> show #!1 models
> select add #2
2455 atoms, 2507 bonds, 306 residues, 2 models selected
> select subtract #2
2 models selected
> close #2
> color name mygreen 72,73,15,20
Color 'mygreen' is 80% transparent: rgba(72%, 73%, 15%, 20%) hex: #b8ba2633
> color name myblue 27,52,53,20
Color 'myblue' is 80% transparent: rgba(27%, 52%, 53%, 20%) hex: #45858733
> color name mygrey 89,89,90,20
Color 'mygrey' is 80% transparent: rgba(89%, 89%, 90%, 20%) hex: #e3e3e633
> color mygrey surfaces
> color grey cartoons
> select
> :1,4,5,7,8,9,11,12,14,15,18,19,21,22,24,52,54,55,56,57,58,59,60,61,62,63,65,66,67,68,69,71,73,87,88,89,91,92,96,97,98,99,100,113,115,118,119,120,121,122,125,142,144,146,151,152,153,155,186,188
471 atoms, 458 bonds, 60 residues, 1 model selected
> color sel myblue surfaces
> select
> :1,4,10,18,20,22,25,27,29,31,34,36,37,38,45,47,49,51,54,56,63,65,74,91,104
190 atoms, 174 bonds, 25 residues, 1 model selected
> color sel mygreen surfaces
> transparency 50 surfaces
> graphics silhouettes true
> transparency 40 surfaces
> transparency 30 surfaces
> select add #1
1596 atoms, 1637 bonds, 198 residues, 2 models selected
> select subtract #1
1 model selected
> transparency 20 surfaces
> transparency 10 surfaces
> transparency 20 surfaces
> save /Users/liyiyuian/Downloads/P80188_UniRef90_A0A174QTT2.tiff width 5000
> height 5000 supersample 3 transparentBackground true
> color name mygreen 72,73,15,20
Color 'mygreen' is 80% transparent: rgba(72%, 73%, 15%, 20%) hex: #b8ba2633
> color name myblue 27,52,53,20
Color 'myblue' is 80% transparent: rgba(27%, 52%, 53%, 20%) hex: #45858733
> color name mygrey 89,89,90,20
Color 'mygrey' is 80% transparent: rgba(89%, 89%, 90%, 20%) hex: #e3e3e633
> color mygrey surfaces
> color grey cartoons
> transparency 20 surfaces
> graphics silhouettes true
> color name mygreen 72,73,15,20
Color 'mygreen' is 80% transparent: rgba(72%, 73%, 15%, 20%) hex: #b8ba2633
> color name myblue 27,52,53,20
Color 'myblue' is 80% transparent: rgba(27%, 52%, 53%, 20%) hex: #45858733
> color name mygrey 89,89,90,20
Color 'mygrey' is 80% transparent: rgba(89%, 89%, 90%, 20%) hex: #e3e3e633
> color mygrey surfaces
> color grey cartoons
> transparency 20 surfaces
> graphics silhouettes true
> save /Users/liyiyuian/Downloads/P80188_UniRef90_A0A174QTT2.tiff width 5000
> height 5000 supersample 3 transparentBackground true
> select
> :1,4,5,7,8,9,11,12,14,15,18,19,21,22,24,52,54,55,56,57,58,59,60,61,62,63,65,66,67,68,69,71,73,87,88,89,91,92,96,97,98,99,100,113,115,118,119,120,121,122,125,142,144,146,151,152,153,155,186,188
471 atoms, 458 bonds, 60 residues, 1 model selected
> color sel myblue surfaces
> select
> :1,4,10,18,20,22,25,27,29,31,34,36,37,38,45,47,49,51,54,56,63,65,74,91,104
190 atoms, 174 bonds, 25 residues, 1 model selected
> color sel mygreen surfaces
> transparency 20 surfaces
> graphics silhouettes true
> save /Users/liyiyuian/Downloads/P80188_UniRef90_A0A174QTT2_interface.tiff
> width 5000 height 5000 supersample 3 transparentBackground true
> select none
Expected an objects specifier or a keyword
> select
1596 atoms, 1637 bonds, 198 residues, 1 model selected
> select none
Expected an objects specifier or a keyword
> color name mygreen 72,73,15,20
Color 'mygreen' is 80% transparent: rgba(72%, 73%, 15%, 20%) hex: #b8ba2633
> color name myblue 27,52,53,20
Color 'myblue' is 80% transparent: rgba(27%, 52%, 53%, 20%) hex: #45858733
> color name mygrey 89,89,90,20
Color 'mygrey' is 80% transparent: rgba(89%, 89%, 90%, 20%) hex: #e3e3e633
> color mygrey surfaces
> color grey cartoons
> transparency 20 surfaces
> graphics silhouettes true
> select subtract #1
1 model selected
> save /Users/liyiyuian/Downloads/P80188_UniRef90_A0A174QTT2.tiff width 5000
> height 5000 supersample 3 transparentBackground true
> select
> :1,4,5,7,8,9,11,12,14,15,18,19,21,22,24,52,54,55,56,57,58,59,60,61,62,63,65,66,67,68,69,71,73,87,88,89,91,92,96,97,98,99,100,113,115,118,119,120,121,122,125,142,144,146,151,152,153,155,186,188
471 atoms, 458 bonds, 60 residues, 1 model selected
> color sel myblue surfaces
> select
> :1,4,10,18,20,22,25,27,29,31,34,36,37,38,45,47,49,51,54,56,63,65,74,91,104
190 atoms, 174 bonds, 25 residues, 1 model selected
> color sel mygreen surfaces
> transparency 20 surfaces
> graphics silhouettes true
> select add #1
1596 atoms, 1637 bonds, 198 residues, 2 models selected
> select subtract #1
1 model selected
> save /Users/liyiyuian/Downloads/P80188_UniRef90_A0A174QTT2_interface.tiff
> width 5000 height 5000 supersample 3 transparentBackground true
> color name mygreen 72,73,15,30
Color 'mygreen' is 70% transparent: rgba(72%, 73%, 15%, 30%) hex: #b8ba264d
> color name myblue 27,52,53,30
Color 'myblue' is 70% transparent: rgba(27%, 52%, 53%, 30%) hex: #4585874d
> color name mygrey 89,89,90,30
Color 'mygrey' is 70% transparent: rgba(89%, 89%, 90%, 30%) hex: #e3e3e64d
> color mygrey surfaces
> color grey cartoons
> transparency 20 surfaces
> graphics silhouettes true
> color name mygreen 72,73,15,30
Color 'mygreen' is 70% transparent: rgba(72%, 73%, 15%, 30%) hex: #b8ba264d
> color name myblue 27,52,53,30
Color 'myblue' is 70% transparent: rgba(27%, 52%, 53%, 30%) hex: #4585874d
> color name mygrey 66,66,66,30
Color 'mygrey' is 70% transparent: rgba(66%, 66%, 66%, 30%) hex: #a8a8a84d
> color mygrey surfaces
> color grey cartoons
> transparency 20 surfaces
> graphics silhouettes true
> save /Users/liyiyuian/Downloads/P80188_UniRef90_A0A174QTT2.tiff width 5000
> height 5000 supersample 3 transparentBackground true
> select
> :1,4,5,7,8,9,11,12,14,15,18,19,21,22,24,52,54,55,56,57,58,59,60,61,62,63,65,66,67,68,69,71,73,87,88,89,91,92,96,97,98,99,100,113,115,118,119,120,121,122,125,142,144,146,151,152,153,155,186,188
471 atoms, 458 bonds, 60 residues, 1 model selected
> color sel myblue surfaces
> select
> :1,4,10,18,20,22,25,27,29,31,34,36,37,38,45,47,49,51,54,56,63,65,74,91,104
190 atoms, 174 bonds, 25 residues, 1 model selected
> color sel mygreen surfaces
> select add #1
1596 atoms, 1637 bonds, 198 residues, 2 models selected
> transparency 30 surfaces
> transparency 40 surfaces
> transparency 20 surfaces
[Repeated 1 time(s)]
> graphics silhouettes true
> select subtract #1
1 model selected
> save /Users/liyiyuian/Downloads/P80188_UniRef90_A0A174QTT2_interface.tiff
> width 5000 height 5000 supersample 3 transparentBackground true
> color name myred 80,13,11,30
Color 'myred' is 70% transparent: rgba(80%, 13%, 11%, 30%) hex: #cc211c4d
> color mygrey surfaces
> color grey cartoons
> transparency 20 surfaces
> graphics silhouettes true
> select
> :1,4,5,7,8,9,11,12,14,15,18,19,21,22,24,52,54,55,56,57,58,59,60,61,62,63,65,66,67,68,69,71,73,87,88,89,91,92,96,97,98,99,100,113,115,118,119,120,121,122,125,142,144,146,151,152,153,155,186,188
471 atoms, 458 bonds, 60 residues, 1 model selected
> color sel mtred surface
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color sel myred surfaces
> undo
[Repeated 3 time(s)]
> color mygrey surfaces
> color grey cartoons
> transparency 20 surfaces
> graphics silhouettes true
> select
> :1,4,5,7,8,9,11,12,14,15,18,19,21,22,24,52,54,55,56,57,58,59,60,61,62,63,65,66,67,68,69,71,73,87,88,89,91,92,96,97,98,99,100,113,115,118,119,120,121,122,125,142,144,146,151,152,153,155,186,188
471 atoms, 458 bonds, 60 residues, 1 model selected
> color sel myred surfaces
> select add #1
1596 atoms, 1637 bonds, 198 residues, 2 models selected
> color name mygreen 72,73,15,50
Color 'mygreen' is 50% transparent: rgba(72%, 73%, 15%, 50%) hex: #b8ba2680
> color name myblue 27,52,53,50
Color 'myblue' is 50% transparent: rgba(27%, 52%, 53%, 50%) hex: #45858780
> color name mygrey 66,66,66,50
Color 'mygrey' is 50% transparent: rgba(66%, 66%, 66%, 50%) hex: #a8a8a880
> color name myred 80,13,11,50
Color 'myred' is 50% transparent: rgba(80%, 13%, 11%, 50%) hex: #cc211c80
> color sel myred surfaces
> color name mygreen 72,73,15,80
Color 'mygreen' is 20% transparent: rgba(72%, 73%, 15%, 80%) hex: #b8ba26cc
> color name myblue 27,52,53,80
Color 'myblue' is 20% transparent: rgba(27%, 52%, 53%, 80%) hex: #458587cc
> color name mygrey 66,66,66,80
Color 'mygrey' is 20% transparent: rgba(66%, 66%, 66%, 80%) hex: #a8a8a8cc
> color name myred 80,13,11,80
Color 'myred' is 20% transparent: rgba(80%, 13%, 11%, 80%) hex: #cc211ccc
> color mygrey surfaces
> color grey cartoons
> color mygrey surfaces
> color grey cartoons
> transparency 20 surfaces
> graphics silhouettes true
> select
> :1,4,5,7,8,9,11,12,14,15,18,19,21,22,24,52,54,55,56,57,58,59,60,61,62,63,65,66,67,68,69,71,73,87,88,89,91,92,96,97,98,99,100,113,115,118,119,120,121,122,125,142,144,146,151,152,153,155,186,188
471 atoms, 458 bonds, 60 residues, 1 model selected
> color sel myred surfaces
> save /Users/liyiyuian/Downloads/P80188_UniRef90_A0A174QTT2_bac.tiff width
> 5000 height 5000 supersample 3 transparentBackground true
> color name mygreen 72,73,15,80
Color 'mygreen' is 20% transparent: rgba(72%, 73%, 15%, 80%) hex: #b8ba26cc
> color name myblue 27,52,53,80
Color 'myblue' is 20% transparent: rgba(27%, 52%, 53%, 80%) hex: #458587cc
> color name mygrey 66,66,66,80
Color 'mygrey' is 20% transparent: rgba(66%, 66%, 66%, 80%) hex: #a8a8a8cc
> color name myred 80,13,11,80
Color 'myred' is 20% transparent: rgba(80%, 13%, 11%, 80%) hex: #cc211ccc
> color mygrey surfaces
> color grey cartoons
> transparency 20 surfaces
> graphics silhouettes true
> select add #1
1596 atoms, 1637 bonds, 198 residues, 2 models selected
> select subtract #1
1 model selected
> save /Users/liyiyuian/Downloads/P80188_UniRef90_A0A174QTT2.tiff width 5000
> height 5000 supersample 3 transparentBackground true
> select
> :1,4,5,7,8,9,11,12,14,15,18,19,21,22,24,52,54,55,56,57,58,59,60,61,62,63,65,66,67,68,69,71,73,87,88,89,91,92,96,97,98,99,100,113,115,118,119,120,121,122,125,142,144,146,151,152,153,155,186,188
471 atoms, 458 bonds, 60 residues, 1 model selected
> color sel myblue surfaces
> select
> :1,4,10,18,20,22,25,27,29,31,34,36,37,38,45,47,49,51,54,56,63,65,74,91,104
190 atoms, 174 bonds, 25 residues, 1 model selected
> color sel mygreen surfaces
> select add #1
1596 atoms, 1637 bonds, 198 residues, 2 models selected
> select subtract #1
1 model selected
> transparency 20 surfaces
> graphics silhouettes true
> save /Users/liyiyuian/Downloads/P80188_UniRef90_A0A174QTT2_interface.tiff
> width 5000 height 5000 supersample 3 transparentBackground true
> color mygrey surfaces
> color grey cartoons
> transparency 20 surfaces
> graphics silhouettes true
> select
> :1,4,5,7,8,9,11,12,14,15,18,19,21,22,24,52,54,55,56,57,58,59,60,61,62,63,65,66,67,68,69,71,73,87,88,89,91,92,96,97,98,99,100,113,115,118,119,120,121,122,125,142,144,146,151,152,153,155,186,188
471 atoms, 458 bonds, 60 residues, 1 model selected
> color sel myred surfaces
> select add #1
1596 atoms, 1637 bonds, 198 residues, 2 models selected
> select subtract #1
1 model selected
> save /Users/liyiyuian/Downloads/P80188_UniRef90_A0A174QTT2_bac.tiff width
> 5000 height 5000 supersample 3 transparentBackground true
> color name mygreen 72,73,15,80
Color 'mygreen' is 20% transparent: rgba(72%, 73%, 15%, 80%) hex: #b8ba26cc
> color name myblue 27,52,53,80
Color 'myblue' is 20% transparent: rgba(27%, 52%, 53%, 80%) hex: #458587cc
> color name mygrey 66,66,66,80
Color 'mygrey' is 20% transparent: rgba(66%, 66%, 66%, 80%) hex: #a8a8a8cc
> color name myred 80,13,11,80
Color 'myred' is 20% transparent: rgba(80%, 13%, 11%, 80%) hex: #cc211ccc
> color mygrey surfaces
> color grey cartoons
> transparency 20 surfaces
> graphics silhouettes true
> color bfactor
1596 atoms, 198 residues, 1 surfaces, atom bfactor range 41.1 to 98.9
> save /Users/liyiyuian/Downloads/P80188_UniRef90_A0A174QTT2_bfactor.tiff
> width 5000 height 5000 supersample 3 transparentBackground true
> save /Users/liyiyuian/Downloads/P80188.cxs
——— End of log from Wed Mar 6 14:38:32 2024 ———
opened ChimeraX session
> color name mygreen 72,73,15,80
Color 'mygreen' is 20% transparent: rgba(72%, 73%, 15%, 80%) hex: #b8ba26cc
> color name myblue 27,52,53,80
Color 'myblue' is 20% transparent: rgba(27%, 52%, 53%, 80%) hex: #458587cc
> color name mygrey 66,66,66,80
Color 'mygrey' is 20% transparent: rgba(66%, 66%, 66%, 80%) hex: #a8a8a8cc
> color name myred 80,13,11,80
Color 'myred' is 20% transparent: rgba(80%, 13%, 11%, 80%) hex: #cc211ccc
> show surfaces
> color mygrey surfaces
> color grey cartoons
> transparency 20 surfaces
> graphics silhouettes true
> color mygrey surfaces
> color grey cartoons
> transparency 20 surfaces
> graphics silhouettes true
> select
> :1,4,5,7,8,9,11,12,14,15,18,19,21,22,24,52,54,55,56,57,58,59,60,61,62,63,65,66,67,68,69,71,73,87,88,89,91,92,96,97,98,99,100,113,115,118,119,120,121,122,125,142,144,146,151,152,153,155,186,188
471 atoms, 458 bonds, 60 residues, 1 model selected
> color sel myred surfaces
> select add #1
1596 atoms, 1637 bonds, 198 residues, 2 models selected
> select subtract #1
1 model selected
> save /Users/liyiyuian/Downloads/P80188_UniRef90_A0A174QTT2_bac.tiff width
> 5000 height 5000 supersample 3 transparentBackground true
> color mygrey surfaces
> color grey cartoons
> transparency 20 surfaces
> graphics silhouettes true
> select
> :1,4,10,18,20,22,25,27,29,31,34,36,37,38,45,47,49,51,54,56,63,65,74,91,104
190 atoms, 174 bonds, 25 residues, 1 model selected
> color sel mygreen surfaces
> select :12,71
16 atoms, 14 bonds, 2 residues, 1 model selected
> color sel myblue surfaces
> select add #1
1596 atoms, 1637 bonds, 198 residues, 2 models selected
> select subtract #1
1 model selected
> save /Users/liyiyuian/Downloads/P80188_UniRef90_A0A174QTT2_interface.tiff
> width 5000 height 5000 supersample 3 transparentBackground true
> color mygrey surfaces
> color grey cartoons
> transparency 20 surfaces
> graphics silhouettes true
> select
> :1,4,5,7,8,9,11,12,14,15,18,19,21,22,24,52,54,55,56,57,58,59,60,61,62,63,65,66,67,68,69,71,73,87,88,89,91,92,96,97,98,99,100,113,115,118,119,120,121,122,125,142,144,146,151,152,153,155,186,188
471 atoms, 458 bonds, 60 residues, 1 model selected
> color sel myred surfaces
> select add #1
1596 atoms, 1637 bonds, 198 residues, 2 models selected
> save /Users/liyiyuian/Downloads/P80188_UniRef90_A0A174QTT2_bac.tiff width
> 5000 height 5000 supersample 3 transparentBackground true
> select subtract #1
1 model selected
> select add #1
1596 atoms, 1637 bonds, 198 residues, 1 model selected
> select subtract #1
1 model selected
> save /Users/liyiyuian/Downloads/P80188_UniRef90_A0A174QTT2_bac.back.tiff
> width 5000 height 5000 supersample 3 transparentBackground true
> color mygrey surfaces
> color grey cartoons
> transparency 20 surfaces
> graphics silhouettes true
> select
> :1,4,10,18,20,22,25,27,29,31,34,36,37,38,45,47,49,51,54,56,63,65,74,91,104
190 atoms, 174 bonds, 25 residues, 1 model selected
> color sel mygreen surfaces
> select :12,71
16 atoms, 14 bonds, 2 residues, 1 model selected
> color sel myblue surfaces
> select add #1
1596 atoms, 1637 bonds, 198 residues, 2 models selected
> save
> /Users/liyiyuian/Downloads/P80188_UniRef90_A0A174QTT2_interface.back.tiff
> width 5000 height 5000 supersample 3 transparentBackground true
===== Log before crash end =====
Log:
Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
UCSF ChimeraX version: 1.7rc202312020245 (2023-12-02)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/liyiyuian/Library/CloudStorage/GoogleDrive-
> liyiyuian@gmail.com/My
> Drive/2024/hbppi_manuscript/AF-P02751-F1-model_v4.pdb"
AF-P02751-F1-model_v4.pdb title:
Alphafold monomer V2.0 prediction for fibronectin (P02751) [more info...]
Chain information for AF-P02751-F1-model_v4.pdb #1
---
Chain | Description | UniProt
A | fibronectin | FINC_HUMAN 1-2477
OpenGL version: 4.1 Metal - 88
OpenGL renderer: Apple M3 Max
OpenGL vendor: Apple
Python: 3.11.2
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: Mac15,8
Model Number: Z1AW001C6LL/A
Chip: Apple M3 Max
Total Number of Cores: 16 (12 performance and 4 efficiency)
Memory: 128 GB
System Firmware Version: 10151.61.4
OS Loader Version: 10151.61.4
Software:
System Software Overview:
System Version: macOS 14.2.1 (23C71)
Kernel Version: Darwin 23.2.0
Time since boot: 15 days, 1 hour, 23 minutes
Graphics/Displays:
Apple M3 Max:
Chipset Model: Apple M3 Max
Type: GPU
Bus: Built-In
Total Number of Cores: 40
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
LG HDR WQHD:
Resolution: 6400 x 2666
UI Looks like: 3200 x 1333 @ 75.00Hz
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Television: Yes
ASUS MB16AH:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.4.1
Babel: 2.13.1
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
blosc2: 2.0.0
build: 0.10.0
certifi: 2022.12.7
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.13
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.1
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.49.1
ChimeraX-AtomicLibrary: 12.1.3
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.10.5
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.3.2
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.5
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.7rc202312020245
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.8
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.1.4
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.13
ChimeraX-ModelPanel: 1.4
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.1
ChimeraX-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.1
ChimeraX-PDB: 2.7.3
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.3
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: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.2
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.12.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.33.2
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.3.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.3
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.0
contourpy: 1.2.0
cxservices: 1.2.2
cycler: 0.12.1
Cython: 0.29.33
debugpy: 1.8.0
decorator: 5.1.1
docutils: 0.19
executing: 2.0.1
filelock: 3.9.0
fonttools: 4.46.0
funcparserlib: 2.0.0a0
glfw: 2.6.3
grako: 3.16.5
h5py: 3.10.0
html2text: 2020.1.16
idna: 3.6
ihm: 0.38
imagecodecs: 2023.9.18
imagesize: 1.4.1
ipykernel: 6.23.2
ipython: 8.14.0
ipython-genutils: 0.2.0
ipywidgets: 8.1.1
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.2.0
jupyter-core: 5.5.0
jupyterlab-widgets: 3.0.9
kiwisolver: 1.4.5
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.3
matplotlib: 3.7.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.8
netCDF4: 1.6.2
networkx: 3.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.7
numpy: 1.25.1
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.9.0
pickleshare: 0.7.5
Pillow: 10.0.1
pip: 23.0
pkginfo: 1.9.6
platformdirs: 4.0.0
prompt-toolkit: 3.0.41
psutil: 5.9.5
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.16.1
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.2801
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
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: 2023.3.post1
pyzmq: 25.1.1
qtconsole: 5.4.3
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.11.1
setuptools: 67.4.0
setuptools-scm: 7.0.5
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.7
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.5
sphinxcontrib-htmlhelp: 2.0.4
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.6
sphinxcontrib-serializinghtml: 1.1.9
stack-data: 0.6.3
superqt: 0.5.0
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2023.7.18
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.4
traitlets: 5.9.0
typing-extensions: 4.8.0
tzdata: 2023.3
urllib3: 2.1.0
wcwidth: 0.2.12
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.9
Change History (2)
comment:1 by , 20 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Window Toolkit |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash running file-save dialog |
comment:2 by , 20 months ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
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