id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
14726	Crash running file-save dialog	chimerax-bug-report@…	Eric Pettersen	"{{{
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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===== 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

}}}
"	defect	closed	normal		Window Toolkit		can't reproduce		Tom Goddard				all	ChimeraX