The following bug report has been submitted:
Platform: macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open /Users/kcervant/Downloads/I_think_it_Crashed.cxs format session
Log from Tue Aug 3 17:31:14 2021UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open /Users/kcervant/Downloads/Session_Try1.cxs format session
Log from Tue Aug 3 16:47:28 2021UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/kcervant/Downloads/6ltj.pdb format pdb
6ltj.pdb title:
Structure of nucleosome-bound human baf complex [more info...]
Chain information for 6ltj.pdb #1
---
Chain | Description
A E | histone H3.3
B F | histone H4
C G | histone H2A type 1
D H | histone H2B
I | transcription activator BRG1
J | actin-like protein 6A
K | β-actin
L | At-rich interactive domain-containing protein 1A
M | swi/SNF-related matrix-associated actin-dependent regulator of chromatin
subfamily B member 1
N O | swi/SNF complex subunit SMARCC2
P | swi/SNF-related matrix-associated actin-dependent regulator of chromatin
subfamily D member 1
Q | swi/SNF-related matrix-associated actin-dependent regulator of chromatin
subfamily E member 1
R | zinc finger protein ubi-D4
X | DNA (119-mer)
Y | DNA (119-mer)
Non-standard residues in 6ltj.pdb #1
---
ZN — zinc ion
> key colorTreatment by attribute
Invalid "colorTreatment" argument: Should be one of 'blended' or 'distinct'
> key colorTreatment byattribute
Invalid "colorTreatment" argument: Should be one of 'blended' or 'distinct'
> 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 show
Illegal color name: ""
> color show slategrey
Color 'slategrey' is opaque, 43.92% red, 50.2% green, and 56.47% blue
> open
> /Users/kcervant/Downloads/cBAF_6ltj_AF_RF_alignment_decipher_ndd_full.pdb
Summary of feedback from opening
/Users/kcervant/Downloads/cBAF_6ltj_AF_RF_alignment_decipher_ndd_full.pdb
---
warnings | Duplicate atom serial number found: 7144
Duplicate atom serial number found: 7145
Duplicate atom serial number found: 7146
Duplicate atom serial number found: 7147
Duplicate atom serial number found: 7318
64 messages similar to the above omitted
Chain information for cBAF_6ltj_AF_RF_alignment_decipher_ndd_full.pdb #2
---
Chain | Description
A E | No description available
B | No description available
C | No description available
D | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
X | No description available
Y | No description available
> show cartoons
> hide surfaces
> show cartoons
> hide surfaces
> hide surfaces
> show surfaces
> style sphere
Changed 91551 atom styles
> select Y
Nothing selected
> select X
Expected an objects specifier or a keyword
> select #2/Y:18-136
2455 atoms, 2757 bonds, 119 residues, 1 model selected
> select #2/X:18-136
2424 atoms, 2715 bonds, 119 residues, 1 model selected
> select #2/R:13-82
580 atoms, 595 bonds, 70 residues, 1 model selected
> select #2/Y:18-136
2455 atoms, 2757 bonds, 119 residues, 1 model selected
> rainbow sel
> color sel bychain
> color bfactor sel
2455 atoms, 119 residues, 1 surfaces, atom bfactor range 0 to 0
> color sel bychain
> rainbow sel
> show sel surfaces
> show sel cartoons
> preset cartoons/nucleotides ribbons/slabs
Changed 91550 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
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 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
> zoom 0.5
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> select #2/C:16-110
726 atoms, 735 bonds, 95 residues, 1 model selected
> select #2/F:25-101
614 atoms, 621 bonds, 77 residues, 1 model selected
> select #2/F:25-101
614 atoms, 621 bonds, 77 residues, 1 model selected
> select #2/G:15-109
727 atoms, 736 bonds, 95 residues, 1 model selected
> lighting simple
> set bgColor white
> set bgColor gray
> set bgColor black
> set bgColor white
> lighting soft
> lighting full
> lighting simple
> graphics silhouettes true
> lighting shadows true
> lighting shadows false
> view sel
> view
> view orient
> view orient
> view orient
> view orient
> ui tool show "Side View"
> ui tool show "Side View"
> view
> view
> view
> view sel
> view
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> ui tool show "Side View"
> ui tool show "Side View"
> zoom 0.9
> zoom 1.1
> zoom 1.1
> zoom 1.1
> zoom 1.1
> zoom 1.1
> lighting simple
> lighting soft
> lighting full
> lighting soft
> lighting full
> lighting flat
> lighting simple
> select #2/H:31-120
700 atoms, 711 bonds, 90 residues, 1 model selected
> select #2/I:350-1366
4640 atoms, 4740 bonds, 11 pseudobonds, 551 residues, 2 models selected
> select #2/H:31-120
700 atoms, 711 bonds, 90 residues, 1 model selected
> select #2/G:15-109
727 atoms, 736 bonds, 95 residues, 1 model selected
> select #2/F:25-101
614 atoms, 621 bonds, 77 residues, 1 model selected
> select #2/D:33-120
682 atoms, 693 bonds, 88 residues, 1 model selected
> select #2/C:16-110
726 atoms, 735 bonds, 95 residues, 1 model selected
> select #2/B:24-101
622 atoms, 629 bonds, 78 residues, 1 model selected
> select #2/G:15-109
727 atoms, 736 bonds, 95 residues, 1 model selected
> select #2/H:31-120
700 atoms, 711 bonds, 90 residues, 1 model selected
> select #2/I:350-1366
4640 atoms, 4740 bonds, 11 pseudobonds, 551 residues, 2 models selected
> select #2/J:1-429
3327 atoms, 3400 bonds, 429 residues, 1 model selected
> select #2/K:1-375
2925 atoms, 2988 bonds, 375 residues, 1 model selected
> select #2/L:1-2285
17018 atoms, 17531 bonds, 2285 residues, 1 model selected
> select #2/M:1-385
3098 atoms, 3163 bonds, 385 residues, 1 model selected
> select #2/N:423-952
2120 atoms, 2158 bonds, 3 pseudobonds, 261 residues, 2 models selected
> select #2/O:423-952
2632 atoms, 2692 bonds, 3 pseudobonds, 325 residues, 2 models selected
> select #2/P:1-515
4094 atoms, 4183 bonds, 515 residues, 1 model selected
> select #2/Q:217-411,1-216
6406 atoms, 6467 bonds, 411 residues, 1 model selected
> select #2/R:13-82
580 atoms, 595 bonds, 70 residues, 1 model selected
> select #2/X:18-136
2424 atoms, 2715 bonds, 119 residues, 1 model selected
> select #2/Y:18-136
2455 atoms, 2757 bonds, 119 residues, 1 model selected
> select #2/X:18-136
2424 atoms, 2715 bonds, 119 residues, 1 model selected
> hide #2.21 models
> hide #2.20 models
> show #2.21 models
> show #2.20 models
> select #2.20
2424 atoms, 119 residues, 1 model selected
> color red
> color sel red
> select #2.21
2455 atoms, 119 residues, 1 model selected
> clor sel red
Unknown command: clor sel red
> color sel red
> select #2.20/2.21
Expected an objects specifier or a keyword
> select #2.20+#2.21
Expected an objects specifier or a keyword
> select #2.20
2424 atoms, 119 residues, 1 model selected
> select add #2.21
4879 atoms, 238 residues, 2 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 sel crimson
> color sel skyblue
> color sel light blue
> color sel spring green
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> ui mousemode right translate
> ui mousemode right translate
> center
Unknown command: center
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.81221,0.094528,0.57565,-107.86,0.17297,0.90339,-0.3924,67.62,-0.55713,0.41828,0.71739,138.22
> ui mousemode right "pick blobs"
> ui mousemode right "tape measure"
> set bgColor black
> set bgColor white
> lighting simple
> lighting soft
> lighting full
> lighting simple
> lighting full
> lighting simple
> save /Users/kcervant/Desktop/image4.png supersample 3
> select
91551 atoms, 94410 bonds, 55 pseudobonds, 10445 residues, 5 models selected
> select #2.20
2424 atoms, 119 residues, 1 model selected
> select add #2.21
4879 atoms, 238 residues, 2 models selected
> colorlist
Unknown command: colorlist
> 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
.
> select maroon
Expected an objects specifier or a keyword
> color sel maroon
> move x
> move x
> move x
> move x
> move x
> move x
> move x
> move x
> move x
> move x
> move x
> move x
> move x
> move x
> move x
> move x
> move x
> move x
> move x
> move x
> move x
> move x
> move x
> move x
> move x
> move x
> move x
> move x
> move x
> move x
> move x
> move x
> move x
> move x
> move x
> move x
> move x
> move x
> move x
> move x
> move x
> move x
> move y
> zoom 0.9
> zoom 0.9
> zoom 0.9
> move y
> move y
> move y
> move y
> move y
> move y
> move y
> move y
> move y
> move y
> move y
> move y
> move y
> move y
> move y
> move y
> move y
> move y
> move y
> move y
> move y
> move y
> move y
> move y
> move y
> move y
> move y
> move y
> move y
> move y
> move y
> move y
> move y
> move y
> save
Missing or invalid "fileName" argument: Expected a file name
> save test_image
Cannot determine format for 'test_image'
> save test_image.jpeg
> save test_image.jpeg
> select #2.19
580 atoms, 70 residues, 1 model selected
> save /Users/kcervant/Desktop/image5.png supersample 3
> ui mousemode right translate
> 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 "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
> color white
> color gray
> 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
> mlp sel
Map values for surface "cBAF_6ltj_AF_RF_alignment_decipher_ndd_full.pdb_R SES
surface": minimum -27.86, mean -3.114, maximum 22.35
To also show corresponding color key, enter the above mlp command and add key
true
> mlp sel
Map values for surface "cBAF_6ltj_AF_RF_alignment_decipher_ndd_full.pdb_R SES
surface": minimum -27.86, mean -3.114, maximum 22.35
To also show corresponding color key, enter the above mlp command and add key
true
> coulombic sel
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/toolbar/tool.py", line 202, in callback
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/toolshed/info.py", line 379, in run_provider
return api._api_caller.run_provider(api, session, name, mgr, **kw)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/toolshed/__init__.py", line 1285, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/shortcuts/__init__.py", line 52, in run_provider
shortcuts.run_provider(session, name)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/shortcuts/shortcuts.py", line 1333, in run_provider
keyboard_shortcuts(session).try_shortcut(name)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/shortcuts/shortcuts.py", line 389, in try_shortcut
self.run_shortcut(keys)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/shortcuts/shortcuts.py", line 407, in run_shortcut
sc.run(self.session, status = self._enabled)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/shortcuts/shortcuts.py", line 326, in run
f(s)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/shortcuts/shortcuts.py", line 61, in func_plus_tip
func(cmd + " %s")(session)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/shortcuts/shortcuts.py", line 568, in run_expanded_command
run(session, cmd)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/shortcuts/shortcuts.py", line 511, in run
run_command(session, command, **kw)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/coulombic/cmd.py", line 90, in cmd_coulombic
assign_charges(session, needs_assignment, his_scheme, charge_method,
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/coulombic/coulombic.py", line 74, in assign_charges
cmd_addh(session, addh_structures, hbond=hbond)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/addh/cmd.py", line 63, in cmd_addh
add_h_func(session, structures, template=template, in_isolation=in_isolation,
**prot_schemes)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/addh/cmd.py", line 170, in hbond_add_hydrogens
add_hydrogens(session, atoms, type_info_for_atom, naming_schemas,
hydrogen_totals,
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/addh/hbond.py", line 245, in add_hydrogens
hbonds = find_hbonds(session, s_list, dist_slop=rec_dist_slop,
angle_slop=rec_angle_slop)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/hbonds/hbond.py", line 577, in find_hbonds
donor_hyds = hyd_positions(donor_atom)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/hbonds/hydpos.py", line 77, in hyd_positions
bond_positions(heavy_loc, geom, bond_len, bonded_locs, coplanar=coplanar))
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/atomic/bond_geom.py", line 73, in bond_positions
return planar_pos(bondee, bonded, bond_len, coplanar, toward, away, toward2,
away2)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/atomic/bond_geom.py", line 129, in planar_pos
pos = angle_pos(bondee, cur_bonded[0], bond_len, 120.0, coplanar)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/atomic/bond_geom.py", line 231, in angle_pos
raise ValueError("More than 2 coplanar positions specified!")
ValueError: More than 2 coplanar positions specified!
ValueError: More than 2 coplanar positions specified!
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/atomic/bond_geom.py", line 231, in angle_pos
raise ValueError("More than 2 coplanar positions specified!")
See log for complete Python traceback.
> surface transparency 50%
Invalid "transparency" argument: Expected a number
> surface transparency 50
> surface transparency 20
> surface transparency 10
> surface transparency 90
> surface transparency 80
> surface transparency 100
> surface transparency 90
> preset "overall look" publication
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
> 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 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
.
> save /Users/kcervant/Downloads/Session_Try1.cxs
——— End of log from Tue Aug 3 16:47:28 2021 ———
opened ChimeraX session
> 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 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
.
> view clip false
> view clip false
> show target m
> show target m
> show target m
> hide #!1 models
> log show
> models hide
Unknown command: models hide
> 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 ghost white
> color white
> hide #!2 models
> show #!1 models
> 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
> set bgColor white
> set bgColor black
> set bgColor white
> lighting simple
> lighting soft
> lighting full
> lighting simple
> select 6ltj.pdb_y SES surface
Expected an objects specifier or a keyword
> select #2.10
4640 atoms, 551 residues, 1 model selected
> select list
Expected an objects specifier or a keyword
> select chains
Expected an objects specifier or a keyword
> preset "initial styles" "original look"
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset "initial styles" sticks
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset "initial styles" cartoon
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> color ghostly white
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> select #1.20
580 atoms, 70 residues, 1 model selected
> close #1.13
> close #1
> close
> open /Users/kcervant/Downloads/6ltj.pdb
6ltj.pdb title:
Structure of nucleosome-bound human baf complex [more info...]
Chain information for 6ltj.pdb #1
---
Chain | Description
A E | histone H3.3
B F | histone H4
C G | histone H2A type 1
D H | histone H2B
I | transcription activator BRG1
J | actin-like protein 6A
K | β-actin
L | At-rich interactive domain-containing protein 1A
M | swi/SNF-related matrix-associated actin-dependent regulator of chromatin
subfamily B member 1
N O | swi/SNF complex subunit SMARCC2
P | swi/SNF-related matrix-associated actin-dependent regulator of chromatin
subfamily D member 1
Q | swi/SNF-related matrix-associated actin-dependent regulator of chromatin
subfamily E member 1
R | zinc finger protein ubi-D4
X | DNA (119-mer)
Y | DNA (119-mer)
Non-standard residues in 6ltj.pdb #1
---
ZN — zinc ion
> ui mousemode right translate
> ui mousemode right select
> select /O:912@CB
1 atom, 1 residue, 1 model selected
> preset "initial styles" cartoon
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> select X
Expected an objects specifier or a keyword
> select X
Expected an objects specifier or a keyword
> select chain X
Expected an objects specifier or a keyword
> select /X:18-136
2424 atoms, 2715 bonds, 119 residues, 1 model selected
> color sel black
> color sel orange
> select /Y:18-136
2455 atoms, 2757 bonds, 119 residues, 1 model selected
> color sel orange
> select /R:13-82
580 atoms, 595 bonds, 70 residues, 1 model selected
> select :ZN
1 atom, 1 residue, 1 model selected
> select /Q:172-276
860 atoms, 871 bonds, 105 residues, 1 model selected
> select /P:125-505
2015 atoms, 2055 bonds, 2 pseudobonds, 239 residues, 2 models selected
> select /O:423-952
2632 atoms, 2692 bonds, 3 pseudobonds, 325 residues, 2 models selected
> select /N:423-952
2120 atoms, 2158 bonds, 3 pseudobonds, 261 residues, 2 models selected
> select /O:423-952
2632 atoms, 2692 bonds, 3 pseudobonds, 325 residues, 2 models selected
> select /N:423-952
2120 atoms, 2158 bonds, 3 pseudobonds, 261 residues, 2 models selected
> select /M:7-381
2277 atoms, 2317 bonds, 4 pseudobonds, 283 residues, 2 models selected
> select /L:1639-2285
3670 atoms, 3739 bonds, 4 pseudobonds, 466 residues, 2 models selected
> select /K:2-372
2482 atoms, 2535 bonds, 3 pseudobonds, 317 residues, 2 models selected
> select /J:12-417
2612 atoms, 2667 bonds, 4 pseudobonds, 334 residues, 2 models selected
> select /I:350-1366
4606 atoms, 4682 bonds, 11 pseudobonds, 551 residues, 2 models selected
> select /H:31-120
700 atoms, 711 bonds, 90 residues, 1 model selected
> select /D:33-120
682 atoms, 693 bonds, 88 residues, 1 model selected
> select /G:15-109
727 atoms, 736 bonds, 95 residues, 1 model selected
> select /C:16-110
726 atoms, 735 bonds, 95 residues, 1 model selected
> select C
20942 atoms, 16285 bonds, 3894 residues, 1 model selected
> select G/
Expected an objects specifier or a keyword
> select G
Expected an objects specifier or a keyword
> select /A:41-131
739 atoms, 747 bonds, 91 residues, 1 model selected
> View G
Unknown command: View G
> View C
Unknown command: View C
> View sel c
Unknown command: View sel c
> View sel C
Unknown command: View sel C
> View sel G
Unknown command: View sel G
> View
Unknown command: View
> view sel 8
> view sel C
Expected an integer >= 1 or a keyword
> 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
.
> select /A:41-131
739 atoms, 747 bonds, 91 residues, 1 model selected
> select /E:44-134
739 atoms, 747 bonds, 91 residues, 1 model selected
> select /B:24-101
622 atoms, 629 bonds, 78 residues, 1 model selected
> select /F:25-101
614 atoms, 621 bonds, 77 residues, 1 model selected
> select /C:16-110
726 atoms, 735 bonds, 95 residues, 1 model selected
> select /G:15-109
727 atoms, 736 bonds, 95 residues, 1 model selected
> select /D:33-120
682 atoms, 693 bonds, 88 residues, 1 model selected
> select /H:31-120
700 atoms, 711 bonds, 90 residues, 1 model selected
> name prt /I/J/K/L/M/N/O/P/Q/R
> name ncp /A/B/C/D/E/F/G/H
> name dna /X/Y
> select dna
4879 atoms, 5472 bonds, 238 residues, 1 model selected
> color dna orange
> select ncp
5549 atoms, 5619 bonds, 705 residues, 1 model selected
> colorlist
Unknown command: colorlist
> 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 mediumblue
> color sel steelblue
> cartoon style width 0.3 thickness 1.0 xsection oval
> cartoon style width 0.25 thickness 1.3 xsection rectangle
> color rgba(229, 229, 229, 1) target c
> ribbon style width 5
> graphics backgroundColor white
> undo
> undo
> color prt white
> color ncp gray
> color dna dimgray
> name actb /K
> name actl6a /J
> name arid1a /L
> name brg1 /I
> name dpf2 /R
> name smarcb1 /M
> name smarcc2 /N/O
> name smarcd1 /P
> name smarce1 /Q
> lighting soft
> lighting simple
> lighting soft
> lighting full
> lighting simple
> 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 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
> transparency 0.7
> show surfaces
> undo
> undo
> hide sel surfaces
> hide sel surfaces
> hide surfaces
> surface #1:dna
No atoms specified by #1:dna
> surface #1:DNA
No atoms specified by #1:DNA
> lighting simple
> lighting soft
> lighting full
> lighting simple
> preset "initial styles" sticks
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset "initial styles" sticks
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset "initial styles" cartoon
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> color dna orange
> color ncp steelblue
> color prt ghostly white
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> color prt ghost white
> color prt white
> color prt white
> 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 ncp ghostwhite
> color ncp steelblue
> color prt whitesmoke
> color prt red
> color prt whitesmoke
> color prt ghostwhite
> view dna
> view prt
> view ncp
> view dna
> view arid1a
> view arid2
Expected an objects specifier or a view name or a keyword
> view arid1b
Expected an objects specifier or a view name or a keyword
> view smarcc2
> view brg1
> view dpf2
> view smarcb
Expected an objects specifier or a view name or a keyword
> view smarcb1
> view actb
> view smarcd1
> view brg1
> select smarccc2
Expected an objects specifier or a keyword
> select smarcc2
4752 atoms, 4850 bonds, 6 pseudobonds, 586 residues, 2 models selected
> select smarcb1
2277 atoms, 2317 bonds, 4 pseudobonds, 283 residues, 2 models selected
> surface smarcb1 gray transparency 70
Expected a keyword
> surface smarcb1 gray transparency 70;
Expected a keyword
> surface smarcb1 gray
Expected a keyword
> surface smarcb1
> surface smarcb1 red
Expected a keyword
> surface smarcb1 transparency 90
> surface smarb1 resolution 200
Expected an atoms specifier or a keyword
> surface smarb1 resolution
Expected an atoms specifier or a keyword
> surface smarcb1 resolution 2000
1 Gaussian surfaces, threshold level 0.000
> select up
34283 atoms, 35402 bonds, 34 pseudobonds, 3895 residues, 3 models selected
> select up
34283 atoms, 35402 bonds, 38 pseudobonds, 3895 residues, 23 models selected
> select down
34283 atoms, 35402 bonds, 34 pseudobonds, 3895 residues, 22 models selected
> surface smarcb1 resolution 2000
1 Gaussian surfaces, threshold level 0.000
> select smarcb1
2277 atoms, 2317 bonds, 4 pseudobonds, 283 residues, 2 models selected
> surface smarcb1 resolution 100
1 Gaussian surfaces, threshold level 0.007
> surface smarcb1 resolution 300
1 Gaussian surfaces, threshold level 0.001
> surface smarcb1 resolution 500
1 Gaussian surfaces, threshold level 0.000
> surface smarcb1 resolution 20
1 Gaussian surfaces, threshold level 0.023
> surface smarcb1 resolution 10
1 Gaussian surfaces, threshold level 0.049
> surface smarcb1 resolution 5
1 Gaussian surfaces, threshold level 0.193
> surface smarcb1 resolution 1
1 Gaussian surfaces, threshold level 15.515
> surface smarcb1 resolution 10
1 Gaussian surfaces, threshold level 0.049
> surface smarcb1 resolution 5
1 Gaussian surfaces, threshold level 0.193
> surface smarcb1 resolution 4
1 Gaussian surfaces, threshold level 0.315
> surface smarcb1 resolution 10
1 Gaussian surfaces, threshold level 0.049
> surface smarcb1 resolution 10 style red
Expected a keyword
> surface smarcb1 resolution 10 style mesh
Expected a keyword
> surface smarcb1 mesh
Expected a keyword
> surface smarcb1 dot
Expected a keyword
> surface style smarcb1 dot
> surface style smarcb1 mesh
> surface style smarcb1 solid
> color surface smarcb1 red
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> color surface smarcb1 red byatom
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> color surface smarcb1 red
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> select smarcb1
2277 atoms, 2317 bonds, 4 pseudobonds, 283 residues, 2 models selected
> color sel pale green
> color zone #1 near #5 distance 5
> surface smarcb1 transparency 90
> surface smarcb1 transparency 80
Drag select of 152 residues, 3 pseudobonds
> color smarcb1 white
> scolor
Unknown command: scolor
> ui tool show "Surface Color"
> surface smarcb1
> color radial #1.15 palette #ff0000:#ffffff:#0000ff
> color radial #1.15 palette 405.6,#ff0000:443.6,#ffffff:481.6,#0000ff
> color single #1.15
> color radial #1.15 palette 405.6,#ff0000:443.6,#ffffff:481.6,#0000ff
> color radial #1.15 palette 20,#ff0000:443.6,#ffffff:481.6,#0000ff
> color radial #1.15 palette 405.6,#ff0000:443.6,#ffffff:481.6,#0000ff
> color radial #1.15 palette 405.6,#00ed0a:443.6,#04ff00:481.6,#00f50d
> color cylindrical #1.15 palette 405.6,#00ed0a:443.6,#04ff00:481.6,#00f50d
No map chosen for coloring
> color radial #1.15 palette 405.6,#00ed0a:443.6,#04ff00:481.6,#00f50d
> surface smarcb1 transparency 90
> select arid1a
3671 atoms, 3739 bonds, 8 pseudobonds, 467 residues, 3 models selected
> surface arid1a
> color radial #1.15 palette 405.6,#e71400:443.6,#f50700:481.6,#ee0002
> select arid1a
3671 atoms, 3739 bonds, 8 pseudobonds, 467 residues, 3 models selected
> color radial #1.15 palette 405.6,#e71400:443.6,#f50700:481.6,#ee0002
> color radial #1.15 palette 405.6,#e71400:443.6,#f50700:481.6,#ee0002
> undo
> color radial #1.15 palette 405.6,#e71400:443.6,#f50700:481.6,#ee0002
> undo
> select arid1a
3671 atoms, 3739 bonds, 8 pseudobonds, 467 residues, 3 models selected
> surface arid1a transparency 80
> color radial #1.15 palette 405.6,#e71400:443.6,#f50700:481.6,#ee0002
> color radial #1.5 palette 405.6,#e71400:443.6,#f50700:481.6,#ee0002
> color radial #1.22 palette 405.6,#e71400:443.6,#f50700:481.6,#ee0002
> select arid1a
3671 atoms, 3739 bonds, 8 pseudobonds, 467 residues, 3 models selected
> color radial palette 405.6,#e71400:443.6,#f50700:481.6,#ee0002
Missing or invalid "surfaces" argument: invalid surfaces specifier
> color radial red
Missing or invalid "surfaces" argument: invalid surfaces specifier
> color radial
Missing or invalid "surfaces" argument: empty atom specifier
> color rainbow
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> ui tool show "Surface Color"
> ui tool show "Surface Zone"
No surface chosen for zoning
> select /L:1728@O
1 atom, 1 residue, 1 model selected
No surface chosen for zoning
> color radial #1.14 palette #ff0000:#ffffff:#0000ff
> undo
> color radial #1.14 palette 366,#edea1d:419.7,#ffffff:473.4,#0000ff
> color radial #1.14 palette 366,#edea1d:419.7,#ffffff:473.4,#dff508
> color radial #1.14 palette 366,#edea1d:419.7,#daff09:473.4,#dff508
> color radial #1.14 palette 350,#0000ff:350,#00ff00:350,#ff0000
> color radial #1.14 palette 350,#0000ff:350,#00ff00:350,#ff0000
> color radial #1.14 palette 350,#ff0000:350,#ffffff:350,#0000ff
> color single #1.14
> key blue-white-red :350 :350 :350
> ui tool show "Color Key"
> ui mousemode left "color key"
An error occurred in drawing the scene. Redrawing graphics is now stopped to
avoid a continuous stream of error messages. To restart graphics use the
command "graphics restart" after changing the settings that caused the error.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/updateloop.py", line 73, in draw_new_frame
view.draw(check_for_changes = False)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/view.py", line 172, in draw
draw_overlays(odrawings, r)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/drawing.py", line 1549, in draw_overlays
_draw_multiple(drawings, r, Drawing.OPAQUE_DRAW_PASS)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/drawing.py", line 1511, in _draw_multiple
d.draw(renderer, draw_pass)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/color_key/model.py", line 98, in draw
self._update_graphics(renderer)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/color_key/model.py", line 454, in _update_graphics
self._update_key_image()
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/color_key/model.py", line 457, in _update_key_image
rgba = self._key_image_rgba()
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/color_key/model.py", line 482, in _key_image_rgba
rect_positions = self._rect_positions(pixels[long_index])
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/color_key/model.py", line 760, in _rect_positions
rect_positions = [long_size * abs(v - values[0])/val_size for v in values]
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/color_key/model.py", line 760, in <listcomp>
rect_positions = [long_size * abs(v - values[0])/val_size for v in values]
ZeroDivisionError: float division by zero
> ui mousemode left rotate
> color radial #1.14 palette 350,#000000:350,#7f7f7f:350,#ffffff
> color radial #1.14 palette 350,#000000:350,#7f7f7f:350,#ffffff
> color radial #1.14 palette 350,#00e504:350,#00fc0a
> color radial #1.14 palette 350,#00e504:350,#00fc0a
> color radial #1.14 palette 350,#00e504:350,#00fc0a
> color (#!1 & sel) red
> select arid1a
3671 atoms, 3739 bonds, 8 pseudobonds, 467 residues, 3 models selected
> ui tool show "Surface Color"
> color radial #1.14 palette #e2ed00:#ffffff:#0000ff
> color radial #1.14 palette 366,#e2ed00:366,#ffffff:366,#0000ff
> color radial #1.14 palette 366,#e2ed00:366,#ffffff:366,#0000ff
> select arid1a
3671 atoms, 3739 bonds, 8 pseudobonds, 467 residues, 3 models selected
> surface arid1a
> color radial #1.14 palette 366,#e2ed00:366,#ffffff:366,#0000ff
> color radial #1.22 palette 405.6,#e71400:443.6,#f50700:481.6,#ee0002
> style sel stick
Changed 3671 atom styles
> show sel atoms
> hide sel atoms
> surface arid1a transparency 80
> hide surfaces
> ui mousemode right translate
> view brg1
> view brg1
> save /Users/kcervant/Downloads/I_think_it_Crashed.cxs
——— End of log from Tue Aug 3 17:31:14 2021 ———
opened ChimeraX session
An error occurred in drawing the scene. Redrawing graphics is now stopped to
avoid a continuous stream of error messages. To restart graphics use the
command "graphics restart" after changing the settings that caused the error.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/updateloop.py", line 73, in draw_new_frame
view.draw(check_for_changes = False)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/view.py", line 172, in draw
draw_overlays(odrawings, r)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/drawing.py", line 1549, in draw_overlays
_draw_multiple(drawings, r, Drawing.OPAQUE_DRAW_PASS)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/drawing.py", line 1511, in _draw_multiple
d.draw(renderer, draw_pass)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/color_key/model.py", line 98, in draw
self._update_graphics(renderer)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/color_key/model.py", line 454, in _update_graphics
self._update_key_image()
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/color_key/model.py", line 457, in _update_key_image
rgba = self._key_image_rgba()
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/color_key/model.py", line 482, in _key_image_rgba
rect_positions = self._rect_positions(pixels[long_index])
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/color_key/model.py", line 760, in _rect_positions
rect_positions = [long_size * abs(v - values[0])/val_size for v in values]
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/color_key/model.py", line 760, in <listcomp>
rect_positions = [long_size * abs(v - values[0])/val_size for v in values]
ZeroDivisionError: float division by zero
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/filehistory.py", line 73, in <lambda>
t.add_handler('frame drawn', lambda *args, s=self: s.capture_thumbnails_cb())
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/filehistory.py", line 85, in capture_thumbnails_cb
fs.capture_image(models, ses)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/filehistory.py", line 173, in capture_image
self.image = models_image(session, models, size)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/filehistory.py", line 231, in models_image
image = v.image(width, height)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/view.py", line 445, in image
self.draw(c, drawings, swap_buffers = False)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/view.py", line 172, in draw
draw_overlays(odrawings, r)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/drawing.py", line 1549, in draw_overlays
_draw_multiple(drawings, r, Drawing.OPAQUE_DRAW_PASS)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/drawing.py", line 1511, in _draw_multiple
d.draw(renderer, draw_pass)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/color_key/model.py", line 98, in draw
self._update_graphics(renderer)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/color_key/model.py", line 454, in _update_graphics
self._update_key_image()
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/color_key/model.py", line 457, in _update_key_image
rgba = self._key_image_rgba()
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/color_key/model.py", line 482, in _key_image_rgba
rect_positions = self._rect_positions(pixels[long_index])
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/color_key/model.py", line 760, in _rect_positions
rect_positions = [long_size * abs(v - values[0])/val_size for v in values]
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/color_key/model.py", line 760, in <listcomp>
rect_positions = [long_size * abs(v - values[0])/val_size for v in values]
ZeroDivisionError: float division by zero
Error processing trigger "frame drawn":
ZeroDivisionError: float division by zero
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/color_key/model.py", line 760, in
rect_positions = [long_size * abs(v - values[0])/val_size for v in values]
See log for complete Python traceback.
OpenGL version: 4.1 ATI-4.5.14
OpenGL renderer: AMD Radeon Pro 5300M OpenGL Engine
OpenGL vendor: ATI Technologies Inc.Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro16,1
Processor Name: 8-Core Intel Core i9
Processor Speed: 2.4 GHz
Number of Processors: 1
Total Number of Cores: 8
L2 Cache (per Core): 256 KB
L3 Cache: 16 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
System Firmware Version: 1554.120.19.0.0 (iBridge: 18.16.14663.0.0,0)
Software:
System Software Overview:
System Version: macOS 11.4 (20F71)
Kernel Version: Darwin 20.5.0
Time since boot: 19 days 8:14
Graphics/Displays:
Intel UHD Graphics 630:
Chipset Model: Intel UHD Graphics 630
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x3e9b
Revision ID: 0x0002
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Family: Supported, Metal GPUFamily macOS 2
AMD Radeon Pro 5300M:
Chipset Model: AMD Radeon Pro 5300M
Type: GPU
Bus: PCIe
PCIe Lane Width: x8
VRAM (Total): 4 GB
Vendor: AMD (0x1002)
Device ID: 0x7340
Revision ID: 0x0043
ROM Revision: 113-D3220E-190
VBIOS Version: 113-D32207P1-020
Option ROM Version: 113-D32207P1-020
EFI Driver Version: 01.A1.190
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Family: Supported, Metal GPUFamily macOS 2
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 3072 x 1920 Retina
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
VE248:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Display Serial Number: G5LMQS089796
Mirror: Off
Online: Yes
Rotation: Supported
Automatically Adjust Brightness: Yes
Connection Type: DVI or HDMI
Adapter Firmware Version: d.1d
Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.2
Babel: 2.9.1
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2020.12.5
cftime: 1.5.0
chardet: 3.0.4
ChimeraX-AddCharge: 1.0.1
ChimeraX-AddH: 2.1.6
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.13.2
ChimeraX-AtomicLibrary: 3.1.3
ChimeraX-AtomSearch: 2.0
ChimeraX-AtomSearchLibrary: 1.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 1.1
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.5.2
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.1
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.1
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.2.1
ChimeraX-CommandLine: 1.1.4
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.2.5
ChimeraX-CoreFormats: 1.0
ChimeraX-coulombic: 1.1.1
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.1
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1.3
ChimeraX-DistUI: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.1
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.0
ChimeraX-Hbonds: 2.1
ChimeraX-Help: 1.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.0
ChimeraX-ImageFormats: 1.1
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-Label: 1.0
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.0.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.0
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 1.2.1
ChimeraX-MDcrds: 2.2
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.3
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.0.1
ChimeraX-ModelPanel: 1.0.1
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.1
ChimeraX-OpenCommand: 1.5
ChimeraX-PDB: 2.4.1
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.1
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0.1
ChimeraX-PubChem: 2.0.1
ChimeraX-ReadPbonds: 1.0
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.4
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SeqView: 2.3
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.0
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.0.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.3.1
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-Struts: 1.0
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.0.1
ChimeraX-ToolshedUtils: 1.2
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.7.6
ChimeraX-uniprot: 2.1
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.0
ChimeraX-Zone: 1.0
colorama: 0.4.3
comtypes: 1.1.7
cxservices: 1.0
cycler: 0.10.0
Cython: 0.29.21
decorator: 5.0.9
distlib: 0.3.1
docutils: 0.16
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 2.10.0
html2text: 2020.1.16
idna: 2.10
ihm: 0.17
imagecodecs: 2020.5.30
imagesize: 1.2.0
ipykernel: 5.3.4
ipython: 7.18.1
ipython-genutils: 0.2.0
jedi: 0.17.2
Jinja2: 2.11.2
jupyter-client: 6.1.7
jupyter-core: 4.7.1
kiwisolver: 1.3.1
line-profiler: 2.1.2
lxml: 4.6.2
lz4: 3.1.0
MarkupSafe: 2.0.1
matplotlib: 3.3.2
matplotlib-inline: 0.1.2
msgpack: 1.0.0
netCDF4: 1.5.4
networkx: 2.5
numexpr: 2.7.3
numpy: 1.19.2
numpydoc: 1.1.0
openvr: 1.14.1501
packaging: 20.9
ParmEd: 3.2.0
parso: 0.7.1
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 7.2.0
pip: 21.0.1
pkginfo: 1.5.0.1
prompt-toolkit: 3.0.18
psutil: 5.7.2
ptyprocess: 0.7.0
pycollada: 0.7.1
pydicom: 2.0.0
Pygments: 2.7.1
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 2.4.7
PyQt5-commercial: 5.15.2
PyQt5-sip: 12.8.1
PyQtWebEngine-commercial: 5.15.2
python-dateutil: 2.8.1
pytz: 2021.1
pyzmq: 22.0.3
qtconsole: 4.7.7
QtPy: 1.9.0
RandomWords: 0.3.0
requests: 2.24.0
scipy: 1.5.2
setuptools: 50.3.2
sfftk-rw: 0.6.7.dev1
six: 1.15.0
snowballstemmer: 2.1.0
sortedcontainers: 2.2.2
Sphinx: 3.2.1
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 2.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
suds-jurko: 0.6
tables: 3.6.1
tifffile: 2020.9.3
tinyarray: 1.2.3
tornado: 6.1
traitlets: 5.0.5
urllib3: 1.25.11
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.36.0
wheel-filename: 1.3.0
![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Creating a key with all the values the same failed. Fixed in tomorrow's daily build. Until then, just create a key with different values.