dark gray vs. gray

[lochuynh@…]

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
It's not a big deal but it seems like Gray and Dark Gray colors are swapped (Dark Gray looks lighter than Gray)

Log:
UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open "/Users/lochuynh/OneDrive - University of Florida/LAB
> RESEARCH/ChimeraX/3Q1R/3Q1R v7.cxs"

Log from Mon Dec 27 20:37:10 2021UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open "/Users/lochuynh/OneDrive - University of Florida/LAB
> RESEARCH/ChimeraX/3Q1R/3Q1R v7.cxs" format session

Log from Mon Dec 27 13:49:00 2021UCSF ChimeraX version: 1.2.5 (2021-05-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open "/Users/lochuynh/OneDrive - University of Florida/LAB
> RESEARCH/ChimeraX/3Q1R/3Q1R v2.cxs"

Log from Wed Aug 5 22:57:52 2020UCSF ChimeraX version: 0.93 (2020-04-03)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open "/Users/LocHuynh/OneDrive - University of Florida/LAB
> RESEARCH/ChimeraX/3Q1R/3Q1R v1 - Mg binding site.cxs"

Log from Thu May 28 14:57:35 2020UCSF ChimeraX version: 0.93 (2020-04-03)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 3Q1R format mmCIF fromDatabase pdb

Summary of feedback from opening 3Q1R fetched from pdb  
---  
notes | Fetching compressed mmCIF 3q1r from
http://files.rcsb.org/download/3q1r.cif  
  
  
  
  
| Summary of feedback from opening
/Users/LocHuynh/Downloads/ChimeraX/PDB/3q1r.cif  
  
---  
  
  
  
  
note | Fetching CCD MG from http://ligand-expo.rcsb.org/reports/M/MG/MG.cif  
  
  
  
  
  
3q1r title:  
Crystal structure of a bacterial RNase P holoenzyme in complex with TRNA and
in the presence of 5' leader [more info...]  
  
Chain information for 3q1r #1  
---  
Chain | Description  
A | Ribonuclease P protein component  
B | RNase P RNA  
C | TRNA (phe)  
D | TRNA 5' leader  
  
Non-standard residues in 3q1r #1  
---  
MG — magnesium ion  
  
  

> set bgColor black

> sequence chain #1/A

Alignment identifier is 1.A  

> sequence chain #1/B

Alignment identifier is 1.B  

> sequence chain #1/A

Destroying pre-existing alignment with identifier 1.A  
Alignment identifier is 1.A  

> show sel cartoons

> sequence chain #1/C

Alignment identifier is 1.C  

> select /C:1-86

1788 atoms, 1994 bonds, 82 pseudobonds, 2 models selected  

> hide sel cartoons

> hide sel atoms

> show sel cartoons

> show sel atoms

> hide sel atoms

> hide sel cartoons

> select /A:6-117

973 atoms, 989 bonds, 1 model selected  

> hide sel atoms

> hide sel cartoons

> select /D:-5--1

40 atoms, 39 bonds, 1 model selected  

> hide sel atoms

> select /B:1-347

7380 atoms, 8253 bonds, 353 pseudobonds, 2 models selected  

> hide sel atoms

> show sel atoms

> style sel stick

Changed 65 atom styles  

> nucleotides sel atoms

> style nucleic & sel stick

Changed 65 atom styles  

> show sel cartoons

> show sel atoms

> color sel bynucleotide

> nucleotides sel atoms

> style nucleic & sel stick

Changed 109 atom styles  

> color sel bynucleotide

> color sel byhetero

> color sel bychain

> color sel byhetero

> hide sel cartoons

> select :MG

5 atoms, 1 model selected  

> color red

> color sel red

> color sel green

> color sel lime

> color sel lime green

> color-spec

Unknown command: color-spec  

> 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 pink

> color sel deep pink

> color sel magenta

> hide sel cartoons

> show sel cartoons

> hide sel cartoons

> color sel bychain

> color sel bychain

> color sel green

> color sel dark green

> color sel sea green

> color sel medium sea green

> color sel sea green

> color sel teal

> color sel dark cyan

> color sel byhetero

> select up

7384 atoms, 8253 bonds, 1 model selected  

> select down

7380 atoms, 8253 bonds, 1 model selected  

> select /B:50@C4'

1 atom, 1 model selected  

> select /B:51@C5

1 atom, 1 model selected  

> select up

65 atoms, 72 bonds, 1 model selected  

> color sel lemonchiffon

> color sel byhetero

> color sel khaki

> color sel wheat

> color sel tan

> color sel byhetero

> color sel teal

> color sel byhetero

> color sel slate blue

> color sel byhetero

> color sel dark slate blue

> color sel byhetero

> color sel bynucleotide

> color sel dark slate blue

> color sel bynucleotide

> color sel byhetero

> mlp sel

mlp: no amino acids specified  

> mlp sel

mlp: no amino acids specified  

> color sel byhetero

> color sel dark slate blue

> color sel byhetero

> set bgColor white

> select :MG

5 atoms, 1 model selected  

> color MG lime green

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword  

> color a/MG lime green

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword  

> color /a MG lime green

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword  

> color sel liime green

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword  

> color sel lime green

> save2 "/Users/LocHuynh/OneDrive - University of Florida/LAB
> RESEARCH/ChimeraX/3Q1R/3Q1R v1 - Mg binding site.cxs"

> show sel cartoons

> hide sel cartoons

> show sel cartoons

> hide sel cartoons

> save2 "/Users/LocHuynh/OneDrive - University of Florida/LAB
> RESEARCH/ChimeraX/3Q1R/3Q1R v1 - Mg binding site.cxs"

> hide sel atoms

> show sel cartoons

> hide sel cartoons

> hide sel cartoons

> show sel cartoons

> hide sel cartoons

> style sel stick

Changed 24 atom styles  

> style sel sphere

Changed 24 atom styles  

> style sel stick

Changed 24 atom styles  

> style sel ball

Changed 24 atom styles  

> style sel stick

Changed 24 atom styles  

> select /D:-5--1

40 atoms, 39 bonds, 1 model selected  

> show sel cartoons

> color sel slate blue

> color sel slateblue midnight blue

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> color sel midnight blue

> color sel red

> show sel atoms

> show sel atoms

> style sel stick

Changed 40 atom styles  

> hide sel cartoons

> show sel cartoons

> style sel stick

Changed 40 atom styles  

> show sel surfaces

> style sel stick

Changed 40 atom styles  

> hide sel surfaces

> nucleotides sel atoms

> style nucleic & sel stick

Changed 40 atom styles  

> show sel atoms

> show sel atoms

> color sel byhetero

> style sel stick

Changed 40 atom styles  

> hide sel cartoons

> sequence chain #1/A

Destroying pre-existing alignment with identifier 1.A  
Alignment identifier is 1.A  

> mlp sel

mlp: no amino acids specified  

> show sel cartoons

> style sel stick

Changed 40 atom styles  

> nucleotides sel atoms

> style nucleic & sel stick

Changed 40 atom styles  

> nucleotides sel atoms

> style nucleic & sel stick

Changed 40 atom styles  

> show sel atoms

> hide sel cartoons

> mlp sel

Map values for surface "3q1r_A SES surface": minimum -23.53, mean -3.612,
maximum 22.92  

> style sel sphere

Changed 973 atom styles  

> mlp sel

Map values for surface "3q1r_A SES surface": minimum -23.53, mean -3.612,
maximum 22.92  

> color sel byhetero

> color sel bychain

> color sel tan

> color sel brown

> color sel chocolate

> color sel burly wood

> color sel burlywood beigh

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> color sel burlywood beige

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> color sel beige

> color sel tan

> select sequence CCCUCGG

146 atoms, 161 bonds, 1 model selected  

> nucleotides sel fill

> style nucleic & sel stick

Changed 146 atom styles  

> show sel atoms

> hide sel atoms

> nucleotides sel slab

> style nucleic & sel stick

Changed 7380 atom styles  

> nucleotides sel ladder

> show sel atoms

> set bgColor black

> select /D:-5--1

40 atoms, 39 bonds, 1 model selected  

> select /C:1-86

1788 atoms, 1994 bonds, 82 pseudobonds, 2 models selected  

> select /B:1-347

7380 atoms, 8253 bonds, 353 pseudobonds, 2 models selected  

> select /A:6-117

973 atoms, 989 bonds, 1 model selected  

> sequence chain #1/D

Alignment identifier is 1.D  

> sequence chain #1/C

Alignment identifier is 1.C  

> sequence chain #1/B

Destroying pre-existing alignment with identifier 1.B  
Alignment identifier is 1.B  

> select sequence AGCGUCGG

174 atoms, 194 bonds, 1 model selected  

> select sequence GGGGGG

138 atoms, 155 bonds, 1 model selected  

> select sequence GGGGGGAA

182 atoms, 205 bonds, 1 model selected  

> select sequence GGGGGGAA

182 atoms, 205 bonds, 1 model selected  

> nucleotides sel ladder

> nucleotides sel fill

> style nucleic & sel stick

Changed 182 atom styles  

> select sequence GGGGGGAAACUUCC

304 atoms, 340 bonds, 15 pseudobonds, 2 models selected  

> nucleotides sel fill

> style nucleic & sel stick

Changed 304 atom styles  

> select clear

> select sequence ggagc

333 atoms, 372 bonds, 1 model selected  

> select sequence ggagcg

134 atoms, 150 bonds, 1 model selected  

> select sequence ggagcg

134 atoms, 150 bonds, 1 model selected  

> nucleotides sel fill

> style nucleic & sel stick

Changed 237 atom styles  

> nucleotides sel atoms

> style nucleic & sel stick

Changed 237 atom styles  

> nucleotides sel fill

> style nucleic & sel stick

Changed 237 atom styles  

> select clear

> select /B:249

20 atoms, 21 bonds, 1 model selected  

> select /B:248

20 atoms, 21 bonds, 1 model selected  

> style sel sphere

Changed 40 atom styles  

> style sel stick

Changed 40 atom styles  

> mlp sel

mlp: no amino acids specified  

> style sel sphere

Changed 40 atom styles  

> style sel sphere

Changed 40 atom styles  

> lighting soft

> lighting simple

> lighting full

> lighting soft

> lighting flat

> lighting flat

> graphics silhouettes false

> lighting soft

> set bgColor white

> show sel cartoons

> style sel stick

Changed 40 atom styles  

> style sel sphere

Changed 40 atom styles  

> style sel stick

Changed 40 atom styles  

> style sel stick

Changed 40 atom styles  

> style sel stick

Changed 40 atom styles  

> hide sel atoms

> hide sel cartoons

> show sel atoms

> style sel sphere

Changed 40 atom styles  

> style sel ball

Changed 40 atom styles  

> set bgColor black

> style sel sphere

Changed 40 atom styles  

> sequence chain #1/A

Alignment identifier is 1.A  

> color sel bychain

> color sel byhetero

> mlp sel

Map values for surface "3q1r_A SES surface": minimum -23.53, mean -3.612,
maximum 22.92  

> color sel bynucleotide

> rainbow sel

> color bfactor sel

973 atoms, 112 residues, 1 surfaces, atom bfactor range 80 to 80  

> color sel byhetero

> color sel bychain

> color sel tan

> show sel surfaces

> style sel stick

Changed 40 atom styles  

> color sel red

> color sel byhetero

> tan

Unknown command: tan  

> color sel byhetero

> color sel tan

> color sel byhetero

> color sel deeppink blue

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> color sel purple

> color sel byhetero

> lighting simple

> lighting simple

> lighting soft

> lighting simple

> hide sel surfaces

> style sel sphere

Changed 40 atom styles  

> select /B:51

23 atoms, 25 bonds, 1 model selected  

> hide sel cartoons

> color sel blue

> color sel navy

> color sel byhetero

> select /B:52

20 atoms, 21 bonds, 1 model selected  

> hide sel cartoons

> show sel cartoons

> show sel atoms

> nucleotides sel atoms

> style nucleic & sel stick

Changed 20 atom styles  

> color sel navy

> color sel byhetero

> lighting soft

> lighting simple

> select /C:1@C3'

1 atom, 1 model selected  

> select up

24 atoms, 26 bonds, 1 model selected  

> select /C:1@P

1 atom, 1 model selected  

> select up

24 atoms, 26 bonds, 1 model selected  

> select /B:52

20 atoms, 21 bonds, 1 model selected  

> select up

2 atoms, 1 bond, 1 model selected  

> select up

23 atoms, 25 bonds, 1 model selected  

> save2 "/Users/LocHuynh/OneDrive - University of Florida/LAB
> RESEARCH/ChimeraX/3Q1R/3Q1R v1 - Mg binding site.cxs"

opened ChimeraX session  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/nucleotides/_data.py", line 525, in rebuild  
_rebuild_molecule('internal', mol)  
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/nucleotides/_data.py", line 652, in _rebuild_molecule  
hide_residues = make_ladder(nd, residues, mol._ladder_params)  
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/nucleotides/_data.py", line 1191, in make_ladder  
midpt = c3p0[1] + mid * (c3p1[1] - c3p0[1])  
TypeError: unsupported operand type(s) for -: 'NoneType' and 'NoneType'  
  
Error processing trigger "new frame":  
TypeError: unsupported operand type(s) for -: 'NoneType' and 'NoneType'  
  
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/nucleotides/_data.py", line 1191, in make_ladder  
midpt = c3p0[1] + mid * (c3p1[1] - c3p0[1])  
  
See log for complete Python traceback.  
  

> set bgColor white

Empty filename passed to function  

> save2 "/Users/LocHuynh/OneDrive - University of Florida/LAB
> RESEARCH/ChimeraX/3Q1R/3Q1R v2.cxs"

> hide sel atoms

> hide sel atoms

> hide sel atoms

> show sel cartoons

> color sel bychain

> color sel bychain

> color bfactor sel

1788 atoms, 86 residues, atom bfactor range 80 to 80.9  

> mlp sel

mlp: no amino acids specified  

> color sel bynucleotide

> color sel bychain

> color sel byhetero

> color sel bychain

> color sel byhetero

> rainbow sel

> color bfactor sel

1788 atoms, 86 residues, atom bfactor range 80 to 80.9  

> mlp sel

mlp: no amino acids specified  

> color sel bynucleotide

> show sel atoms

> hide sel atoms

> color sel bynucleotide

> nucleotides sel ladder

> ui favorite true Toolbar

> toolshed show Toolbar

> ui favorite false Toolbar

> color sel silver

> show sel atoms

> nucleotides sel atoms

> style nucleic & sel stick

Changed 1788 atom styles  

> nucleotides sel tube/slab shape box

> nucleotides sel tube/slab shape box

> nucleotides sel tube/slab shape box

> nucleotides sel ladder

> nucleotides sel ladder

> nucleotides sel atoms

> style nucleic & sel stick

Changed 1788 atom styles  

> hide sel atoms

> show sel atoms

> nucleotides sel atoms

> style nucleic & sel stick

Changed 1788 atom styles  

> nucleotides sel atoms

> style nucleic & sel stick

Changed 1788 atom styles  

> hide sel atoms

> nucleotides sel ladder

> show sel atoms

> color sel silver

> show sel atoms

> nucleotides sel ladder

> hide sel atoms

> show sel atoms

> color sel red

> color sel red

> hide sel atoms

> style sel stick

Changed 40 atom styles  

> show sel cartoons

> cartoon style sel xsection oval modeHelix default

> cartoon hide sel

> cartoon hide sel

> hide sel atoms

> cartoon sel

> nucleotides sel ladder

> show sel atoms

> cartoon style (sel & coil) xsection oval

> cartoon style sel xsection barbell modeHelix default

> cartoon style sel xsection oval modeHelix default

> cartoon style sel modeHelix tube sides 20

> select clear

> color sel dark grey

> color sel blue

> color sel navy

> color sel green

> color sel green

> color sel dark green

> save2 "/Users/LocHuynh/OneDrive - University of Florida/LAB
> RESEARCH/ChimeraX/3Q1R/3Q1R v2.cxs"

——— End of log from Wed Aug 5 22:57:52 2020 ———

opened ChimeraX session  

> save "/Users/lochuynh/OneDrive - University of Florida/LAB
> RESEARCH/ChimeraX/3Q1R/3Q1R v7.cxs"

> select /C:86

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select /C:1-86

1788 atoms, 1994 bonds, 82 pseudobonds, 86 residues, 2 models selected  

> ui tool show "Color Actions"

> color sel light gray

> color sel gray

> select /B:302-347

913 atoms, 1012 bonds, 46 residues, 1 model selected  

> select /B:1-347

7380 atoms, 8253 bonds, 353 pseudobonds, 347 residues, 2 models selected  

> color sel dark blue

> color sel navy

> color sel medium blue

> color sel blue

> color sel navy

> color sel indigo

> color sel navy

> color sel midnight blue

> select /B:264-347

1726 atoms, 1921 bonds, 25 pseudobonds, 84 residues, 2 models selected  

> select /B:1-347

7380 atoms, 8253 bonds, 353 pseudobonds, 347 residues, 2 models selected  

> cartoon style (#!1 & sel) xsection oval modeHelix default

> cartoon style (#!1 & sel) modeHelix tube sides 20

> cartoon style (#!1 & sel & coil) xsection oval

> cartoon style (#!1 & sel) xsection barbell modeHelix default

> cartoon hide (#!1 & sel)

> cartoon style (#!1 & sel) xsection oval modeHelix default

> cartoon (#!1 & sel)

> cartoon style (#!1 & sel & coil) xsection oval

> cartoon style (#!1 & sel) xsection barbell modeHelix default

> cartoon style (#!1 & sel) modeHelix tube sides 20

> cartoon style (#!1 & sel) xsection oval modeHelix default

> cartoon style (#!1 & sel & coil) xsection oval

> cartoon style (#!1 & sel) xsection barbell modeHelix default

> save "/Users/lochuynh/OneDrive - University of Florida/LAB
> RESEARCH/ChimeraX/3Q1R/3Q1R v7.cxs"

——— End of log from Mon Dec 27 13:49:00 2021 ———

opened ChimeraX session  

> alias nucrib cartoon style nucleic xsect oval width 1.6 thick 1.6

> cartoon style initial defaults

Expected an atoms specifier or a keyword  

> cartoon style nucleic xsection oval width 1.6 thickness 1.6

> cartoon style nucleic xsection oval width 2.0 thickness 2.0

> help help:user/preferences.html#startup

> save "/Users/lochuynh/OneDrive - University of Florida/LAB
> RESEARCH/ChimeraX/3Q1R/3Q1R v7.cxs"

[Repeated 1 time(s)]

——— End of log from Mon Dec 27 20:37:10 2021 ———

opened ChimeraX session  

> preset cartoons/nucleotides cylinders/stubs

Changed 973 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

  

> cartoon style nucleic xsection oval width 1.0 thickness 1.0

> cartoon style nucleic xsection oval width 3.0 thickness 3.0

> cartoon style nucleic xsection oval width 2.0 thickness 2.0

> select clear

> select /A:117

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select /A:6-117

973 atoms, 989 bonds, 112 residues, 1 model selected  

> select /C:86

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select /C:1-86

1788 atoms, 1994 bonds, 82 pseudobonds, 86 residues, 2 models selected  

> ui tool show "Color Actions"

> color sel light gray

> color sel gray

> color sel dark gray

> color sel gray

> color sel dark gray

> select /B:1-347

7380 atoms, 8253 bonds, 353 pseudobonds, 347 residues, 2 models selected  

> select /B:347

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select /B:1-347

7380 atoms, 8253 bonds, 353 pseudobonds, 347 residues, 2 models selected  

> surface (#!1 & sel)

> transparency (#!1 & sel) 50

> cartoon hide (#!1 & sel)

> hide (#!1 & sel) target a

> color sel cornflower blue

> color sel medium blue

> color sel dark blue




OpenGL version: 4.1 Metal - 71.7.1
OpenGL renderer: Apple M1
OpenGL vendor: AppleHardware:

    Hardware Overview:

      Model Name: Mac mini
      Model Identifier: Macmini9,1
      Processor Name: Unknown
      Processor Speed: 2.4 GHz
      Number of Processors: 1
      Total Number of Cores: 8
      L2 Cache (per Core): 4 MB
      Memory: 16 GB

Software:

    System Software Overview:

      System Version: macOS 11.6.1 (20G224)
      Kernel Version: Darwin 20.6.0
      Time since boot: 17:37

Graphics/Displays:

    Apple M1:

      Chipset Model: Apple M1
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 8
      Vendor: Apple (0x106b)
      Metal Family: Supported, Metal GPUFamily Apple 7
      Displays:
        LG HDR 4K:
          Resolution: 5120 x 2880 (5K/UHD+ - Ultra High Definition Plus)
          UI Looks like: 2560 x 1440 @ 60.00Hz
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
        LG HDR 4K:
          Resolution: 5120 x 2880 (5K/UHD+ - Ultra High Definition Plus)
          UI Looks like: 2560 x 1440 @ 60.00Hz
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes

Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.2
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.5.30
    cftime: 1.5.1.1
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    ChimeraX-AddCharge: 1.2.2
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.31
    ChimeraX-AtomicLibrary: 4.2
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.6.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
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    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.2
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5
    ChimeraX-CommandLine: 1.1.5
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.4
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.4
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.4
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.2.6
    ChimeraX-ModelPanel: 1.2.1
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.7
    ChimeraX-PDB: 2.6.5
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.6
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.6.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.13.7
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0.1
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    cxservices: 1.1
    cycler: 0.11.0
    Cython: 0.29.24
    decorator: 5.1.0
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.6.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.21
    imagecodecs: 2021.4.28
    imagesize: 1.3.0
    ipykernel: 5.5.5
    ipython: 7.23.1
    ipython-genutils: 0.2.0
    jedi: 0.18.0
    Jinja2: 3.0.1
    jupyter-client: 6.1.12
    jupyter-core: 4.9.1
    kiwisolver: 1.3.2
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 2.0.1
    matplotlib: 3.4.3
    matplotlib-inline: 0.1.3
    msgpack: 1.0.2
    netCDF4: 1.5.7
    networkx: 2.6.3
    numexpr: 2.8.0
    numpy: 1.21.2
    openvr: 1.16.801
    packaging: 21.0
    ParmEd: 3.2.0
    parso: 0.8.3
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 8.3.2
    pip: 21.2.4
    pkginfo: 1.7.1
    prompt-toolkit: 3.0.23
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    pydicom: 2.1.2
    Pygments: 2.10.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.6
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.2
    pytz: 2021.3
    pyzmq: 22.3.0
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    scipy: 1.7.1
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    tinyarray: 1.2.3
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    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.0
    wheel-filename: 1.3.0

[pett]

Reported by Loc Huynh

[Elaine Meng]

Hi Loc,
It's true that "dark gray" is darker than "gray" which seems silly, but it is not a bug, simply that we are using a common set of color names (that we did not define ourselves) and that is actually the way that they are defined.  There are other similar examples, like "dark sea green" looks lighter than "sea green."

here are the names and the colors that go with them:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/colornames.html>

Best,
Elaine