Status bar destruction: wrapped C/C++ object of type QScreen has been deleted

[lochuynh@…]

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
Error processing trigger "modified":
RuntimeError: wrapped C/C++ object of type QScreen has been deleted

File "/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/graphics/opengl.py", line 125, in _initialize_context
qc.setScreen(self._screen)

See log for complete Python traceback.

Log:
UCSF 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 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  

> /a

Unknown command: /a  

> /A

Unknown command: /A  

> /A

Unknown command: /A  

> /A

Unknown command: /A  

> /B

Unknown command: /B  

> chain /A

Unknown command: chain /A  

> select clear

> /a

Unknown command: /a  

> chain /a

Unknown command: chain /a  

> chain /b

Unknown command: chain /b  

> chain/a

Unknown command: chain/a  

> chain/.a

Unknown command: chain/.a  

> chain /.a

Unknown command: chain /.a  

> alias ribbon #1/A

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/cmd_line/tool.py", line 280, in execute  
cmd.run(cmd_text)  
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/std_commands/alias.py", line 35, in alias  
cli.create_alias(name, text, user=True, logger=logger)  
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 3464, in create_alias  
register(name, alias.cmd_desc(synopsis='alias of "%s"' % text, url=url),  
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 2297, in register  
_parent_info.add_subcommand(words[-1], name, cmd_desc, logger=logger)  
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 2210, in add_subcommand  
logger.info("FYI: alias is hiding existing command" %  
TypeError: not all arguments converted during string formatting  
  
TypeError: not all arguments converted during string formatting  
  
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 2210, in add_subcommand  
logger.info("FYI: alias is hiding existing command" %  
  
See log for complete Python traceback.  
  

> alias ribbon #1/A

> alias ribbon #1/A

> alias ribbon #1/A

> help

> help command

No help found for 'command'  

> 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  

> style nucrib

Expected fewer arguments  

> nucrib

Unknown command: nucrib  

> nucrib\

Unknown command: nucrib\  

> nucrib

Unknown command: nucrib  

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

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

> select clear

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

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

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

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

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

> select

10186 atoms, 11275 bonds, 454 pseudobonds, 555 residues, 3 models selected  

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

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

> close

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/seqalign/alignment.py", line 635, in _mmap_mod_cb  
self.disassociate(self._sseq_to_chain[match_map.struct_seq], demotion=True)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/alignment.py", line 392, in disassociate  
self.session.alignments.destroy_alignment(self)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/manager.py", line 108, in destroy_alignment  
alignment._destroy()  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/alignment.py", line 603, in _destroy  
self._notify_observers(self.NOTE_DESTROYED, None)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/alignment.py", line 652, in _notify_observers  
recipient.alignment_notification(note_name, note_data)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/tool.py", line 474, in alignment_notification  
self.delete()  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/tool.py", line 512, in delete  
ToolInstance.delete(self)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/tools.py", line 154, in delete  
self.session.ui.remove_tool(self)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 345, in remove_tool  
self.main_window.remove_tool(tool_instance)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 725, in remove_tool  
tw._destroy()  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 2049, in _destroy  
self.__toolkit.destroy()  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 2189, in destroy  
sbar.destroy()  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/statusbar.py", line 51, in destroy  
v.delete()  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/opengl.py", line 438, in delete  
self.make_current()  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/opengl.py", line 478, in make_current  
return self._opengl_context.make_current()  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/opengl.py", line 99, in make_current  
qc = self._initialize_context()  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/opengl.py", line 125, in _initialize_context  
qc.setScreen(self._screen)  
RuntimeError: wrapped C/C++ object of type QScreen has been deleted  
  
Error processing trigger "modified":  
RuntimeError: wrapped C/C++ object of type QScreen has been deleted  
  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/opengl.py", line 125, in _initialize_context  
qc.setScreen(self._screen)  
  
See log for complete Python traceback.  
  
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/seqalign/alignment.py", line 635, in _mmap_mod_cb  
self.disassociate(self._sseq_to_chain[match_map.struct_seq], demotion=True)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/alignment.py", line 392, in disassociate  
self.session.alignments.destroy_alignment(self)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/manager.py", line 108, in destroy_alignment  
alignment._destroy()  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/alignment.py", line 603, in _destroy  
self._notify_observers(self.NOTE_DESTROYED, None)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/alignment.py", line 652, in _notify_observers  
recipient.alignment_notification(note_name, note_data)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/tool.py", line 474, in alignment_notification  
self.delete()  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/tool.py", line 512, in delete  
ToolInstance.delete(self)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/tools.py", line 154, in delete  
self.session.ui.remove_tool(self)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 345, in remove_tool  
self.main_window.remove_tool(tool_instance)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 725, in remove_tool  
tw._destroy()  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 2049, in _destroy  
self.__toolkit.destroy()  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 2189, in destroy  
sbar.destroy()  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/statusbar.py", line 51, in destroy  
v.delete()  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/opengl.py", line 438, in delete  
self.make_current()  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/opengl.py", line 478, in make_current  
return self._opengl_context.make_current()  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/opengl.py", line 99, in make_current  
qc = self._initialize_context()  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/opengl.py", line 125, in _initialize_context  
qc.setScreen(self._screen)  
RuntimeError: wrapped C/C++ object of type QScreen has been deleted  
  
Error processing trigger "modified":  
RuntimeError: wrapped C/C++ object of type QScreen has been deleted  
  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/opengl.py", line 125, in _initialize_context  
qc.setScreen(self._screen)  
  
See log for complete Python traceback.  
  
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/seqalign/alignment.py", line 635, in _mmap_mod_cb  
self.disassociate(self._sseq_to_chain[match_map.struct_seq], demotion=True)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/alignment.py", line 392, in disassociate  
self.session.alignments.destroy_alignment(self)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/manager.py", line 108, in destroy_alignment  
alignment._destroy()  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/alignment.py", line 603, in _destroy  
self._notify_observers(self.NOTE_DESTROYED, None)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/alignment.py", line 652, in _notify_observers  
recipient.alignment_notification(note_name, note_data)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/tool.py", line 474, in alignment_notification  
self.delete()  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/tool.py", line 512, in delete  
ToolInstance.delete(self)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/tools.py", line 154, in delete  
self.session.ui.remove_tool(self)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 345, in remove_tool  
self.main_window.remove_tool(tool_instance)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 725, in remove_tool  
tw._destroy()  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 2049, in _destroy  
self.__toolkit.destroy()  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 2189, in destroy  
sbar.destroy()  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/statusbar.py", line 51, in destroy  
v.delete()  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/opengl.py", line 438, in delete  
self.make_current()  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/opengl.py", line 478, in make_current  
return self._opengl_context.make_current()  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/opengl.py", line 99, in make_current  
qc = self._initialize_context()  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/opengl.py", line 125, in _initialize_context  
qc.setScreen(self._screen)  
RuntimeError: wrapped C/C++ object of type QScreen has been deleted  
  
Error processing trigger "modified":  
RuntimeError: wrapped C/C++ object of type QScreen has been deleted  
  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/opengl.py", line 125, in _initialize_context  
qc.setScreen(self._screen)  
  
See log for complete Python traceback.  
  
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/seqalign/alignment.py", line 635, in _mmap_mod_cb  
self.disassociate(self._sseq_to_chain[match_map.struct_seq], demotion=True)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/alignment.py", line 392, in disassociate  
self.session.alignments.destroy_alignment(self)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/manager.py", line 108, in destroy_alignment  
alignment._destroy()  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/alignment.py", line 603, in _destroy  
self._notify_observers(self.NOTE_DESTROYED, None)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/alignment.py", line 652, in _notify_observers  
recipient.alignment_notification(note_name, note_data)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/tool.py", line 474, in alignment_notification  
self.delete()  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/tool.py", line 512, in delete  
ToolInstance.delete(self)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/tools.py", line 154, in delete  
self.session.ui.remove_tool(self)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 345, in remove_tool  
self.main_window.remove_tool(tool_instance)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 725, in remove_tool  
tw._destroy()  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 2049, in _destroy  
self.__toolkit.destroy()  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 2189, in destroy  
sbar.destroy()  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/statusbar.py", line 51, in destroy  
v.delete()  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/opengl.py", line 438, in delete  
self.make_current()  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/opengl.py", line 478, in make_current  
return self._opengl_context.make_current()  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/opengl.py", line 99, in make_current  
qc = self._initialize_context()  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/opengl.py", line 125, in _initialize_context  
qc.setScreen(self._screen)  
RuntimeError: wrapped C/C++ object of type QScreen has been deleted  
  
Error processing trigger "modified":  
RuntimeError: wrapped C/C++ object of type QScreen has been deleted  
  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/opengl.py", line 125, in _initialize_context  
qc.setScreen(self._screen)  
  
See log for complete Python traceback.  
  




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: 29 days 1:46

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: 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

[Eric Pettersen]

Reported by Loc Huynh

[Tom Goddard]

This ChimeraX error is fixed in the current version 1.3, was fixed about 6 months ago, happens after an external screen is disconnected and a sequence panel is closed.