id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
15910	Crash on Mac waking from sleep	sandelpi@…	Tom Goddard	"{{{
The following bug report has been submitted:
Platform:        macOS-14.6.1-x86_64-i386-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
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    ""size"" : 241656,
    ""uuid"" : ""54b50613-cc4b-3ace-a9ec-919ea83d5e5f"",
    ""path"" : ""\/usr\/lib\/system\/libsystem_kernel.dylib"",
    ""name"" : ""libsystem_kernel.dylib""
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    ""name"" : ""libsystem_pthread.dylib""
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    ""size"" : 503796,
    ""uuid"" : ""69eca28c-bfb7-35bf-ad4f-1bece712d239"",
    ""path"" : ""\/usr\/lib\/libc++.1.dylib"",
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===== Log before crash start =====
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 1bm8 fromDatabase pdb format mmcif

Summary of feedback from opening 1bm8 fetched from pdb  
---  
warning | Atom H1 is not in the residue template for GLN /A:4  
note | Fetching compressed mmCIF 1bm8 from http://files.rcsb.org/download/1bm8.cif  
  
1bm8 title:  
Dna-binding domain of MBP1 [more info...]  
  
Chain information for 1bm8 #1  
---  
Chain | Description | UniProt  
A | TRANSCRIPTION FACTOR MBP1 | MBP1_YEAST 4-102  
  

> color sequential ÷a palette blue:cornflower:gray:pink:red

Expected one of 'chains', 'polymers', 'residues', or 'structures' or a keyword  

> color sequential /a palette blue:cornflower:gray:pink:red

> ui tool show ""Show Sequence Viewer""

> sequence chain /A

Alignment identifier is 1/A  

> ui autostart false ""Map Coordinates""

> select /A:13

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:13-19

70 atoms, 71 bonds, 7 residues, 1 model selected  

> select /A:21-71

513 atoms, 518 bonds, 51 residues, 1 model selected  

> select /A:21-73

540 atoms, 546 bonds, 53 residues, 1 model selected  

> select clear

> select /A:49

13 atoms, 12 bonds, 1 residue, 1 model selected  

> select /A:49-74

278 atoms, 280 bonds, 26 residues, 1 model selected  

> show sel atoms

> hbonds sel reveal true

45 hydrogen bonds found  

> ~hbonds

> show sel atoms, bonds

> hide H

> color sel byelement

> preset ""overall look"" ""publication 1 (silhouettes)""

Using preset: Overall Look / Publication 1 (Silhouettes)  
Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes t
    lighting depthCue f

  

> select clear

> camera walleye

> ui tool show ""Side View""

> view orient

> view

> view orient

> help help:user

> camera crosseye

> view orient

> view

> close session

> open /Users/Pino/Dropbox/Docs/LAB/MAT/ESPECTROS:ESTRUCTURA/PDB/MATrat.cxs
> format session

Exception ignored in:   
Traceback (most recent call last):  
File
""/Applications/CIENCIA/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py"", line 2218, in __del__  
raise OpenGLError('OpenGL framebuffer ""%s"" was not deleted before
graphics.Framebuffer destroyed'  
chimerax.graphics.opengl.OpenGLError: OpenGL framebuffer ""stereo camera"" was
not deleted before graphics.Framebuffer destroyed  
Exception ignored in:   
Traceback (most recent call last):  
File
""/Applications/CIENCIA/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py"", line 2218, in __del__  
raise OpenGLError('OpenGL framebuffer ""%s"" was not deleted before
graphics.Framebuffer destroyed'  
chimerax.graphics.opengl.OpenGLError: OpenGL framebuffer ""stereo camera"" was
not deleted before graphics.Framebuffer destroyed  
opened ChimeraX session  

> view orient

> preset ""overall look"" ""publication 1 (silhouettes)""

Using preset: Overall Look / Publication 1 (Silhouettes)  
Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes t
    lighting depthCue f

  

> save /Users/Pino/Downloads/matSil.png width 1790 height 1640 supersample 3
> transparentBackground true

> close session

> open /Users/Pino/Dropbox/Docs/LAB/MAT/ESPECTROS:ESTRUCTURA/PDB/MATrat.cxs
> format session

opened ChimeraX session  

> graphics silhouettes true

> graphics silhouettes false

> lighting full

> lighting false

Expected one of 'default', 'flat', 'full', 'gentle', 'simple', or 'soft' or a
keyword  

> lighting simple

> lighting soft

> lighting full

> lighting flat

> lighting simple

> graphics silhouettes false

> lighting shadows true

> lighting shadows false

> lighting simple

> close session

> open 1bm8 format mmcif fromDatabase pdb

Summary of feedback from opening 1bm8 fetched from pdb  
---  
warning | Atom H1 is not in the residue template for GLN /A:4  
  
1bm8 title:  
Dna-binding domain of MBP1 [more info...]  
  
Chain information for 1bm8 #1  
---  
Chain | Description | UniProt  
A | TRANSCRIPTION FACTOR MBP1 | MBP1_YEAST 4-102  
  

> preset ""overall look"" ""publication 1 (silhouettes)""

Using preset: Overall Look / Publication 1 (Silhouettes)  
Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes t
    lighting depthCue f

  

> lighting simple

> lighting full

> close session

> open 1bm8 format mmcif fromDatabase pdb

Summary of feedback from opening 1bm8 fetched from pdb  
---  
warning | Atom H1 is not in the residue template for GLN /A:4  
  
1bm8 title:  
Dna-binding domain of MBP1 [more info...]  
  
Chain information for 1bm8 #1  
---  
Chain | Description | UniProt  
A | TRANSCRIPTION FACTOR MBP1 | MBP1_YEAST 4-102  
  

> view orient

> preset cartoons/nucleotides ribbons/slabs

Using preset: Cartoons/Nucleotides / Ribbons/Slabs  
Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    ~worm
    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 ""initial styles"" ""original look""

Using preset: Initial Styles / Original Look  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> preset cartoons/nucleotides ribbons/slabs

Using preset: Cartoons/Nucleotides / Ribbons/Slabs  
Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    ~worm
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    nucleotides tube/slab shape box

  

> preset cartoons/nucleotides cylinders/stubs

Using preset: Cartoons/Nucleotides / Cylinders/Stubs  
Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    ~worm
    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 licorice/ovals

Using preset: Cartoons/Nucleotides / Licorice/Ovals  
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
    ~worm
    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 default arrows f x round width 1 thick 1
    cartoon style nucleic x round width 1.6 thick 1.6
    nucleotides tube/slab shape ellipsoid

  

> preset ""initial styles"" ""original look""

Using preset: Initial Styles / Original Look  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> preset ""initial styles"" sticks

Using preset: Initial Styles / Sticks  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> preset ""initial styles"" cartoon

Using preset: Initial Styles / Cartoon  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> preset ""initial styles"" ""space-filling (chain colors)""

Using preset: Initial Styles / Space-Filling (Chain Colors)  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> preset ""initial styles"" ""space-filling (single color)""

Using preset: Initial Styles / Space-Filling (Single Color)  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> preset ""molecular surfaces"" ""ghostly white""

Using preset: Molecular Surfaces / Ghostly White  
Changed 1256 atom styles  
Preset expands to these ChimeraX commands:

    
    
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    surface
    color white targ s trans 80

  

> preset ""molecular surfaces"" ""atomic coloring (transparent)""

Using preset: Molecular Surfaces / Atomic Coloring (Transparent)  
Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    surface
    color fromatoms targ s trans 70

  

> preset ""molecular surfaces"" ""chain id coloring (opaque)""

Using preset: Molecular Surfaces / Chain ID Coloring (Opaque)  
Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    surface
    color bychain targ s trans 0

  

> preset ""overall look"" ""publication 2 (depth-cued)""

Using preset: Overall Look / Publication 2 (Depth-Cued)  
Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes f
    lighting depthCue t

  

> preset ""overall look"" interactive

Using preset: Overall Look / Interactive  
Preset expands to these ChimeraX commands:

    
    
    ~set bg
    graphics silhouettes f
    lighting depthCue t

  

> preset ""overall look"" ""publication 1 (silhouettes)""

Using preset: Overall Look / Publication 1 (Silhouettes)  
Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes t
    lighting depthCue f

  

> hide surfaces

> show cartoons

> hide atoms

> rainbow

> show cartoons

> preset apply pub 1

No preset name matches 'apply pub 1'  

> color hotpink pink,r helix; color dark magenta,r strand; color grey,r
> coiland colour the protein by secondary structure

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

> help help:user

> ui tool show Toolbar

> worm

> cartoon byattribute

Missing or invalid ""attrName"" argument: Expected a text string  

> ~worm

> cartoon hide

> show cartoons

> cartoon ~worm hide

Expected an atoms specifier or a keyword  

> cartoon /a ~worm hide

Expected a keyword  

> cartoon ~worm hide

Expected an atoms specifier or a keyword  

> cartoon all ~worm hide

Expected a keyword  

> cartoon helix

> show cartoons

> worm off

> show cartoons

> show atoms

> hide cartoons

> preset ""initial styles"" cartoon

Using preset: Initial Styles / Cartoon  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> preset cartoons/nucleotides cylinders/stubs

Using preset: Cartoons/Nucleotides / Cylinders/Stubs  
Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    ~worm
    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 licorice/ovals

Using preset: Cartoons/Nucleotides / Licorice/Ovals  
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
    ~worm
    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 default arrows f x round width 1 thick 1
    cartoon style nucleic x round width 1.6 thick 1.6
    nucleotides tube/slab shape ellipsoid

  

> preset cartoons/nucleotides ribbons/slabs

Using preset: Cartoons/Nucleotides / Ribbons/Slabs  
Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    ~worm
    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 black

> view orient

> close session

> open /Users/Pino/Dropbox/Docs/LAB/MAT/ESPECTROS:ESTRUCTURA/PDB/MATrat.cxs
> format session

opened ChimeraX session  

> view orient

> color bychain

> select :AMB

9 atoms, 8 bonds, 1 residue, 1 model selected  

> color sel byhetero

> color sel byelement

> select :SO4

15 atoms, 12 bonds, 3 residues, 1 model selected  

> hide #1.1 models

> show #1.1 models

> hide #1.2 models

> show #1.2 models

> hide #1.2 models

> show #1.2 models

> hide sel atoms

> select :K

3 atoms, 3 residues, 1 model selected  

> hide sel atoms

> select :MG

2 atoms, 2 residues, 1 model selected  

> hide sel atoms

> select :amb

9 atoms, 8 bonds, 1 residue, 1 model selected  

> style sel sphere

Changed 9 atom styles  

> ui tool show ""Show Sequence Viewer""

> sequence chain /A /B

Alignment identifier is 1  

> select /A-B:265

22 atoms, 20 bonds, 2 residues, 1 model selected  

> select /A-B:265

22 atoms, 20 bonds, 2 residues, 1 model selected  

> select /a,b

5918 atoms, 5822 bonds, 10 pseudobonds, 942 residues, 3 models selected  

> hide sel atoms

> select :amb

9 atoms, 8 bonds, 1 residue, 1 model selected  

> show sel atoms

> select /A-B:265

22 atoms, 20 bonds, 2 residues, 1 model selected  

> select /A-B:265

22 atoms, 20 bonds, 2 residues, 1 model selected  

> show sel atoms

> style sel ball

Changed 22 atom styles  

> style sel stick

Changed 22 atom styles  

> style sel sphere

Changed 22 atom styles  

> select /A-B:58

18 atoms, 16 bonds, 2 residues, 1 model selected  

> select /A-B:58

18 atoms, 16 bonds, 2 residues, 1 model selected  

> show sel atoms

> style sel sphere

Changed 18 atom styles  

> select clear

> select /a,b

5918 atoms, 5822 bonds, 10 pseudobonds, 942 residues, 3 models selected  

> show sel cartoons

> hide sel cartoons

> show sel cartoons

> show sel surfaces

> hide sel surfaces

> select clear

> select /A-B:265

22 atoms, 20 bonds, 2 residues, 1 model selected  

> select /A-B:265

22 atoms, 20 bonds, 2 residues, 1 model selected  

> select clear

> select /A-B:265

22 atoms, 20 bonds, 2 residues, 1 model selected  

> select /A-B:265

22 atoms, 20 bonds, 2 residues, 1 model selected  

> view /A:265

> view orient

> view

> view sel

> view

> select /a,b

5918 atoms, 5822 bonds, 10 pseudobonds, 942 residues, 3 models selected  

> view sel

> view orient

> movie record

> turn y 2 180

> wait 180

> movie encode /Users/Pino/Desktop/movie1.mp4

Movie saved to /Users/Pino/Desktop/movie1.mp4  
  

> movie record

> turn y 2 180

> wait 180

> movie encode /Users/Pino/Desktop/movie2.mp4

Movie saved to /Users/Pino/Desktop/movie2.mp4  
  

> select clear

> select /a:265

11 atoms, 10 bonds, 1 residue, 1 model selected  

> view orient

> style sel stick

Changed 11 atom styles  

> select /b:265

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select /b:58

9 atoms, 8 bonds, 1 residue, 1 model selected  

> style sel stick

Changed 9 atom styles  

> hbonds sel reveal true

5 hydrogen bonds found  

> select subtract #1.4

1 model selected  

> select /a:265

11 atoms, 10 bonds, 1 residue, 1 model selected  

> hbonds sel reveal true

7 hydrogen bonds found  

> ~hbonds

> select /b:58

9 atoms, 8 bonds, 1 residue, 1 model selected  

> hbonds sel reveal true

5 hydrogen bonds found  

> view sel

> ~hbonds

> hbonds sel reveal true

5 hydrogen bonds found  

> view orient

> select solvent

197 atoms, 197 residues, 1 model selected  

> select /a:58

9 atoms, 8 bonds, 1 residue, 1 model selected  

> style sel stick

Changed 9 atom styles  

> select /a:265

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select /b:58

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /b:265

11 atoms, 10 bonds, 1 residue, 1 model selected  

> style sel stick

Changed 11 atom styles  

> hbonds sel reveal true

6 hydrogen bonds found  

> ~hbonds

> select /b:58

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /a:58

9 atoms, 8 bonds, 1 residue, 1 model selected  

> hbonds sel reveal true

5 hydrogen bonds found  

> select clear

> ~hbonds

> hbonds reveal true

990 hydrogen bonds found  

> ~hbonds

> select /a:58

9 atoms, 8 bonds, 1 residue, 1 model selected  

> hbonds sel reveal true

5 hydrogen bonds found  

> select clear

> select /b:58

9 atoms, 8 bonds, 1 residue, 1 model selected  

> hbonds sel reveal true

5 hydrogen bonds found  

> select /b:58,a:58

9 atoms, 8 bonds, 1 residue, 1 model selected  

> view sel

> view orient

> select /a,b

5918 atoms, 5822 bonds, 15 pseudobonds, 942 residues, 4 models selected  

> hide sel atoms

> select /a:58

9 atoms, 8 bonds, 1 residue, 1 model selected  

> style sel stick

Changed 9 atom styles  

> style sel stick

Changed 9 atom styles  

> show sel atoms

> hbonds sel reveal true

5 hydrogen bonds found  

> select /b:58

9 atoms, 8 bonds, 1 residue, 1 model selected  

> style sel stick

Changed 9 atom styles  

> show sel atoms

> hbonds sel reveal true

5 hydrogen bonds found  

> select /b:58, /a:58

Expected an objects specifier or a keyword  

> select /b:58 & /a:58

Nothing selected  

> select /A-B:58

18 atoms, 16 bonds, 2 residues, 1 model selected  

> select /A-B:58

18 atoms, 16 bonds, 2 residues, 1 model selected  

> select /a-b:58

18 atoms, 16 bonds, 2 residues, 1 model selected  

> hbonds sel reveal true

10 hydrogen bonds found  

> select clear

> select :amb

9 atoms, 8 bonds, 1 residue, 1 model selected  

> show sel atoms

> select clear

> select /b

2945 atoms, 2905 bonds, 5 pseudobonds, 463 residues, 4 models selected  

> ui tool show ""Color Actions""

> select clear

> set bgColor white

> graphics silhouettes true

> movie record

> turn y 2 180

> wait 180

> movie encode /Users/Pino/Desktop/movie3.mp4

Movie saved to /Users/Pino/Desktop/movie3.mp4  
  

> select /a-b:69

12 atoms, 10 bonds, 2 residues, 1 model selected  

> ~hbonds

> select /a-b:58

18 atoms, 16 bonds, 2 residues, 1 model selected  

> hbonds sel reveal true

10 hydrogen bonds found  

> hbonds /a-b:58 restrict protein reveal true

8 hydrogen bonds found  

> select /a-b:58

18 atoms, 16 bonds, 2 residues, 1 model selected  

> hbonds sel reveal true

10 hydrogen bonds found  

> hbonds /a-b:69 reveal false

5 hydrogen bonds found  

> hbonds /a-b:69 reveal hide

Invalid ""reveal"" argument: Expected true or false (or 1 or 0)  

> hbonds /a-b:69 hide

Expected a keyword  

> hbonds /a-b:58

10 hydrogen bonds found  

> hbonds /a-b:58 sidechain restrict

Expected a keyword  

> hbonds sidechain restrict /a-b:58

4 hydrogen bonds found  

> select solvent

197 atoms, 197 residues, 1 model selected  

> hide sel atoms

> view orient

> select /a-b:265

22 atoms, 20 bonds, 2 residues, 1 model selected  

> color sel blue

> select /a-b:58

18 atoms, 16 bonds, 2 residues, 1 model selected  

> color sel red

> select clear

> view name side_initial

> movie record

> turn y 2 180

> wait 180

> movie encode /Users/Pino/Desktop/movie3.mp4

Movie saved to /Users/Pino/Desktop/movie3.mp4  
  

> save /Users/Pino/Downloads/MATside_initial.png width 1790 height 1640
> supersample 3 transparentBackground true

> view side_initial

Downloading file AMB_ideal.sdf  
Downloading file AMB_model.sdf  
Downloading file AMB.cif  

> view side_initial

> view top

> help help:user

> fly 200 side_initial top

> record fly 200 side_initial top

Unknown command: record fly 200 side_initial top  

> fly 200 side_initial top

> fly 200 side_initial top

Unknown command: movie fly 200 side_initial top  

> fly 200 side_initial top

> movie record fly 200 side_initial top

Expected a keyword  

> fly 200 side_initial top

> record

Unknown command: record  

> fly 200 side_initial top

> movie record

> fly 200 side_initial top

> movie stop

> movie encode /Users/Pino/Desktop/movie3.mp4

Movie saved to /Users/Pino/Desktop/movie3.mp4  
  

> roll y 2 180

> fly 200 side_initial top

> view side_initial

> roll y 2 180

> roll y 1 180

> roll y 1 360

> view side_initial

> roll y 1 360

> roll y 0.5 360

> view side_initial

> roll y 0.5 720

> record movie

Unknown command: record movie  

> movie record

> view side_initial

> roll y 0.5 720

> fly 200 side_initial top

> movie encode /Users/Pino/Desktop/movie3.mp4

Movie saved to /Users/Pino/Desktop/movie3.mp4  
  

> movie stop

No movie being recorded.  

> movie record

> movie stop

> view side_initial

> movie record

> roll y 2 180

> fly 200 side_initial top

> movie stop

> movie encode /Users/Pino/Desktop/movie3.mp4

Movie saved to /Users/Pino/Desktop/movie3.mp4  
  

> fly 200 top side_initial

> roll z 2 90

> roll x 2 90

> roll x 1 90

> movie stop

No movie being recorded.  

> view top

> roll x 1 90

> roll x -1 90

> roll y 2 180

> view top

> movie record

> roll x -1 90

> roll y 2 180

> movie stop

> movie encode /Users/Pino/Desktop/movie3.mp4

Movie saved to /Users/Pino/Desktop/movie3.mp4  
  

> view side_initial

> turn z90

Expected an axis vector or a keyword  

> turn x 90

> roll x -1 90

> view side_initial

> turn x 90

> view top

> movie record

> fly 90 top side_initial

> roll y 2 180

> view side_initial

> movie stop

> movie encode /Users/Pino/Desktop/movie3.mp4

Movie saved to /Users/Pino/Desktop/movie3.mp4  
  

> select /a

2973 atoms, 2917 bonds, 7 pseudobonds, 479 residues, 3 models selected  

> mlp sel

Map values for surface ""1qm4_A SES surface"": minimum -27.14, mean -5.217,
maximum 27.21  
To also show corresponding color key, enter the above mlp command and add key
true  

> mlp sel

Map values for surface ""1qm4_A SES surface"": minimum -27.14, mean -5.217,
maximum 27.21  
To also show corresponding color key, enter the above mlp command and add key
true  

> hide sel surfaces

> select clear

> view side_initial

> turn x -90

> view orient

> turn x -90

> turn x 90

> turn y 90

> view side_initial


===== Log before crash end =====

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.1 ATI-5.5.17
OpenGL renderer: AMD Radeon Pro 560X OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro15,1
      Processor Name: 6-Core Intel Core i7
      Processor Speed: 2,6 GHz
      Number of Processors: 1
      Total Number of Cores: 6
      L2 Cache (per Core): 256 KB
      L3 Cache: 9 MB
      Hyper-Threading Technology: Enabled
      Memory: 32 GB
      System Firmware Version: 2022.140.5.0.0 (iBridge: 21.16.6074.0.0,0)
      OS Loader Version: 580.140.1~8

Software:

    System Software Overview:

      System Version: macOS 14.6.1 (23G93)
      Kernel Version: Darwin 23.6.0
      Time since boot: 1 día, 23 horas y 9 minutos

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: 0x0000
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal Support: Metal 3

    Radeon Pro 560X:

      Chipset Model: Radeon Pro 560X
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x8
      VRAM (Total): 4 GB
      Vendor: AMD (0x1002)
      Device ID: 0x67ef
      Revision ID: 0x00c2
      ROM Revision: 113-C980AL-075
      VBIOS Version: 113-C97501U-005
      EFI Driver Version: 01.A1.075
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2880 x 1800 Retina
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal
        DELL U2913WM:
          Resolution: 2560 x 1080 (UW-UXGA - Ultra Wide - Ultra Extended Graphics Array)
          UI Looks like: 2560 x 1080 @ 60.00Hz
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Display Serial Number: 5YD8C42I226L
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Connection Type: DVI or HDMI
          Adapter Firmware Version: 7,55


Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 2.4.1
    Babel: 2.15.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 1.2.1
    certifi: 2023.11.17
    cftime: 1.6.4
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.17
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.7
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.57.1
    ChimeraX-AtomicLibrary: 14.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.4.6
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.12.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.7
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.8
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.3
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.4
    ChimeraX-DiffPlot: 1.0
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.10
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.3
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.1
    ChimeraX-MedicalToolbar: 1.0.3
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.17
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.5
    ChimeraX-PDB: 2.7.5
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.1
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.4.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-ScholAR: 0.4.2
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.0.15
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.16.5
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.39.1
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.3
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.2.1
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.1
    decorator: 5.1.1
    docutils: 0.20.1
    executing: 2.0.1
    filelock: 3.13.4
    fonttools: 4.53.0
    funcparserlib: 2.0.0a0
    glfw: 2.7.0
    grako: 3.16.5
    h5py: 3.11.0
    html2text: 2024.2.26
    idna: 3.7
    ihm: 1.0
    imagecodecs: 2024.1.1
    imagesize: 1.4.1
    ipykernel: 6.29.2
    ipython: 8.21.0
    ipywidgets: 8.1.3
    jedi: 0.19.1
    jinja2: 3.1.4
    jupyter-client: 8.6.0
    jupyter-core: 5.7.2
    jupyterlab-widgets: 3.0.11
    kiwisolver: 1.4.5
    line-profiler: 4.1.2
    lxml: 5.2.1
    lz4: 4.3.3
    MarkupSafe: 2.1.5
    matplotlib: 3.8.4
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.0
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 23.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.3.0
    pip: 24.0
    pkginfo: 1.10.0
    platformdirs: 4.2.2
    prompt-toolkit: 3.0.47
    psutil: 5.9.8
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pygments: 2.17.2
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.1.2
    pyproject-hooks: 1.1.0
    PyQt6-commercial: 6.6.1
    PyQt6-Qt6: 6.6.3
    PyQt6-sip: 13.6.0
    PyQt6-WebEngine-commercial: 6.6.0
    PyQt6-WebEngine-Qt6: 6.6.3
    python-dateutil: 2.9.0.post0
    pytz: 2024.1
    pyzmq: 26.0.3
    qtconsole: 5.5.1
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.13.0
    setuptools: 69.5.1
    setuptools-scm: 8.0.4
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 7.2.6
    sphinx-autodoc-typehints: 2.0.1
    sphinxcontrib-applehelp: 1.0.8
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.6
    sphinxcontrib-htmlhelp: 2.0.5
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.7
    sphinxcontrib-serializinghtml: 1.1.10
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2024.1.30
    tinyarray: 1.2.4
    tornado: 6.4.1
    traitlets: 5.14.2
    typing-extensions: 4.12.2
    tzdata: 2024.1
    urllib3: 2.2.1
    wcwidth: 0.2.13
    webcolors: 1.13
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.11
}}}
"	defect	closed	normal		Window Toolkit		duplicate						all	ChimeraX