[chimerax-users] [Chimera-users] Using ChimeraX in no-gui mode

[James Starlight]

P.S. sorry I forgot to mention that I have not yet updated Chimera-X
since the version which had been installed at first time. So I will
now do it today and will report the result!

J.

пт, 28 июн. 2019 г. в 10:44, James Starlight <jmsstarlight at gmail.com>:
>
> Hi Greg,
>
> sorry for some delay :-)
>
> Actually I just checked and indeed, there is still problem with
> rendering of the images with chimera-X using
>
> here is the detailed output if it would help
>
>
> chimerax-daily --offscreen --nogui "${output}/!temp/chimeraX.${pdb_name}.cxc"
>
> INFO:
> Offscreen rendering is not available.
> INFO:
> module 'OpenGL.osmesa' has no attribute 'OSMESA_DEPTH_BITS'
> INFO:
> UCSF ChimeraX version: 0.9 (2019-04-03)
> INFO:
> © 2016-2019 Regents of the University of California.  All rights reserved.
> INFO:
> Executing: open /home_pers/novikov/Bureau/test/test/!temp/chimeraX.0476.cxc
> INFO:
> Executing: open /home_pers/novikov/Bureau/test/test/!temp/B-factors_0476.pdb
> INFO:
> Summary of feedback from opening
> /home_pers/novikov/Bureau/test/test/!temp/B-factors_0476.pdb
> ---
> _warning_ |  Ignored bad PDB record found on line 2
> REMARK THIS IS A SIMULATION BOX
>
>
> INFO:
> _B-factors_0476.pdb_ title:
>  **Gallium Rubidium Oxygen Manganese Argon Carbon Silicon**
> [[more info...]](cxcmd:log metadata #1)
>
>
> INFO:
> Chain information for B-factors_0476.pdb #1
> ---
> Chain | Description
> [ ](cxcmd:select :1-219 "Select chain") | [No description
> available](cxcmd:sequence chain #1/  "Show sequence")
>
>
> INFO:
> Executing: open /home_pers/novikov/Bureau/test/test/florence.pdb
> INFO:
> Chain information for florence.pdb #2
> ---
> Chain | Description
> [ ](cxcmd:select #2:1-219 "Select chain") | [No description
> available](cxcmd:sequence chain #2/  "Show sequence")
>
>
> INFO:
> Executing: mmaker #1 to #2
> INFO:
> Parameters
> ---
> Chain pairing | bb
> Alignment algorithm | Needleman-Wunsch
> Similarity matrix | BLOSUM-62
> SS fraction | 0.3
> Gap open (HH/SS/other) | 18/18/6
> Gap extend | 1
> SS matrix |  |  | H | S | O
> ---|---|---|---
> H | 6 | -9 | -6
> S |  | 6 | -6
> O |  |  | 4
> Iteration cutoff | 2
>
>
> INFO:
> Matchmaker florence.pdb, chain (blank) (#2) with B-factors_0476.pdb,
> chain (blank) (#1), sequence alignment score = 1131.8
> STATUS:
> Matchmaker florence.pdb, chain (blank) (#2) with B-factors_0476.pdb,
> chain (blank) (#1), sequence alignment score = 1131.8
> STATUS:
> RMSD between 194 pruned atom pairs is 0.859 angstroms; (across all 219
> pairs: 2.266)
> INFO:
> RMSD between 194 pruned atom pairs is 0.859 angstroms; (across all 219
> pairs: 2.266)
> INFO:
>
> INFO:
> Executing: hide #2 models
> INFO:
> Executing: wait
> ERROR:
> wait requires a frame count argument unless motion is in progress
> ERROR:
> wait requires a frame count argument unless motion is in progress
> INFO:
> Executing: dssp #1
> INFO:
> Executing: zoom 1.3
> ERROR:
> turn x 15 y 15 z -40
> ERROR:
> ..........^
> ERROR:
> Expected an integer >= 1 or a keyword
> ERROR:
> Expected an integer >= 1 or a keyword
> INFO:
> Executing: wait
> ERROR:
> wait requires a frame count argument unless motion is in progress
> ERROR:
> wait requires a frame count argument unless motion is in progress
> INFO:
> Executing: preset "'overall look'" publication
> INFO:
> Preset expands to these ChimeraX commands: _set bg white; set silhouettes t_
>
> INFO:
> Executing: set silhouettes true
> INFO:
> Executing: set silhouetteColor indigo
> INFO:
> Executing: set silhouetteDepthJump 0.02
> INFO:
> Executing: color byattribute bfactor palette rainbow range 2,100
> INFO:
> 16875 atoms, 4661 residues, atom bfactor range 0 to 367
> STATUS:
> 16875 atoms, 4661 residues, atom bfactor range 0 to 367
> INFO:
> Executing: cartoon style width 2.4 thickness 0.50 xsection barbell
> INFO:
> Executing: 2dlabels create title text '"Cluster 0476"' color red font
> gothic xpos .01 ypos .90 size 36
> INFO:
> Executing: lighting depthCueStart .4 depthCueEnd .8
> INFO:
> Executing: lighting full intensity 1.4 shadows true qualityOfShadows finer
> INFO:
> Executing: save image
> /home_pers/novikov/Bureau/test/test/!plots/visu_0476.png format png
> width 600 height 600 supersample 4 transparentBackground false
>
>
> and this is my script
>
> open /home_pers/novikov/Bureau/test/test/!temp/B-factors_0472.pdb
> open /home_pers/novikov/Bureau/test/test/florence.pdb
> mm #1 to #2
> hide #2 models
> wait
> dssp #1
> #view
> zoom 1.3
> turn x 15 y 15 z -40
> wait
> # options for appearance
> preset 'overall look' publication
> # set bg powder blue
> set silhouettes t; set silhouetteColor indigo; set silhouetteDepthJump 0.02
> color byattribute bfactor palette rainbow range 2,100
> cartoon style width 2.4 thickness 0.50 xsection barbell
>
> # make info of the screen
> 2dlab create title text "Cluster 0472" color red font gothic xpos .01
> ypos .90 size 36
>
> # options for light
> light depthcuestart .4 depthcueend .8; lighting full intensity 1.4
> shadows true qualityOfShadows finer
>
> save image /home_pers/novikov/Bureau/test/test/!plots/visu_0472.png
> format png width 600 height 600 supersample 4 transparentBackground
> false
> exit
>
> пн, 22 апр. 2019 г. в 23:38, Greg Couch <gregc at cgl.ucsf.edu>:
> >
> > Salut,
> >
> > Does ChimeraX work in offscreen mode for you now?  I believe it is fixed.
> >
> >      -- Greg
> >