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

[James Starlight]

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
>