[chimerax-users] [Chimera-users] Using ChimeraX in no-gui mode
James Starlight
jmsstarlight at gmail.com
Mon Jul 8 02:26:56 PDT 2019
hello,
just tested with 0.91 version of Chimera-X. There is still a problem
with making of the image while execution of chimeraX in --offscreen
-nogui
(with the same script there is not problems in no gui mode). Here is
the detailed outputs:
INFO:
UCSF ChimeraX version: 0.91 (2019-07-07)
INFO:
© 2016-2019 Regents of the University of California. All rights reserved.
INFO:
[How to cite UCSF ChimeraX](cxcmd:help help:credits.html)
INFO:
Executing: open chimeraX.0062_310K.cxc
INFO:
Executing: open B-factors_0062_310K.pdb
INFO:
Summary of feedback from opening B-factors_0062_310K.pdb
---
_warning_ | Ignored bad PDB record found on line 2
REMARK THIS IS A SIMULATION BOX
INFO:
_B-factors_0062_310K.pdb_ title:
**Good gRace! Old Maple Actually Chews Slate** [[more info...]](cxcmd:log
metadata #1)
INFO:
Chain information for B-factors_0062_310K.pdb #1
---
Chain | Description
[ ](cxcmd:select :1-219 "Select chain") | [No description
available](cxcmd:sequence chain #1/ "Show sequence")
INFO:
Executing: open 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: hide #2 models
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_0062_310K.pdb, chain (blank) (#1), sequence alignment score
= 1132.4
STATUS:
Matchmaker florence.pdb, chain (blank) (#2) with
B-factors_0062_310K.pdb, chain (blank) (#1), sequence alignment score
= 1132.4
STATUS:
RMSD between 193 pruned atom pairs is 0.874 angstroms; (across all 219
pairs: 2.260)
INFO:
RMSD between 193 pruned atom pairs is 0.874 angstroms; (across all 219
pairs: 2.260)
INFO:
INFO:
Executing: close #2
INFO:
Executing: wait 1
INFO:
Executing: dssp #1
INFO:
Executing: view
INFO:
Executing: zoom 1.5
INFO:
Executing: turn x 15
INFO:
Executing: wait 1
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:
877 atoms, 219 residues, atom bfactor range 3.49 to 377
STATUS:
877 atoms, 219 residues, atom bfactor range 3.49 to 377
INFO:
Executing: cartoon style width 2.4 thickness 0.50 xsection barbell
INFO:
Executing: distance #1:56 at ca #1:152 at ca color maroon
INFO:
Distance between LEU 56 CA and ASN 152 CA: 11.674Å
INFO:
Executing: distance #1:56 at ca #1:107 at ca color "dark green"
INFO:
Distance between LEU 56 CA and ASN 107 CA: 31.617Å
INFO:
Executing: distance style #1 radius 0.088 dashes 12 decimalPlaces 1
INFO:
Executing: 2dlabels create title text "Cluster 0062_310K" color red
font gothic xpos .20 ypos .88 size 40
INFO:
Executing: lighting depthCueStart .4 depthCueEnd .8
INFO:
Executing: lighting full intensity 1.4 shadows true qualityOfShadows finer
INFO:
Executing: save image ./visu_0062_310K.png format png width 600 height
600 supersample 4 transparentBackground false
0.00% done: Initializing core
50.00% done: Initializing bundles
100.00% done: Finished initialization
QObject::startTimer: Timers can only be used with threads started with QThread
Fatal Python error: Segmentation fault
Thread 0x00007fb1866d2700 (most recent call first):
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/threading.py", line
300 in wait
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/threading.py", line
552 in wait
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/threading.py", line
1156 in run
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/threading.py", line
917 in _bootstrap_inner
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/threading.py", line
885 in _bootstrap
Current thread 0x00007fb1abfef700 (most recent call first):
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/graphics/drawing.py",
line 2058 in text_image_rgba
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/label/label3d.py",
line 625 in _label_image
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/label/label3d.py",
line 427 in <listcomp>
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/label/label3d.py",
line 427 in _packed_texture
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/label/label3d.py",
line 409 in _rebuild_label_graphics
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/label/label3d.py",
line 401 in _update_graphics_if_needed
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/triggerset.py",
line 130 in invoke
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/triggerset.py",
line 190 in activate
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/triggerset.py",
line 325 in activate_trigger
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/graphics/view.py",
line 258 in check_for_drawing_change
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/updateloop.py",
line 64 in draw_new_frame
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/updateloop.py",
line 139 in update_graphics_now
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/commands/save.py",
line 56 in save
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/commands/cli.py",
line 2646 in run
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/commands/run.py",
line 31 in run
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/scripting.py",
line 147 in open_command_script
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/io.py",
line 433 in open_data
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/io.py",
line 479 in open_multiple_data
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/models.py",
line 616 in open
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/commands/open.py",
line 68 in open
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/commands/cli.py",
line 2646 in run
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/commands/run.py",
line 31 in run
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/ChimeraX_main.py",
line 729 in init
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/ChimeraX_main.py",
line 869 in <module>
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/runpy.py", line 85
in _run_code
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/runpy.py", line 193
in _run_module_as_main
Erreur de segmentation (core dumped)
пт, 28 июн. 2019 г. в 10:51, James Starlight <jmsstarlight at gmail.com>:
>
> 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
> > >
More information about the ChimeraX-users
mailing list