[chimerax-users] [Chimera-users] Using ChimeraX in no-gui mode
Eric Pettersen
pett at cgl.ucsf.edu
Mon Jul 8 10:45:20 PDT 2019
Hi James,
Bugs should actually be reported to chimerax-bugs, not chimerax-users. I have opened a ticket for this problem in our bug-tracking database, and you should have received information about the ticket via email.
—Eric
Eric Pettersen
UCSF Computer Graphics Lab
> On Jul 8, 2019, at 2:26 AM, James Starlight <jmsstarlight at gmail.com> wrote:
>
> 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
>>>>
>
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