Re: [chimerax-users] [Chimera-users] Using ChimeraX in no-gui mode
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@cgl.ucsf.edu:
Salut,
Does ChimeraX work in offscreen mode for you now? I believe it is fixed.
-- Greg
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@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@cgl.ucsf.edu:
Salut,
Does ChimeraX work in offscreen mode for you now? I believe it is fixed.
-- Greg
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@ca #1:152@ca color maroon INFO: Distance between LEU 56 CA and ASN 152 CA: 11.674Å INFO: Executing: distance #1:56@ca #1:107@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@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@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@cgl.ucsf.edu:
Salut,
Does ChimeraX work in offscreen mode for you now? I believe it is fixed.
-- Greg
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@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@ca #1:152@ca color maroon INFO: Distance between LEU 56 CA and ASN 152 CA: 11.674Å INFO: Executing: distance #1:56@ca #1:107@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@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@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@cgl.ucsf.edu:
Salut,
Does ChimeraX work in offscreen mode for you now? I believe it is fixed.
-- Greg
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participants (2)
-
Eric Pettersen -
James Starlight