<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Hi James,<div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>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.</div><div class=""><br class=""></div><div class="">—Eric<br class=""><div class="">
<div style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><span class="Apple-tab-span" style="white-space: pre;"><br class="Apple-interchange-newline"> </span>Eric Pettersen</div><div style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><span class="Apple-tab-span" style="white-space: pre;"> </span>UCSF Computer Graphics Lab</div><div style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><br class=""></div><br class="Apple-interchange-newline">
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<div><br class=""><blockquote type="cite" class=""><div class="">On Jul 8, 2019, at 2:26 AM, James Starlight <<a href="mailto:jmsstarlight@gmail.com" class="">jmsstarlight@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div class="">hello,<br class="">just tested with 0.91 version of Chimera-X. There is still a problem<br class="">with making of the image while execution of chimeraX in --offscreen<br class="">-nogui<br class="">(with the same script there is not problems in no gui mode). Here is<br class="">the detailed outputs:<br class=""><br class="">INFO:<br class="">UCSF ChimeraX version: 0.91 (2019-07-07)<br class="">INFO:<br class="">© 2016-2019 Regents of the University of California. All rights reserved.<br class="">INFO:<br class="">[How to cite UCSF ChimeraX](cxcmd:help help:credits.html)<br class=""><br class="">INFO:<br class="">Executing: open chimeraX.0062_310K.cxc<br class="">INFO:<br class="">Executing: open B-factors_0062_310K.pdb<br class="">INFO:<br class="">Summary of feedback from opening B-factors_0062_310K.pdb<br class="">---<br class="">_warning_ | Ignored bad PDB record found on line 2<br class="">REMARK THIS IS A SIMULATION BOX<br class=""><br class=""><br class="">INFO:<br class="">_B-factors_0062_310K.pdb_ title:<br class=""> **Good gRace! Old Maple Actually Chews Slate** [[more info...]](cxcmd:log<br class="">metadata #1)<br class=""><br class=""><br class="">INFO:<br class="">Chain information for B-factors_0062_310K.pdb #1<br class="">---<br class="">Chain | Description<br class="">[ ](cxcmd:select :1-219 "Select chain") | [No description<br class="">available](cxcmd:sequence chain #1/ "Show sequence")<br class=""><br class=""><br class="">INFO:<br class="">Executing: open florence.pdb<br class="">INFO:<br class="">Chain information for florence.pdb #2<br class="">---<br class="">Chain | Description<br class="">[ ](cxcmd:select #2:1-219 "Select chain") | [No description<br class="">available](cxcmd:sequence chain #2/ "Show sequence")<br class=""><br class=""><br class="">INFO:<br class="">Executing: hide #2 models<br class="">INFO:<br class="">Executing: mmaker #1 to #2<br class="">INFO:<br class="">Parameters<br class="">---<br class="">Chain pairing | bb<br class="">Alignment algorithm | Needleman-Wunsch<br class="">Similarity matrix | BLOSUM-62<br class="">SS fraction | 0.3<br class="">Gap open (HH/SS/other) | 18/18/6<br class="">Gap extend | 1<br class="">SS matrix | | | H | S | O<br class="">---|---|---|---<br class="">H | 6 | -9 | -6<br class="">S | | 6 | -6<br class="">O | | | 4<br class="">Iteration cutoff | 2<br class=""><br class=""><br class="">INFO:<br class="">Matchmaker florence.pdb, chain (blank) (#2) with<br class="">B-factors_0062_310K.pdb, chain (blank) (#1), sequence alignment score<br class="">= 1132.4<br class="">STATUS:<br class="">Matchmaker florence.pdb, chain (blank) (#2) with<br class="">B-factors_0062_310K.pdb, chain (blank) (#1), sequence alignment score<br class="">= 1132.4<br class="">STATUS:<br class="">RMSD between 193 pruned atom pairs is 0.874 angstroms; (across all 219<br class="">pairs: 2.260)<br class="">INFO:<br class="">RMSD between 193 pruned atom pairs is 0.874 angstroms; (across all 219<br class="">pairs: 2.260)<br class="">INFO:<br class=""><br class="">INFO:<br class="">Executing: close #2<br class="">INFO:<br class="">Executing: wait 1<br class="">INFO:<br class="">Executing: dssp #1<br class="">INFO:<br class="">Executing: view<br class="">INFO:<br class="">Executing: zoom 1.5<br class="">INFO:<br class="">Executing: turn x 15<br class="">INFO:<br class="">Executing: wait 1<br class="">INFO:<br class="">Executing: preset "overall look" publication<br class="">INFO:<br class="">Preset expands to these ChimeraX commands:<br class=""><br class=""><br class=""><br class=""> set bg white<br class=""> set silhouettes t<br class=""><br class=""><br class=""><br class="">INFO:<br class="">Executing: set silhouettes true<br class="">INFO:<br class="">Executing: set silhouetteColor indigo<br class="">INFO:<br class="">Executing: set silhouetteDepthJump 0.02<br class="">INFO:<br class="">Executing: color byattribute bfactor palette rainbow range 2,100<br class="">INFO:<br class="">877 atoms, 219 residues, atom bfactor range 3.49 to 377<br class="">STATUS:<br class="">877 atoms, 219 residues, atom bfactor range 3.49 to 377<br class="">INFO:<br class="">Executing: cartoon style width 2.4 thickness 0.50 xsection barbell<br class="">INFO:<br class="">Executing: distance #1:56@ca #1:152@ca color maroon<br class="">INFO:<br class="">Distance between LEU 56 CA and ASN 152 CA: 11.674Å<br class="">INFO:<br class="">Executing: distance #1:56@ca #1:107@ca color "dark green"<br class="">INFO:<br class="">Distance between LEU 56 CA and ASN 107 CA: 31.617Å<br class="">INFO:<br class="">Executing: distance style #1 radius 0.088 dashes 12 decimalPlaces 1<br class="">INFO:<br class="">Executing: 2dlabels create title text "Cluster 0062_310K" color red<br class="">font gothic xpos .20 ypos .88 size 40<br class="">INFO:<br class="">Executing: lighting depthCueStart .4 depthCueEnd .8<br class="">INFO:<br class="">Executing: lighting full intensity 1.4 shadows true qualityOfShadows finer<br class="">INFO:<br class="">Executing: save image ./visu_0062_310K.png format png width 600 height<br class="">600 supersample 4 transparentBackground false<br class=""><br class=""><br class="">0.00% done: Initializing core<br class="">50.00% done: Initializing bundles<br class="">100.00% done: Finished initialization<br class="">QObject::startTimer: Timers can only be used with threads started with QThread<br class="">Fatal Python error: Segmentation fault<br class=""><br class="">Thread 0x00007fb1866d2700 (most recent call first):<br class=""> File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/threading.py", line<br class="">300 in wait<br class=""> File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/threading.py", line<br class="">552 in wait<br class=""> File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/threading.py", line<br class="">1156 in run<br class=""> File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/threading.py", line<br class="">917 in _bootstrap_inner<br class=""> File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/threading.py", line<br class="">885 in _bootstrap<br class=""><br class="">Current thread 0x00007fb1abfef700 (most recent call first):<br class=""> File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/graphics/drawing.py",<br class="">line 2058 in text_image_rgba<br class=""> File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/label/label3d.py",<br class="">line 625 in _label_image<br class=""> File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/label/label3d.py",<br class="">line 427 in <listcomp><br class=""> File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/label/label3d.py",<br class="">line 427 in _packed_texture<br class=""> File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/label/label3d.py",<br class="">line 409 in _rebuild_label_graphics<br class=""> File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/label/label3d.py",<br class="">line 401 in _update_graphics_if_needed<br class=""> File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/triggerset.py",<br class="">line 130 in invoke<br class=""> File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/triggerset.py",<br class="">line 190 in activate<br class=""> File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/triggerset.py",<br class="">line 325 in activate_trigger<br class=""> File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/graphics/view.py",<br class="">line 258 in check_for_drawing_change<br class=""> File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/updateloop.py",<br class="">line 64 in draw_new_frame<br class=""> File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/updateloop.py",<br class="">line 139 in update_graphics_now<br class=""> File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/commands/save.py",<br class="">line 56 in save<br class=""> File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/commands/cli.py",<br class="">line 2646 in run<br class=""> File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/commands/run.py",<br class="">line 31 in run<br class=""> File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/scripting.py",<br class="">line 147 in open_command_script<br class=""> File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/io.py",<br class="">line 433 in open_data<br class=""> File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/io.py",<br class="">line 479 in open_multiple_data<br class=""> File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/models.py",<br class="">line 616 in open<br class=""> File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/commands/open.py",<br class="">line 68 in open<br class=""> File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/commands/cli.py",<br class="">line 2646 in run<br class=""> File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/commands/run.py",<br class="">line 31 in run<br class=""> File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/ChimeraX_main.py",<br class="">line 729 in init<br class=""> File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/ChimeraX_main.py",<br class="">line 869 in <module><br class=""> File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/runpy.py", line 85<br class="">in _run_code<br class=""> File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/runpy.py", line 193<br class="">in _run_module_as_main<br class="">Erreur de segmentation (core dumped)<br class=""><br class="">пт, 28 июн. 2019 г. в 10:51, James Starlight <<a href="mailto:jmsstarlight@gmail.com" class="">jmsstarlight@gmail.com</a>>:<br class=""><blockquote type="cite" class=""><br class="">P.S. sorry I forgot to mention that I have not yet updated Chimera-X<br class="">since the version which had been installed at first time. So I will<br class="">now do it today and will report the result!<br class=""><br class="">J.<br class=""><br class="">пт, 28 июн. 2019 г. в 10:44, James Starlight <<a href="mailto:jmsstarlight@gmail.com" class="">jmsstarlight@gmail.com</a>>:<br class=""><blockquote type="cite" class=""><br class="">Hi Greg,<br class=""><br class="">sorry for some delay :-)<br class=""><br class="">Actually I just checked and indeed, there is still problem with<br class="">rendering of the images with chimera-X using<br class=""><br class="">here is the detailed output if it would help<br class=""><br class=""><br class="">chimerax-daily --offscreen --nogui "${output}/!temp/chimeraX.${pdb_name}.cxc"<br class=""><br class="">INFO:<br class="">Offscreen rendering is not available.<br class="">INFO:<br class="">module 'OpenGL.osmesa' has no attribute 'OSMESA_DEPTH_BITS'<br class="">INFO:<br class="">UCSF ChimeraX version: 0.9 (2019-04-03)<br class="">INFO:<br class="">© 2016-2019 Regents of the University of California. All rights reserved.<br class="">INFO:<br class="">Executing: open /home_pers/novikov/Bureau/test/test/!temp/chimeraX.0476.cxc<br class="">INFO:<br class="">Executing: open /home_pers/novikov/Bureau/test/test/!temp/B-factors_0476.pdb<br class="">INFO:<br class="">Summary of feedback from opening<br class="">/home_pers/novikov/Bureau/test/test/!temp/B-factors_0476.pdb<br class="">---<br class="">_warning_ | Ignored bad PDB record found on line 2<br class="">REMARK THIS IS A SIMULATION BOX<br class=""><br class=""><br class="">INFO:<br class="">_B-factors_0476.pdb_ title:<br class=""> **Gallium Rubidium Oxygen Manganese Argon Carbon Silicon**<br class="">[[more info...]](cxcmd:log metadata #1)<br class=""><br class=""><br class="">INFO:<br class="">Chain information for B-factors_0476.pdb #1<br class="">---<br class="">Chain | Description<br class="">[ ](cxcmd:select :1-219 "Select chain") | [No description<br class="">available](cxcmd:sequence chain #1/ "Show sequence")<br class=""><br class=""><br class="">INFO:<br class="">Executing: open /home_pers/novikov/Bureau/test/test/florence.pdb<br class="">INFO:<br class="">Chain information for florence.pdb #2<br class="">---<br class="">Chain | Description<br class="">[ ](cxcmd:select #2:1-219 "Select chain") | [No description<br class="">available](cxcmd:sequence chain #2/ "Show sequence")<br class=""><br class=""><br class="">INFO:<br class="">Executing: mmaker #1 to #2<br class="">INFO:<br class="">Parameters<br class="">---<br class="">Chain pairing | bb<br class="">Alignment algorithm | Needleman-Wunsch<br class="">Similarity matrix | BLOSUM-62<br class="">SS fraction | 0.3<br class="">Gap open (HH/SS/other) | 18/18/6<br class="">Gap extend | 1<br class="">SS matrix | | | H | S | O<br class="">---|---|---|---<br class="">H | 6 | -9 | -6<br class="">S | | 6 | -6<br class="">O | | | 4<br class="">Iteration cutoff | 2<br class=""><br class=""><br class="">INFO:<br class="">Matchmaker florence.pdb, chain (blank) (#2) with B-factors_0476.pdb,<br class="">chain (blank) (#1), sequence alignment score = 1131.8<br class="">STATUS:<br class="">Matchmaker florence.pdb, chain (blank) (#2) with B-factors_0476.pdb,<br class="">chain (blank) (#1), sequence alignment score = 1131.8<br class="">STATUS:<br class="">RMSD between 194 pruned atom pairs is 0.859 angstroms; (across all 219<br class="">pairs: 2.266)<br class="">INFO:<br class="">RMSD between 194 pruned atom pairs is 0.859 angstroms; (across all 219<br class="">pairs: 2.266)<br class="">INFO:<br class=""><br class="">INFO:<br class="">Executing: hide #2 models<br class="">INFO:<br class="">Executing: wait<br class="">ERROR:<br class="">wait requires a frame count argument unless motion is in progress<br class="">ERROR:<br class="">wait requires a frame count argument unless motion is in progress<br class="">INFO:<br class="">Executing: dssp #1<br class="">INFO:<br class="">Executing: zoom 1.3<br class="">ERROR:<br class="">turn x 15 y 15 z -40<br class="">ERROR:<br class="">..........^<br class="">ERROR:<br class="">Expected an integer >= 1 or a keyword<br class="">ERROR:<br class="">Expected an integer >= 1 or a keyword<br class="">INFO:<br class="">Executing: wait<br class="">ERROR:<br class="">wait requires a frame count argument unless motion is in progress<br class="">ERROR:<br class="">wait requires a frame count argument unless motion is in progress<br class="">INFO:<br class="">Executing: preset "'overall look'" publication<br class="">INFO:<br class="">Preset expands to these ChimeraX commands: _set bg white; set silhouettes t_<br class=""><br class="">INFO:<br class="">Executing: set silhouettes true<br class="">INFO:<br class="">Executing: set silhouetteColor indigo<br class="">INFO:<br class="">Executing: set silhouetteDepthJump 0.02<br class="">INFO:<br class="">Executing: color byattribute bfactor palette rainbow range 2,100<br class="">INFO:<br class="">16875 atoms, 4661 residues, atom bfactor range 0 to 367<br class="">STATUS:<br class="">16875 atoms, 4661 residues, atom bfactor range 0 to 367<br class="">INFO:<br class="">Executing: cartoon style width 2.4 thickness 0.50 xsection barbell<br class="">INFO:<br class="">Executing: 2dlabels create title text '"Cluster 0476"' color red font<br class="">gothic xpos .01 ypos .90 size 36<br class="">INFO:<br class="">Executing: lighting depthCueStart .4 depthCueEnd .8<br class="">INFO:<br class="">Executing: lighting full intensity 1.4 shadows true qualityOfShadows finer<br class="">INFO:<br class="">Executing: save image<br class="">/home_pers/novikov/Bureau/test/test/!plots/visu_0476.png format png<br class="">width 600 height 600 supersample 4 transparentBackground false<br class=""><br class=""><br class="">and this is my script<br class=""><br class="">open /home_pers/novikov/Bureau/test/test/!temp/B-factors_0472.pdb<br class="">open /home_pers/novikov/Bureau/test/test/florence.pdb<br class="">mm #1 to #2<br class="">hide #2 models<br class="">wait<br class="">dssp #1<br class="">#view<br class="">zoom 1.3<br class="">turn x 15 y 15 z -40<br class="">wait<br class=""># options for appearance<br class="">preset 'overall look' publication<br class=""># set bg powder blue<br class="">set silhouettes t; set silhouetteColor indigo; set silhouetteDepthJump 0.02<br class="">color byattribute bfactor palette rainbow range 2,100<br class="">cartoon style width 2.4 thickness 0.50 xsection barbell<br class=""><br class=""># make info of the screen<br class="">2dlab create title text "Cluster 0472" color red font gothic xpos .01<br class="">ypos .90 size 36<br class=""><br class=""># options for light<br class="">light depthcuestart .4 depthcueend .8; lighting full intensity 1.4<br class="">shadows true qualityOfShadows finer<br class=""><br class="">save image /home_pers/novikov/Bureau/test/test/!plots/visu_0472.png<br class="">format png width 600 height 600 supersample 4 transparentBackground<br class="">false<br class="">exit<br class=""><br class="">пн, 22 апр. 2019 г. в 23:38, Greg Couch <<a href="mailto:gregc@cgl.ucsf.edu" class="">gregc@cgl.ucsf.edu</a>>:<br class=""><blockquote type="cite" class=""><br class="">Salut,<br class=""><br class="">Does ChimeraX work in offscreen mode for you now? I believe it is fixed.<br class=""><br class=""> -- Greg<br class=""><br class=""></blockquote></blockquote></blockquote><br class="">_______________________________________________<br class="">ChimeraX-users mailing list<br class=""><a href="mailto:ChimeraX-users@cgl.ucsf.edu" class="">ChimeraX-users@cgl.ucsf.edu</a><br class="">Manage subscription:<br class="">http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users<br class=""><br class=""></div></div></blockquote></div><br class=""></div></body></html>