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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