Here is some update! :-) following tutorials found on the web, I have made a test.cxc file with all of the commands: # chimeraX script for B-factor coloring and saving of the image windowsize 800 600 open ./test.pdb view; zoom 1.0; turn x 90; turn z -80; preset 'overall look' publication color byattribute bfactor palette rainbow range 2,100 # make info 2dlab create title text "B-factors for" xpos .04 ypos .93 size 30 # options for light light depthcuestart .4 depthcueend .8; lighting full save image ./test.png format png width 800 height 600 supersample 4 transparentBackground false exit Briefly it looks fine being executing in GUI interphace hovewer in the precence of --nogui i got the following error during image rendering: chimerax-daily --nogui test.cxc Executing: save image ./test.png format png width 800 height 600 supersample 4 transparentBackground false Traceback (most recent call last): File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/ChimeraX_main.py", line 699, in init commands.run(sess, 'open %s' % arg) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/commands/run.py", line 31, in run results = command.run(text, log=log) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/commands/cli.py", line 2616, in run result = ci.function(session, **kw_args) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/commands/open.py", line 41, in open from_database=from_database, ignore_cache=ignore_cache, **kw)) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/commands/open.py", line 117, in open models = handle_unknown_kw(session.models.open, paths, format=format, name=name, **kw) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/commands/open.py", line 62, in handle_unknown_kw return f(*args, **kw) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/models.py", line 601, in open session, filenames, format=format, name=name, **kw) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/io.py", line 467, in open_multiple_data models, status = open_data(session, fspec, format=format, name=name, **kw) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/io.py", line 421, in open_data models, status = open_func(*args, **kw) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/scripting.py", line 115, in open_command_script run(session, text) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/commands/run.py", line 31, in run results = command.run(text, log=log) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/commands/cli.py", line 2616, in run result = ci.function(session, **kw_args) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/commands/save.py", line 61, in save fmt.export(session, filename, fmt.nicknames[0], **kw) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/io.py", line 203, in export result = self.export_func(session, path, **kw) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/image.py", line 43, in save_image raise LimitationError("Unable to render images to save them") chimerax.core.errors.LimitationError: Unable to render images to save them is it a bug? пн, 15 апр. 2019 г. в 11:14, James Starlight <jmsstarlight@gmail.com>:
Dear Chimera users!
Would be possible to use new ChimeraX for execution of some simple scripts for structure visualisation and imaging via no-gui mode?
I am using bash script to loop over pdbs and would like to
1) open each pdb which contains b-factors info in chimeraX 2) apply preset publication 3) colour the pdb using "color byattribute bfactor palette rainbow ave residue" 4) save high quality image at the selected directory using chimera render
Would it be possible to do these things directly from linux terminal providing each time pdb and some script file with the list of the applied commands?
chimerax-daily ${pdb} ${script}
Thank you in advance!