[Chimera-users] Using ChimeraX in no-gui mode

[James Starlight]

P.S. just forgot also to ask - how it would be possible to place bar
diagram to range b-factors colouring gradient in the manner of the
"key" option in the previous version of chimera?

пн, 15 апр. 2019 г. в 18:41, James Starlight <jmsstarlight at gmail.com>:
>
> 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 at 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!