[chimerax-users] ChimeraX python crush in no-gui mode

[James Starlight]

Elaine,

i have got a bug while trying to report a bug :-)

Failed to send bug report. Error while sending follows:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/bug_reporter/bug_reporter_gui.py",
line 231, in submit
errcode, errmsg, headers, body = post_multipart_formdata(BUG_HOST,
BUG_SELECTOR, fields)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/bug_reporter/post_form.py",
line 36, in post_multipart_formdata
h = HTTPConnection(realhost)
UnboundLocalError: local variable 'HTTPConnection' referenced before assignment

вт, 16 апр. 2019 г. в 18:11, Elaine Meng <meng at cgl.ucsf.edu>:
>
> Hi Gleb/James,
> You should use the Report a Bug dialog, not this e-mail list, when you have a bug.  Both ChimeraX and Chimera have this dialog in their Help menus, and it is also a button on the error dialog in most cases.
> Best,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
> > On Apr 16, 2019, at 1:30 AM, James Starlight <jmsstarlight at gmail.com> wrote:
> >
> > Dear ChimeraX users!
> >
> > I am using a cxc script together with the following options to run
> > ChimeraX in no-gui mode.
> > chimerax-daily --offscreen --nogui test.cxc
> >
> > here is my scrript
> >
> > # chimeraX script
> > 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" color red font gothic xpos .04
> > ypos .90 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
> >
> > This script works fine with GUI producing very good picture but with
> > the --nogui it gave me error:
> >
> > 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
> >
> > could you help me how it may be fixed?
> >
> > Thank you in advance!
> >
> > Gleb
>
>
>