Jason,
many thanks for your quick response!
The example you sent worked; I will try to rewrite our scripts as Python
commands and embed them in "python" blocks...
Thanks again, and have a nice weekend,
-Markus
On Mit, 10 Mär 2010, Jason Vertrees wrote:
> Markus,
>
> PyMOL is a multithreaded application and it'll accept input from the
> two locations asynchronously. Sync works until the next command is
> done--so, a script, a series of single commands will not do. Embed
> your scripts inside "python" blocks:
>
> # your_script.py
> python
> cmd.fetch("1rsy")
> cmd.show_as("surface")
> for x in range(10): cmd.ray(1000,1000)
> python end
>
> While that is running input the following into the terminal:
>
> cmd.sync(); dele *
>
> This will sync PyMOL and then delete everything. If your session ends
> up blank, it worked.
>
> Cheers,
>
> -- Jason
>
>
> On Wed, Mar 10, 2010 at 3:41 AM, Markus Wiederstein
> <mar...@came.sbg.ac.at> wrote:
> > Hi,
> >
> > starting PyMOL with the '-p' option to let it accept input from stdin is a
> > convenient way to trigger it from external programs.
> > However, it seems that one can run into synchronization problems when this
> > is combined with the '@' command for running scripts.
> > For example, the following setup led to a race condition between script
> > handling and standard input:
> >
> > 1. pymol -p (let PyMOL accept input from standard input)
> >
> > 2. External program sends commands, PyMOL reacts.
> > At some point, PyMOL sends "@ pymol_script.p1m" in order to run commands
> > stored in a script file.
> >
> > 3. When further commands are sent by the external program, they intervene
> > with the commands of the script file.
> > In other words, as soon as the "@" command is sent, PyMOL accepts further
> > input from stdin and seemingly ignores the fact that the commands from the
> > script file may not be finished.
> >
> > Is there a way to temporarily block acceptance of standard input? I have
> > tried to use the "cmd.sync()" command, but did not have any success with it.
> >
> >
> > Thanks for any help on this,
> > kind regards,
> > -Markus
> >
> > --
> > Dr. Markus Wiederstein
> > University of Salzburg
> > Department of Molecular Biology
> > Division of Bioinformatics /
> > Center of Applied Molecular Engineering
> > Hellbrunnerstr. 34
> > A-5020 Salzburg
> > Tel: +43 662 8044 5794
> > Fax: +43 662 8044 176
> >
> > ------------------------------------------------------------------------------
> > Download Intel® Parallel Studio Eval
> > Try the new software tools for yourself. Speed compiling, find bugs
> > proactively, and fine-tune applications for parallel performance.
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> > _______________________________________________
> > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
> > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
> >
>
>
>
> --
> Jason Vertrees, PhD
> PyMOL Product Manager
> Schrodinger, LLC
>
> (e) jason.vertr...@schrodinger.com
> (o) +1 (603) 374-7120
>
------------------------------------------------------------------------------
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Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
See why Intel Parallel Studio got high marks during beta.
http://p.sf.net/sfu/intel-sw-dev
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