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
>
> ------------------------------------------------------------------------------
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> _______________________________________________
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--
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC
(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120
------------------------------------------------------------------------------
Download Intel® Parallel Studio Eval
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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