Re: [PyMOL] Running scripts with the '@' command

[Jason V. <jas...@sc...>]

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
<ma...@ca...> 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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-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

(e) Jas...@sc...
(o) +1 (603) 374-7120