[Chimera-users] Scripting with Chimera

[Lockwood, Svetlana]

Thank you!
--sv

________________________________________
From: Elaine Meng [meng at cgl.ucsf.edu]
Sent: Thursday, August 13, 2009 2:05 PM
To: Lockwood, Svetlana
Cc: chimera-users at cgl.ucsf.edu
Subject: Re: [Chimera-users] Scripting with Chimera

Hi Svetlana,
Every Chimera command can be pythonized with runCommand, as detailed
in this previous post by Eric:

<http://www.cgl.ucsf.edu/pipermail/chimera-users/2009-March/003729.html>

We have reproduced the Ubuntu problem and are looking into it.

Best,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
                      http://www.cgl.ucsf.edu/home/meng/index.html

On Aug 13, 2009, at 1:40 PM, Lockwood, Svetlana wrote:

> Hi All,
>
> Here's my problem: I need to calculate hydrogen bonds for several
> thousand PDB files. Chimera has nice hbonds command line command -
> sweet! Since Chimera was vanishing from Ubuntu, I had to switch to
> other available tools, i.e. Windows. After I got my python up and
> running and communicating with Chimera modules. Here's my very
> simple pseudo-idea:
>
> foreach file in the list:
>     open PDB file
>     construct output filename from input filename
>     calculate & and write out hydrogen bonds using hbonds command
>     close file
> end foreach
>
> Short and sweet. Except that one cannot use a command line command
> within python code. Command files don't work either because they do
> not understand python commands. Someone must have run into the same
> problem before me :-) Is there a way around this problem?
>
> Thank you,
> Svetlana