[Chimera-users] Scripting with Chimera

Elaine Meng meng at cgl.ucsf.edu
Thu Aug 13 14:05:37 PDT 2009

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


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

Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

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

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