[Chimera-users] Scripting with Chimera

Lockwood, Svetlana svetlana.lockwood at email.wsu.edu
Thu Aug 13 13:40:05 PDT 2009

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,
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