[Chimera-users] Using runCommand outputs

Tom Goddard goddard at sonic.net
Wed Nov 13 09:52:36 PST 2013

Hi Ahir,

  Unfortunately runCommand() does not return any Python objects resulting from the command -- would be convenient if it worked that way. If you want return values from a command you need to call the Python function that does that command.  Most of those are in file


with the function name matching the command name, e.g. rmsd() for the "rmsd" command, or match() for the "match" command.  So open that file in a text editor and search for the command you want.  We unfortunately don't have documentation on the Python functions so this can be troublesome and I'm sure is why you prefer runCommand().  We will provide documentation for all the Python functions in our next generation Chimera that we are working on now.


On Nov 13, 2013, at 8:40 AM, a.pushpanath at mail.cryst.bbk.ac.uk wrote:

> Hello all, I am getting confused by the runCommand() functionality when I am trying to run scripts. When I run my python script through IDLE(From Tools-General), the ouput of runcommand commands like rmsd etc are given the IDLE. I want to store the output from runcommand into a variable dynamically. I dont want to save from the ReplyLog (by running program without IDLE) or output to file, is there something in python itself that I am not understanding and hence, not using, or is it not possible to store the output of runcommand into a variable/list etc, as it is possible for the midas.rmsd function for example. I only ask because I prefer to use the command line functionality over the midas command. If it is only possible with the direct midas, how do I find out the equivalent command of the runcommand for the midas python formatting?
> Thank you
> Sorry if my question is a bit confusing!
> Ahir
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