[Chimera-users] redirecting runCommands output

Eric Pettersen pett at cgl.ucsf.edu
Thu Jun 10 13:53:32 PDT 2010

On Jun 10, 2010, at 4:36 AM, Bala subramanian wrote:

> Friends,
> I wrote a small script to calculate the distance between two atoms  
> in a list of pdb files. I would like to know how i can redirect the  
> message that appears in replyobj to a text file. Some chimera  
> commands like findhbon has option to save the result in file. But  
> distance command dosent have the same.
>  import glob
>  from chimera import runCommand as rc
>  filenames=[ fn for fn in glob.glob('*.pdb.*')]
>  for fn in filenames:
>      rc("open " + fn)
>      rc("distance :1 at CA :166 at CA")  # I have to write this distance  
> to a file.
>      rc("close all")

Hi Bala,
	Since you are using a Python script, you can use the saveReplyLog  
method in the chimera.tkgui module to save the contents of the reply  
log to a file, e.g.:

for fn in filenames:
	rc("open " + fn)
	rc("distance :1 at ca :166 at ca")
	rc("close all")
from chimera.tkgui import saveReplyLog

	In tomorrow's build there will also be a clearReplyLog method, so you  
would be able to save a distance file for each structure with:

from chimera.tkgui import saveReplyLog, clearReplyLog
for fn in filenames:
	rc("open " + fn)
	rc("distance :1 at ca :166 at ca")
	saveReplyLog(fn[:-3] + "distance")
	rc("close all")


                         Eric Pettersen
                         UCSF Computer Graphics Lab

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