[Chimera-users] [chimera-dev] chimera help

Elaine Meng meng at cgl.ucsf.edu
Thu Sep 28 09:14:35 PDT 2006

Hi Vishal,
Actually you can do this with a Chimera command script, as opposed to  
programming in Python.  A command script just contains the same  
commands you would enter in the Command Line.  I'm not sure of what  
type of saving you had in mind, " but the  "copy" command can be used  
to save an image file, "save" to save a session, and "write" to save  
a PDB file.

This page links to all the command man pages, plus it discusses  
command scripts (at the bottom):

Just opening the command file will execute the commands.
Here are links to a couple of example command files:

And here is another, between the dashed lines:
open 1hxx
open 1pho
modelcolor coral #0
modelcolor cornflower blue #1
~disp; rep bs; ribbon; ribrepr smooth
matchmaker #0 #1

I guess the main difficulty if you are saving images is how to get a  
good view of the structures. Usually some rotation, scaling, etc. is  
done interactively to make a better picture.
I hope this helps,

On Sep 27, 2006, at 7:29 PM, Vishal Pua wrote:

> Hi, I was wondering if there was a way to create a script, that  
> would open pdb files, render them to look a certain way ex. wire or  
> ribbon, then save, automatically? this would have to work for a  
> number of pdb files? I have little programming experience, and  
> wonder if there was an easy way to do this, thanks
> Vishal Pua
> _______________________________________________
> Chimera-dev mailing list
> Chimera-dev at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev

Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

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