[Chimera-users] running command scripts

Elaine Meng meng at cgl.ucsf.edu
Wed Jan 27 11:43:29 PST 2010

Hi Mike,
Eric is exactly right, you would just open the command file in  
Chimera, similar to opening a PDB file.  Just thought I'd point out  
the explanation of Chimera command files and how to execute them:


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

On Jan 27, 2010, at 10:50 AM, Eric Pettersen wrote:

> On Jan 27, 2010, at 10:02 AM, Michael Zimmermann wrote:
>> Dear Chimera users,
>> I am getting to know Chimera a bit more and was just going through  
>> the
>> scripting tutorial here:
>> http://www.cgl.ucsf.edu/Outreach/Workshops/UCSF-Fall-2005/09- 
>> ScriptDemo/Scripting_Tutorial.html
>> For the command line script 1gfl.com, the tutorial just says "run it"
>> but does not say how.  I just typed "run 1gfl.com" in the chimera
>> command line, but I get a syntax error in the script.  I can't  
>> seem to
>> copy the error text, so a screenshot is attached.  Is this an issue
>> with the script or how I am running it?
>> I use chimera v. 1.4 on win XP - 64bit
> It's an issue with how you are running it.  There is no "run"  
> command per se, but since Chimera allows you to shorten command  
> names "run" is equivalent to "runscript", which executes a Python  
> script (optionally with arguments).  Since the script is Chimera  
> commands, not Python, you naturally get a syntax error.  To run the  
> script you should use the "open" command or File...Open in the menus.
> --Eric

More information about the Chimera-users mailing list