[Chimera-users] Python -send command and IDLE

Elaine Meng meng at cgl.ucsf.edu
Fri May 29 15:48:08 PDT 2009

Hi Chris,
I was hoping the others would answer, since I'm not a programmer.   
However, I'll take a stab at this and maybe they can correct or add  
to the answer as needed.

1. There is a relatively new command (in daily builds but not the 1.3  
release) "runscript" for running python scripts with arguments.  This  
is used as a Chimera command, not in IDLE, but see #2...

2. There is a "ReadStdin" feature (start by choosing it from the  
Tools... Utilities menu) that allows you to feed in Chimera commands  
through standard input.  I guess you could combine it with the above.

I'm not sure if these will meet your needs, however.  Programmers,  
feel free to pipe up!
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On May 28, 2009, at 11:10 PM, cdlau at ucsd.edu wrote:
> Hi,
> I have 2 questions:
> 1. Is it possible to use send python scripts (with arguments) to an
> already running Chimera instance?  I know that it is possible to  
> use to
> use the --send feature, however I wasn't able to send argument in  
> with my
> python script
> (http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/options.html).  I  
> want to
> be able to pass arguments to a already running instance of chimera  
> similar
> to the --script feature (but this feature forces a new instance of  
> chimera
> to open).
> 2. Along the same lines as the first question, is it possible to use
> terminal and python commands to manipulate color, rotation, etc. in  
> place
> of using the IDLE?  Currently I am working on a project to that  
> requires
> communicating with a computer running Chimera through "ssh"ing into  
> the
> computer.  I want to be able to use terminal commands to do basic
> manipulations of the molecules from the other machine.
> Thanks for all your help in advanced,
> Chris

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