[Chimera-users] Python -send command and IDLE

Tom Goddard goddard at cgl.ucsf.edu
Fri May 29 16:10:36 PDT 2009

Hi Chris,

  Would be nice if you could use --send and pass a script and script 
arguments but it's not possible now.  The --send mechanism was intended 
for a web browser to send a PDB file to Chimera.  You could go the more 
cumbersome route of writing a one line file "runscript myscript.py 
[args...]" and send that file with chimera --send.  If you had to do 
this a lot you might make a script in a language of your choice 
"sendtochimera myscript.py [args...]" that writes the one line temporary 
file and does the chimera --send.

  For question 2) the ReadStdin is closest to what you want.  It allows 
you to enter Chimera commands from a shell where you started Chimera.  
It doesn't allow you to send Python code to Chimera.  If you need to run 
python scripts you can write them to a file on the machine where Chimera 
is running and then use the "runscript" command via the ReadStdin 
mechanism.  There is currently no way to type Python code in an 
operating system shell and have it directly interpreted by Chimera.


-------- Original Message --------
Subject: Re: [Chimera-users] Python -send command and IDLE
From: Elaine Meng <meng at cgl.ucsf.edu>
To: cdlau at ucsd.edu
Date: 5/29/09 3:48 PM
> 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...
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/runscript.html>
> 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.
> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/readstdin/ 
> readstdin.html>
> I'm not sure if these will meet your needs, however.  Programmers,  
> feel free to pipe up!
> Elaine
> -----
> 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
>                        http://www.cgl.ucsf.edu/home/meng/index.html
> 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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