[Chimera-users] Motion of an atom

Elaine Meng meng at cgl.ucsf.edu
Tue Jul 10 09:17:59 PDT 2012

Hi Raju,
It sounds like you are trying to do some programming, but instead you could just use Chimera commands, e.g. "move" to translate atom(s).  Chimera commands can be entered into the Command Line (show using Favorites menu), or you can put them into a plain text file named *.cmd -- then opening the file in Chimera will execute the commands in the file.

< http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/movies.html#moviecommands>

Example command: move x .1 50

... to move along laboratory X axis 0.1 angstroms for each of 50 frames.  I hope this helps,
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Jul 10, 2012, at 9:07 AM, Raju Purohit wrote:

> Hello friends,
> I need some help here.
> I created a basic model having just an atom and set its coordinates as (0,0,0). Now I want to make it move along a certain path defined mathematically (say, along x axis) and I need to see it move. So I used a for loop. But I couldn't see and motion and soon realised that the loop is very quick in executing and thus I could see the atom at its last coordinates. So I tried to add delay of 0.5 seconds for each loop by importing time module and useing time.sleep. But still I couldn't see any motion and the coordinates of the atom is set only at the end of the for loop. I could not see the intermediate path. I am sure you people must have tried this earlier and this problem has a solution but I just couldn't figure it out. 
> Can you please help me out?
> Thank you in advance.
> -- 
> Raju R.N.
> Third Year, B.Tech
> Mechanical Engineering
> National Institute of Technology Karnataka, Surathkal

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