[Chimera-users] Motion of an atom

Raju Purohit rajurnpurohit at gmail.com
Tue Jul 10 09:33:22 PDT 2012

Hi Elaine,

Thanks for your quick reply. The method you suggested is nice but
I actually want to change the coordinates of the atom. In the present case,
there is only one atom. In my next step, I will have to work with molecules
and will have to make just a few atoms to move. And moreover, my project
work uses chimera python for everything, so I would be glad if you can
suggest me a python command.


On Tue, Jul 10, 2012 at 6:17 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> 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
> >
> <
> http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/indexcommand.html#cmdfile
> >
> 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
> ----------
> 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
> >

Raju R.N.
Third Year, B.Tech
Mechanical Engineering
National Institute of Technology Karnataka, Surathkal
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