[Chimera-users] Help in MD movie

Elaine Meng meng at cgl.ucsf.edu
Sat Apr 18 08:51:54 PDT 2015


Hi Ankit,
This doesn’t really make sense (to me, anyway), because when you open the trajectory in Chimera, the atomic structure is automatically displayed.  So unless your script did something to hide it, the molecule should be shown.  The only other idea I have is that maybe the ellipsoid is surrounding the molecule, but it seems unlikely that it would surround all of the atoms.  Although I doubt that’s the problem, with the “measure inertia” command you can set the color of the ellipsoid to a transparent color so you could still see the atoms if they were inside:

<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#inertia>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/color.html#colorname>

It is impossible to know what is happening without more information, such as your script.  Also, the chimera-dev at cgl.ucsf.edu list is probably better for python scripting questions than this chimera-users list.  I don’t know python, but others may be able to advise.

<http://www.rbvi.ucsf.edu/chimera/docs/feedback.html>

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 Apr 18, 2015, at 2:10 AM, Ankit Agrawal <aka895 at gmail.com> wrote:

> Hi
> I have trajectory file from gromacs and opened in chimera.
> Now I am doing inertia calculation. I wrote a python script to show the ellipsoid. But this script is showing only the ellipsoid. I want ellipsoid as well as the molecular structure of that frame, i.e. both ellipsoid and the molecule. so that I can show the how molecule is changing its position. This is like a structure overlay but I want it with ellipsoid.
> thanks
> regards
> Ankit Agrawal




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