[Chimera-users] origin of sphere in MDmovie

Edward Brignole brignole at scripps.edu
Wed Jul 16 21:34:20 PDT 2008

Hey Chimera-folks,

I've got a nice movie with morph conformations, and then wrote a script that goes along with it that generates tranparent multiscale models (molmap) and displays a ligand with solid atom spheres for each frame in the movie.  But I'd like to make a sphere that tracks along with the domain movement - it can't be transparent because the model is transparent already. The shape command looks like it can do this, make a sphere with a specified radius in mesh, but I can't figure out how to specify the origin according to a particular atom's coordinates, and then script it so that it tracks with the conformational changes in the movie.  And it would be really cumbersome to write a bild file for each of the ~200 frames in the movie.

I'm guessing something like "getcrd" will get the coordinates that I'd like to use for the origin but "shape sphere" doesn't allow me to specify origin.

Alternatively I could render the atom I'm tracking as a radius 25 sphere, but am unable to display an atom as mesh.

Can you point me in the right direction?

Ed Brignole
Asturias Lab
The Scripps Research Institute
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