[Chimera-users] origin of sphere in MDmovie

Tom Goddard goddard at cgl.ucsf.edu
Wed Jul 16 21:59:05 PDT 2008

Hi Ed,

  To make a mesh sphere centered at a specific atom, say the CA atom of 
residue 283 of model #0 how about

    molmap #0:283 at CA 10 gridSpacing 1 modelId 5
    volume #5 style mesh color yellow

You can do this each frame of the MD trajectory and the molmap will by 
default replace the sphere so you don't have to worry about removing the 
previous sphere.  This makes a map from one atom with resolution 10.  
Not sure what radius that produces.  You could figure it out from the 
molmap documentation or simply adjust the resolution value until you get 
a radius that looks right.


Edward Brignole wrote:
> 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?
> Thanks,
> Ed Brignole
> Asturias Lab
> The Scripps Research Institute

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