[Chimera-users] centering a volume to an atom's coordinate

Tom Goddard goddard at sonic.net
Mon May 23 11:17:51 PDT 2011

Hi Roni,

   The origin set in the Chimera volume dialog coordinates panel is the 
volume grid index corresponding to x,y,z position 0,0,0.  So it requires 
a little calculation to figure out what to set that to to make the 
center of the volume box land on a specific atom (x,y,z) position.  
Here's an example

     volume grid size (201,201,201)
     volume center grid index (100,100,100) (indices start at 0 in Chimera)
     atom position xyz = (25, 50, 75)
     volume grid spacing 2.5 Angstroms
     atom position xyz divided by grid spacing (10, 20, 30)
     set volume origin in coordinates panel to (90,80,70) will make grid 
index (100,100,100) align with atom.


> Hi,
> I am trying to center volumes (cylinders and spheres that I created using spider) to an atom from a pdb file.
>   When I created the volumes I made sure that their center is in the middle of the box containing the volume.
> I tried to set the coordinate of the volume to the atom's coordinate (in the coordinate tab under volume viewer) but the position of the volume was not centered to the coordinates provided.
> Any idea on how to do that?
> Thank you
> Roni

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