[Chimera-users] precise overlay of ligands

Elaine Meng meng at cgl.ucsf.edu
Mon Jan 12 13:33:18 PST 2009

Hi Dave,
With the "match" command you can specify the exact atoms to fit, and  
the resulting RMSD will be reported in the Reply Log. The main thing  
to be careful about is specifying the atoms in the proper order.  One  
way is by name, another is to pick them in order from the graphics  
window (Shift-Ctrl-click).

Specifics on how to use the "match" command:

More general information on various matching methods:

I hope this helps,
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Jan 12, 2009, at 1:32 PM, David Chenoweth wrote:

> Dear Chimera team,
> Hi! I have two ligands in two different PDB files which have a very  
> similar core structure. I have constructed a framework of dummy  
> atoms based on the centroids of several aromatic rings to use as a  
> positioning system for the two ligands. I have three points/dummy  
> atoms for each ligand in space in their respective pdb files and I  
> would like to overlay or map the three points of one onto the three  
> points of the other so I can make measurements in chimera. Is there  
> a simple way to open the two pdb files, select the three points that  
> belong to each ligand and overlay them (maybe even minimize the rms  
> deviation between them with some kind of fit to the plane defined by  
> the three points). I can do this by hand and get them close but not  
> exact. I would also like to be able to calculate the rms deviation  
> between similar atoms in the core structure if possible.
> Thanks in advance,
> Dave Chenoweth

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