[Chimera-users] precise overlay of ligands

David Chenoweth dchen at caltech.edu
Mon Jan 12 13:32:26 PST 2009

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

David M. Chenoweth
California Institute of Technology
Division of Chemistry and Chemical Engineering
Mail Code: 164-30
1200 California Boulevard, 91125 Pasadena
California, USA

Phone: 626-395-6074
Email: dchen at caltech.edu
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