[Chimera-users] precise overlay of ligands

Elaine Meng meng at cgl.ucsf.edu
Mon Jan 12 18:35:22 PST 2009

Hi Dave,
Me again - I forgot to mention that there is also a command to measure  
RMSD between sets of atoms without fitting them (it just uses their  
current positions):


You could fit on the three pairs of atoms using the "match" command,  
then use this "rmsd" command to measure RMSD between other sets of  
atoms without changing the fit. I wasn't sure from your mail whether  
that was something you wanted to do.

On Jan 12, 2009, at 1:33 PM, Elaine Meng wrote:

> 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:
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html>
> More general information on various matching methods:
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/superposition.html>
> I hope this helps,
> Elaine
> -----
> 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
>                      http://www.cgl.ucsf.edu/home/meng/index.html
> 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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