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):

<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/rmsd.html>

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.
Best,
Elaine

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@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