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

Hi Elaine, Thanks so much for all the advice. I'm still having trouble getting the match/alignment command to work and I'm not quite sure what I'm doing wrong but I think it's in my pdb format. I have attached two files with four atoms in each that I would like to overlay and get the rms deviation for. Maybe you could look at the files and let me know where my formatting mistake is. The files are attached and the coordinates are listed below. They both open in Chimera and work fine but I think maybe the problem lies in chain id #'s or something. Thanks again for your help, Dave 1st pdb file: 2to1_coordinates_test.pdb HETATM 114 B2 CE2 22 8.649 -5.055 13.615 1.00 1.00 B HETATM 115 B3 CE2 22 10.976 -7.450 8.675 1.00 1.00 B HETATM 117 S1 CE3 22 8.845 -8.275 11.641 1.00 1.00 S HETATM 118 S2 CE3 22 10.227 -5.377 10.923 1.00 1.00 S END 2nd pdb file: Cycle_coordinates_test.pdb HETATM 96 B2 CE2 Z 1 -3.480 14.686 -11.018 1.00 1.00 B HETATM 97 B3 CE2 Z 1 -5.877 19.992 -9.560 1.00 1.00 B HETATM 99 S1 CE3 G 1 -6.701 16.412 -10.234 1.00 1.00 S HETATM 107 S9 CE3 G 1 -3.731 17.766 -10.322 1.00 1.00 S END On Jan 12, 2009, at 6:35 PM, Elaine Meng wrote:

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