Hi Dave, If I open the file 2to1... as model 0 and Cycle... as model 1, then the command in Chimera to fit the 4 pairs of atoms and get the RMSD is: match #0@b2@b3@s1@s2 #1@b2@b3@s1@s9 or vice versa. The above will move #0 and keep #1 fixed. The RMSD is 0.035 angstroms. If you are using a relatively recent daily build, the following command gives exactly the same result: match #0@b2,b3,s1,s2 #1@b2,b3,s1,s9 I was assuming you wanted the atoms to pair in the same order as they are listed in the files. If you wanted to pair the atoms differently, change the order of their names. I'm not sure what you were doing, so I don't know what was causing the problem. Best, 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 13, 2009, at 11:31 AM, David Chenoweth wrote:
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