[Chimera-users] precise overlay of ligands

[Elaine Meng]

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 at b2@b3 at s1@s2 #1 at b2@b3 at 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 at b2,b3,s1,s2 #1 at 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 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 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