[Chimera-users] Calculating RMSD for ligand

Elaine Meng meng at cgl.ucsf.edu
Sat Sep 27 11:34:07 PDT 2008

Hi Chao Wu,
The ordering is changed by the intersection (&) because the two sets  
of intersected atoms have different orders: in your case you wanted to  
keep the order in residue :1.het, but the set of all nonhydrogen atoms  
( ~ element.H ) is in a different order.

One way to do what you want is to delete the hydrogens before doing  
the RMSD calculation (be careful not to overwrite your original  
results files that includes the hydrogens, of course), for example:

del :1.het & element.H      (or maybe even just "del element.H" to  
delete all hydrogens)
rmsd #0:1.het #1:1.het

The disadvantage is that some other steps you do later might require  
the hydrogens, so you would have to close those files and open the  
original ones with hydrogens.

If you don't delete the hydrogens, the only way I can think of is to  
specify all the atoms by name in the same order (brute force  
approach), for example:

rmsd #0:1.het at c1@c2 at c3@c4 at c5@c6 at o1@o2 at o3@o4 at o5@o6  
#1:1.het at c1@c2 at c3@c4 at c5@c6 at o1@o2 at o3@o4 at o5@o6

which can be hard to type and ugly.  When I do something like that I  
usually text-edit to put it in a command file and then open the  
command file so I don't have to type it over and over.

I hope this helps,
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Sep 27, 2008, at 7:04 AM, 吴超 wrote:

> Hi, dear folks,
> I want to evaluate the docking performance by calculating the RMSD  
> of heavy atoms between ligand crystal conformation and docked  
> conformation.
> I use the following command:
> rmsd #0:1.het & ~element.H #1:1.het & ~element.H
> But Chimera seems to forget the correct order and give a pairwise  
> alignment not the way I want .
> I wonder if there is a way that I can get the correct selection  
> order so as to calculate RMSD.
> Best
> -- 
> Chao Wu

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