[Chimera-users] RMSD

Julien Orts jort at nmr.mpibpc.mpg.de
Tue Nov 13 08:52:16 PST 2007

Dear all,

First thanks a lot for the great software you provide us!!!

I would like to compare structures after an MD simulation.
There is a function called match which can be used to calculate the  
RMSD between selected atoms.

The protocol is the following;
I select atoms within 5 Angstrom to a reference atom in the structure  
1: 300 atoms selected. I do the same for the structure 2 (reference  
atom is the same): 311 atoms selected

The problem is then I can not use the match function since the atom  
number is different.

I selected then residues (the one which are 5A away from the  
reference atom) instead of atoms but it is a bit fastidious plus it  
is not the same as a "zone selection" (some atoms are coming even if  
they are at 5.6A)
I print out (from a pdb) the number of desired proton but the command  
sel @123 do not work because atom selection is done by name and not  
by number (if it is really the case then it would be nice to have  
this possibility as well ;-)
The last solution would be really easy and quick to do if the  
selection on atoms can also be done by number.

Is there any way to solve this? I need to use all the atoms, so the  
matchMaker give me an RMSD but it does not use all of the atoms in  
the calculation of the RMSD.

Basically I need the intersection of the two sets (two structures) of  
selected atoms.

In reality I have much more than 2 structures so the protocol should  
also be scriptable, but I guess everything is scriptable in Chimera  

thank in advance
many greetings


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