VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Fri Apr 18 2008 - 09:20:29 CDT

On Fri, 18 Apr 2008, Aurelie.DeLuca_at_sanofi-aventis.com wrote:

AD> Hy everybody,

dear aurelie,

AD> I want to do a script what calcul RMSD between two structures what they
AD> haven't the same number of atoms. I can do it if structures have the

that is not possible. please think of what an RMSD stands for!
it is not just a "magic number" is made up but there is an algorithm...

the RMSD is computed atom-by-atom, so you have to create two selections
which contain the same number of atoms, i.e. take only the c-alpha or
the backbone so that it doesn't matter if the amino acids are different
and then make sure that you compare two peptide sections that have the
exact same number of amino acids. this will work.

cheers,
   axel.
AD> same number with a VMD script as following :
AD>
AD> set out [open
AD> "/global/home/i0028932/plos//CROSSED_RMSD/crossed_rmsd.dat" a]
AD>
AD> mol delete all
AD>
AD> mol load pdb file1.pdb
AD>
AD> set sel0 [atomselect 0 "backbone"]
AD>
AD> mol load pdb file2.pdb
AD>
AD> set sel1 [atomselect 1 "backbone"]
AD>
AD> set rmsd [measure rmsd $sel0 $sel1]
AD>
AD> set rmsd [format "%-10.5f" $rmsd]
AD>
AD> puts $rmsd
AD>
AD> puts $out "1 $rmsd PAK1_DFGsemiout.pdb"
AD>
AD> close $out
AD>
AD> mol delete all
AD>
AD>
AD>
AD> Thanks for your help.
AD>
AD> Aurelie
AD>
AD> 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.