Re: [ccp4bb]: rmsd calculation

[Gerard DVD Kleywegt <gerard@xray.bmc.uu.se>]

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> In LASQMAN programme,"rmsd m1 a26-36 m2 a26" command mean that it will 
> calculate the rmsd of molecule 1 A chain 26-36, and the rmsd of molecule 
> 2 A chain 26-36. Please tell me.

first you need to align the two molecules, e.g. using the CA atoms (see e.g.
http://xray.bmc.uu.se/usf/lsqman_man.html#H6). after that you can use the RMsd
command to calculate the rmsd of arbitrary subsets of atoms, e.g. the active
site residues, or the ligands, or one domain at a time, or whatever

--dvd

******************************************************************
                        Gerard J.  Kleywegt
    [Research Fellow of the Royal  Swedish Academy of Sciences]
Dept. of Cell & Molecular Biology  University of Uppsala
                Biomedical Centre  Box 596
                SE-751 24 Uppsala  SWEDEN

    http://xray.bmc.uu.se/gerard/  mailto:gerard@xray.bmc.uu.se
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