Andrea,
PyMOL really can't do this job generally well because you'd need to
specify an atom-by-atom correspondance between the two ligands. Unless
the ligands are identical and have identical atom names, the numbers you
get will be misleading. =20
If that is in fact the case, then I think you're on the right track.
Cheers,
Warren
--
Warren L. DeLano, Ph.D. =20
Principal Scientist
. DeLano Scientific LLC =20
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=20
> -----Original Message-----
> From: pym...@li...=20
> [mailto:pym...@li...] On Behalf Of=20
> Andrea Spitaleri
> Sent: Thursday, November 17, 2005 4:11 PM
> To: pymol-users
> Subject: [PyMOL] combine align and rms_cur to calculate rms=20
> for complexes
>=20
> Hi all,
> could someone confirm this:
> I have some complexes protein+ligand and I'd like to perform=20
> rms calculation for the position of the ligand. This what I have done:
>=20
> load reference.pdb
> select proteinreference, segi A
> select ligreference, segi B
> load compare.pdb
> select proteincomapre, segi A
> select ligcompare, segi B
> align proteinreference,proteincompare
> rms_cur ligreference,ligcompare
>=20
> is rms_cur the right command to calculate the rms for the=20
> ligand position? then, is the procedure "chemically" correct?
>=20
> thanks
>=20
> regards,
>=20
> andrea
>=20
> --
> "La conoscenza libera il genere umano dalla superstizione"
> J. Watson
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