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.
If that is in fact the case, then I think you're on the right track. Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 USA . Biz:(650)-872-0942 Tech:(650)-872-0834 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:war...@delsci.com > -----Original Message----- > From: pymol-users-ad...@lists.sourceforge.net > [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of > Andrea Spitaleri > Sent: Thursday, November 17, 2005 4:11 PM > To: pymol-users > Subject: [PyMOL] combine align and rms_cur to calculate rms > for complexes > > Hi all, > could someone confirm this: > I have some complexes protein+ligand and I'd like to perform > rms calculation for the position of the ligand. This what I have done: > > 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 > > is rms_cur the right command to calculate the rms for the > ligand position? then, is the procedure "chemically" correct? > > thanks > > regards, > > andrea > > -- > "La conoscenza libera il genere umano dalla superstizione" > J. Watson > > > ------------------------------------------------------- > This SF.Net email is sponsored by the JBoss Inc. Get > Certified Today Register for a JBoss Training Course. Free > Certification Exam for All Training Attendees Through End of > 2005. For more info visit: > http://ads.osdn.com/?ad_idv28&alloc_id845&op=ick > _______________________________________________ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users > > > >
