Horacio, PyMOL cannot currently superimpose small molecules unless:
1. either the identifiers match between the two molecules (fit commmand) or 2. the pairwise correspondance between the two is explicitly specified (pair_fit command or pair fitting wizard) Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:del...@delsci.info > -----Original Message----- > From: pymol-users-boun...@lists.sourceforge.net > [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf > Of Horacio Emilio Pérez Sánchez > Sent: Thursday, February 21, 2008 6:58 AM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] RMSD between two ligands > > Hi, > > I need to calculate the RMSD between two ligands (around 50 > atoms). For proteins works very well but it seems that for > small molecules it gives errors. I looked through the forum > and I did not find any useful info. I tried rms , rms_cur and > so between the atoms selections but I get errors (it gets > wron number of atoms. Do you know if this is possible in pymol ? > > P.D. I also tried to load in pymol some fitting.py script, > but when pymol restarts I get errors and it does not regonise > the new plugin/script. > > Thanks > > > > > > -------------------------------------------------------------- > ----------- > This SF.net email is sponsored by: Microsoft Defy all > challenges. Microsoft(R) Visual Studio 2008. > http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > _______________________________________________ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users
