Hi Sasi, for "pair_fit" you have to match all atom pairs manually. I guess what you want is "align" on the full monomers and then "rms_cur" (or just distance measure) on each CA pair.
Have a look at the "rmsd_b.py" script from http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/ It writes per residue deviation to the b-factor column. Example: fetch 2hv1, async=0 extract mono2, chain B align mono2, 2hv1, cycles=0, object=aln rmsd_b mono2 & aln, 2hv1 & aln iterate mono2 and name CA, print (resi,b) Hope that helps. Cheers, Thomas sasi kodathala wrote, On 12/27/11 01:37: > dear pymol users, > > i have a homodimer, with two identical monomers. i would like to know > the rmsd of each residue in the first monomer with respect to each > residue in the second monomer. > > i guess pair_fit should give the rmsd. > > is there a better command to look at the per residue rmsd. > > thank you. > > sasi -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen ------------------------------------------------------------------------------ Write once. Port to many. Get the SDK and tools to simplify cross-platform app development. Create new or port existing apps to sell to consumers worldwide. Explore the Intel AppUpSM program developer opportunity. appdeveloper.intel.com/join http://p.sf.net/sfu/intel-appdev _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
