> I want to align the > first 100 residues (resi 1-100) to the last 100 (51-150) ... > and try to run the following commands:
> load structure.pdb > create s1, resi 1-100 and structure > create s2, resi 51-150 and structure > align s1, s2 > resi 1-50 of s1 TO resi 51-100 of s2 > resi 51-100 of s1 TO resi 101 to 150 of s2 align s1//1-100//CA, s2//51-150//CA However, that is an adaptive fit that will match the sequence using DP, superimpose, and then toss outliers. In constrast, pair_fit s1//1-100//CA, s2//51-150//CA is a straight pairwise RMS fit, with the only catch being that all residues in the indicated ranges must exist. 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 > Douglas Kojetin > Sent: Thursday, March 02, 2006 8:14 AM > To: Pymol > Subject: [PyMOL] alignment in pymol > > Hi All- > > If I have a protein with 150 residues (three 50 residue > repeats; 1-50, 51-100, 101-150), and I want to align the > first 100 residues (resi 1-100) to the last 100 (51-150) ... > and try to run the following commands: > > load structure.pdb > create s1, resi 1-100 and structure > create s2, resi 51-150 and structure > align s1, s2 > > PyMOL aligns residues 50-100 of s1 to residues 50-100 of s2 > (the region in common between s1 and s2). What I want to > happen is for PyMOL to align the entire structure of s1 > (1-100) to s2 (50-150), so that essentially the following > sequences are aligned simultaneously: > > resi 1-50 of s1 TO resi 51-100 of s2 > resi 51-100 of s1 TO resi 101 to 150 of s2 > > Does anyone know how I can do this? > > Thanks, > Doug > > > > ------------------------------------------------------- > This SF.Net email is sponsored by xPML, a groundbreaking > scripting language that extends applications into web and > mobile media. Attend the live webcast and join the prime > developer group breaking into this new coding territory! > http://sel.as-us.falkag.net/sel?cmd=lnk&kid=110944&bid=241720&; > dat=121642 > _______________________________________________ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users > > > >
