Joel, > align 1kjg & i. 1-99 & n. ca, 1kjh & i. 1-99 & n. ca
pair_fit 1kjg///1-99/ca, 1kjh///1-99/ca pair_fit will use all atoms, whereas align will only use atoms that are matched with respect to a dynamic-programming sequence alignment. 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 > Joel Tyndall > Sent: Sunday, June 26, 2005 4:08 PM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] align/fit > > Hi folks, > > Been sitting here getting a little confused with the > seemingly endless possibilities of the fit and align > commands. What I want to do is a pairwise alignment of the > ca atoms of protein portion of some HIV complexes ie 2 chains > of 99 residues). > > When I use the command > > align 1kjg & i. 1-99 & n. ca, 1kjh & i. 1-99 & n. ca > > pinched from robert campbells website (ta) I get the > following results: > > Match: read scoring matrix. > Match: assigning 208 x 209 pairwise scores. > MatchAlign: aligning residues (208 vs 209)... > ExecutiveAlign: 195 atoms aligned. > ExecutiveRMS: 5 atoms rejected during cycle 1 (RMS=2.49). > ExecutiveRMS: 6 atoms rejected during cycle 2 (RMS=0.67). > Executive: RMS = 0.475 (184 to 184 atoms) > > I know how to turn off the refinement so thats and that > aligns 195 atoms without refinement. (This can be also > complicated when the 2 chains are A and B or 1-99 and > 101-199). So what I am after is the protein alignment which > will align 198 atoms (2 x chain of 99 residues) to give me a > pairwise alignment to compare _multiple _structures. > > Could someone point me in the right direction please. > > Many thanks > > Joel > > -- > Joel Tyndall, PhD > > Lecturer > National School of Pharmacy > University of Otago > PO Box 913 Dunedin > New Zealand > > Pukenga > Te Kura Taiwhanga Putaiao > Te Whare Wananga o Otago > Pouaka Poutapeta 913 Otepoti > Aotearoa > > Ph / Waea +64 3 4797293 > Fax / Waeawhakaahua +64 3 4797034 > > > > > ------------------------------------------------------- > SF.Net email is sponsored by: Discover Easy Linux Migration > Strategies from IBM. Find simple to follow Roadmaps, > straightforward articles, informative Webcasts and more! Get > everything you need to get up to speed, fast. > http://ads.osdn.com/?ad_id=7477&alloc_id=16492&op=click > _______________________________________________ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users > > >
