Andreas > ExecutiveAlign: 2889 atoms aligned. > ExecutiveRMS: 95 atoms rejected during cycle 1 (RMS=6.10). > ExecutiveRMS: 152 atoms rejected during cycle 2 (RMS=2.98).
means: 2889 atoms were aligned intially, then after looking at the quality of the alignment, 95 atoms were rejected as outliers and the alignment was run again with 2794 atoms. On cycle two, 152 more atoms were rejected and the fit was performed with the remaining 2642 atoms with a final RMS of 2.98. align (protein1 and name ca), (protein2 and name ca), object=alignment will show you visually the atoms used in the final fit. Cheers, Warren -- mailto:war...@delsci.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC 400 Oyster Pt. Blvd., Ste 213 South San Francisco, CA 94080 (650)-346-1154 Fax:(650)-593-4020 > -----Original Message----- > From: pymol-users-ad...@lists.sourceforge.net > [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of > Andreas Förster > Sent: Wednesday, September 29, 2004 8:23 AM > To: pymol > Subject: [PyMOL] align output > > Hey Warren, world, > > I want to make sure that I understand the output from the > align command correctly. Here is an example: > > > align (protein1 and name ca), (protein2 and name ca) > Match: read scoring matrix. > Match: assigning 3194 x 3010 pairwise scores. > MatchAlign: aligning residues (3194 vs 3010)... > ExecutiveAlign: 2889 atoms aligned. > ExecutiveRMS: 95 atoms rejected during cycle 1 (RMS=6.10). > ExecutiveRMS: 152 atoms rejected during cycle 2 (RMS=2.98). > > > Does this mean that in the end, 2642 atoms (2889 - 95 - 152) > are aligned? Or are 2889 atoms aligned? > > > Thanks > > > Andreas > > > > -- > Andreas Förster > Dept of Biochem, Univ of Utah, 20N 1900E, #2460 Eccles Bldg. > Salt Lake City, UT 84132, phone: 001.801.585.3919 > home: 465 3rd Av, SLC, UT 84103, 001.801.364.0529 > http://www.biochem.utah.edu/~andreas > > > > ------------------------------------------------------- > This SF.net email is sponsored by: IT Product Guide on > ITManagersJournal Use IT products in your business? Tell us > what you think of them. Give us Your Opinions, Get Free > ThinkGeek Gift Certificates! Click to find out more > http://productguide.itmanagersjournal.com/guidepromo.tmpl > _______________________________________________ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users >
