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


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