From: Andreas <andreas@bi...> - 2004-09-07 01:33:07
Hey all, and especially Warren,
I've been playing around with alignment recently and was wondering what
exactly is going on when I run the command 'align'. As I understand it,
a combination of sequence and structural alignment is performed. Here
is my output from a recent alignment:
Match: read scoring matrix.
Match: assigning 200 x 219 pairwise scores.
MatchAlign: aligning residues (200 vs 219)...
ExecutiveAlign: 168 atoms aligned.
ExecutiveRMS: 11 atoms rejected during cycle 1 (RMS=3D5.82).
ExecutiveRMS: 6 atoms rejected during cycle 2 (RMS=3D4.73).
Executive: RMS =3D 4.391 (151 to 151 atoms)
Now, my questions are: How is the number of cycles determined? By
which criteria are atoms (outliers) rejected? Which are the atoms that
are used for the final alignment (in my case 151?, and can I select them
What I want to do eventually is run the 'distance' command on all pairs
of matching atoms (CAs in this case) and show those pairs whose members
are within or outside a set cutoff. Which was trivial if I knew how to
select the pairs.
I know that I can manually rename residues that look like they are
structurally equivalent, but I'm wondering if there is a more elegant
Thanks for your help.
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