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From: Irene Newhouse (einew_at_hotmail.com)
Date: Tue Sep 23 2008 - 16:21:02 CDT

I'm working up a trimeric protein, and have calculated the average structure over
the trajectory for each monomer. I have several such computations, and taking
the RMSD of various loops between monomer a & b, a & c, b & c works just fine.
 
However, in one example, a particular loop refuses to compute. I get an error
message saying the vectors are of different size. The loop encompasses residues
210 to 220. There's no problem doing the RMSD of this loop between monomers a &
b. a & c gives the error message, but oddly enough I can get an RMSD for residues 206 to 220!
However, this trick doesn't work for b & c. Each of the 3 pdb files contains the same
number of lines. In each of b & c, residue 200 starts on the same line in both files
& residue 220 ends on the same line of both files...
 
Can anyone please explain what might be going on?
 
Thanks!
Irene Newhouse
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