From: Irene Newhouse (
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?
Irene Newhouse
See how Windows Mobile brings your life together—at home, work, or on the go.