VMD-L Mailing List

From: Sally Fisher (sally.fisher_at_richmond.edu)
Date: Wed May 26 2010 - 10:15:20 CDT

Hi all:

I am looking at a desmond trajectory for a 200 residue protein. The protein
was originally built in Maestro. When I import the protein into VMD, it
appears correctly by visual inspection and VMD correctly identifies the
entire protein as one chain. However, when I look at the sequence using
Sequence Viewer, it displays the sequence out of order. It lists the residue
numbers and names and correctly identifies their corresponding structures,
just out of order. MultiSeq also lists the sequence out of order. Is there
anyway I can reorder these numbers? How does VMD determine the order in
which to list the residues, if not residue number? Should I be concerned
about the structure file being incorrect?

Thanks,
Sally Fisher
Department of Chemistry
University of Richmond, VA 23173