VMD-L Mailing List

From: Wallace Chan (wallakin_at_umich.edu)
Date: Fri Sep 06 2019 - 12:56:35 CDT

Dear All,

I am working with a structure generated from CHARMM-GUI in which there are
over 19,000 water molecules. As the standard PDB format only uses 4 columns
for the residue number, CHARMM-GUI uses one more column after it for
residues over 9,999, totaling to 5 columns. VMD doesn't appear to like
this, so every time I query a set of waters, it only returns only four
numbers, understandably because it adheres strictly to the four-column
residue number format.

As a result, I re-encoded all residues over 9,999. For example, 10,000
would be A000. When I try to query once again, I get that the residue
number is 0. In fact, this happens for every residue that has a residue
number that is alphanumeric. Is there a way to query the residue number so
that it returns the alphanumeric string?

Thank you for any advice that may be provided. 

-- 
Wallace Chan
Post-Doctoral Research Fellow
Traynor Lab
Department of Pharmacology
University of Michigan
wallakin_at_umich.edu