From: Dennis N (
Date: Thu Nov 07 2013 - 16:53:42 CST

Hi all,

I'd like to follow up on a question raised in early 2011:

This issue had not been completely resolved at the time, but perhaps VMD
and Multiseq now include the needed functionality:

I would like to run Multiseq and STAMP structural alignment in a text-only
mode so that I can script it without having to invoke the graphical
interface. I have many clusters of sequence-similar PDBs (hundreds), and
I'd like to perform structural alignment within each sequence cluster
(using STAMP), and then print out Qres values for specific residues of
certain pdbs. I'm also hoping to do the same for sequence alignment too -
ie, perform sequence alignment of pdbs within each cluster and print out
sequence conservation of specific residues.

As noted in responses to the 2011 post, I could run STAMP by itself, and
write my own script to calculate Qres values from the output, but it would
save a lot of time if I could do all this through a text-only workflow for
Multiseq. In addition, my impression from the 2011 thread was that a
text-only version of Multiseq was in the works (in addition to changes to
STAMP within Multiseq).

Have such changes been introduced to VMD & Multiseq, and if so, how may I
implement such a text-only Multiseq?

Many thanks in advance.