From: Paul R Brenner (
Date: Wed Oct 18 2006 - 10:08:49 CDT

I have read through the mailing list with respect to structural alignments prior
to RMSD calculations. It seems in 2004 there were recommendations to peform a
'center' translation prior to measuring a fit. I am computing RMSDs for a set
of conformations from a Replica Exchange Simulation, thus each frame may require
significant alignment prior to RMSD. In the current VMD code is a 'measure fit'
style alignment sufficient or is a 'centering' operation still recommended prior
to the 'measure fit'?

My protein has stable secondary structure (beta sheets) which I have been using
for the alignment prior to an RMSD over the entire protein. I am suprised by
the frequency of 'Matrix: Warning: no convergence' messages from the measure
fit function.

Is there a way to script in the functions from the 'Multiple Alignment' plugin.
Comments or thoughts on the suitability of this method for alignment prior to
RMSD calculation?

Any guidance would be appreciated.

Paul R Brenner, P.E.
Computer Science and Engineering
The University of Notre Dame
"Computers are incredibly fast, accurate, and stupid; humans are incredibly
slow, inaccurate and brilliant; together they are powerful beyond imagination."
-Albert Einstein