From: Vijay Vammi (
Date: Fri Sep 16 2011 - 08:13:49 CDT


I have a 8ns simulation with about 16000 frames. I want to cluster these
frames to get representative structures.

I want to use the QR factorization method as described in "Evolutionary
Profiles Derived from the QR Factorization of Multiple Structural Alignments
Gives an Economy of Information" by Patrick O’Donoghue and Zaida
Luthey-Schulten. I see that this has been part of multiseq plugin in VMD. I
have couple of questions regarding its use :

1). Since we are dealing with rather large number of PDB's, is it advisable
that I run this via command line instead of GUI. I tried using the GUI but I
see that multiseq did not load all the frames but only 2000 of them.

2). In the actual implementation the problem becomes multi-dimmensional
because of gaps, since I dont have gaps in the structure alignment the
problem should be reducible to traditional QR factorization. (noofCAAtoms*3
X numframes would be the size of matrix I am trying to decompose.). Would be
it be much faster and better if I use numpy or Matlab instead of VMD to get
this done? Please correct me if I am wrong here.

Any help or advice on this is appreciated.