VMD-L Mailing List

From: Kirby Vandivort (kvandivo_at_ks.uiuc.edu)
Date: Tue Oct 19 2010 - 11:54:26 CDT

Raul,

A couple of things...

If you could:

a) Try the latest alpha version of 1.8.8 for linux available at:

http://www.ks.uiuc.edu/Research/vmd/alpha/

We have made a few changes to the code that does that particular work.
Hopefully you will find that your problem has been solved.

b) If that doesn't work, please send me a small sample, if possible, of the
files that you are using and the exact steps you are following to create
this problem. That will give me what I need to do additional debugging.

Thanks,

Kirby

On Sun, Oct 17, 2010 at 6:52 PM, Raul Araya <arayasecchi_at_gmail.com> wrote:

> Dear VMD users and developers:
>
> I have 200 pdb structures taken each 50ps from an MD trajectory. I want to
> eliminate the redundancy and find the non-overlaping set of structures that
> represents the dynamics of my system. The problem is that when I try to
> search for the non-redundant set using the srtucture QR(after aligning my
> structures with STAMP) (with what ever QH cut-off) I dont get nothing,
> actually it looks as if nothing happens at all. If I use the sequence QR
> instead I get results but I will get one representative only.
>
> Im I doing something wrong? Should I get a selection after the process? It
> is enough to use the Qres tree from the pylogeneric tree menu??
>
> Any help will be appreciated.
>
> PS: I've done this same proces with VMD 1.87 in lunux and mac...
>
>
> Raúl Araya Secchi
> B.Sc Molecular Biotechnology.
> Molecular Biotechnology Engineer.
> PhD Student (Biotechnology Program. UNAB, Chile)
> Computational Biology Lab (DLab)
> Center for Mathematical Modeling (CMM)
> Facultad de Ciencias Físicas y Matemáticas.
> Universidad de Chile.
> 

-- 
Kirby Vandivort