Re: [AMBER-Developers] [AMBER] Visualizing ptraj eigenvectors

From: <>
Date: Thu, 24 May 2012 08:51:03 -0400 (EDT)

Hi all,

to summarize this weeks discussion. I tried out PCAsuite, Bio3D and IED.
My personal conclusion would be:

Bio3D is powerful, but does so much more than I needed that it would be
overkill to learn just to do PCA animations. I tried to get IED to work.
Thanks to Mark for the detailed description, but already on Fedora11 (not
the most exotic environment) I couldn't get it to compile and gave up
after 60 min (maximum attention span of the youtube generation). I have
the feeling that IED is not really maintained and supported anymore, apart
from the fact that it is a mess to get to work on any new machine/distro.
PCAsuite is straightforward to use, freely available and works well with
Amber formats and VMD.

So why not make PCAsuite the suggested 'default' tool for PCA
visualisations in Amber? It seems designed with that in mind, so no new
coding in AT would be needed and no more than a PCA tutorial for our
website would be required...


Dr. Thomas Steinbrecher
formerly at the
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854

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Received on Thu May 24 2012 - 06:00:02 PDT
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