From: Giovanni Bellesia (gbellesia_at_chem.ucsb.edu)
Date: Thu Dec 06 2007 - 12:25:37 CST
Principal Components Analysis.
See
Annu. Rev. Phys. Chem. 1995. 46: 223-50
or
Curr. Op. Struct. Biology 1999, 9:164-169
-g
> Hi all,
>
> I am curious as to what you mean by "PCA".
>
> Richard
>
> Richard L. Wood, Ph. D.
> University of Minnesota
> Dept. of Medicinal Chemistry,
> College of Pharmacy
> 717 Delaware St. SE
> Minneapolis, MN 55419-2959
> rwoodphd_at_yahoo.com
>
>
> ----- Original Message ----
> From: patrick wintrode <pat_wde2_at_yahoo.com>
> To: L. Michel Espinoza-Fonseca <mef_at_ddt.biochem.umn.edu>
> Cc: namd-l_at_ks.uiuc.edu
> Sent: Thursday, December 6, 2007 8:54:25 AM
> Subject: Re: namd-l: Generating a gromacs topology file for analyzing
> NAMD trajectories
>
> Thanks for the replies. I was able to do PCA using just a pdb file and
> the .trr trajectory.
>
> Now for another question. I did PCA on just the alpha carbons. When I
> generate a trajectory (of the alpha carbons) along the different
> components, it is displayed in VMD as just a collection of points.
> I've tried displaying as "trace", "tube" and various other options.
> Anyone know how to get VMD to draw connections between the alpha carbons?
> Thanks again.
>
> Patrick L. Wintrode
> Dept. of Physiology & Biophysics
> Case Western Reserve University
> Cleveland, OH 44106
>
>
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