From: maria goranovic (mariagoranovic_at_gmail.com)
Date: Wed Nov 23 2011 - 04:25:08 CST

Dear All

Thank you for the suggestions. I will look into IED, and try to make some
visualizations.

Maria

On Tue, Nov 22, 2011 at 3:13 PM, Vlad Cojocaru <
vlad.cojocaru_at_mpi-muenster.mpg.de> wrote:

> I.E.D. (Interactive Essential Dynamics) should still be a good piece of
> code to visualize PCA modes from ptraj and gromacs ...
> I know it requires (or at least used to require) source compilation of VMD
> and I also know its not being developed further (pity) but I find it good
> for visualization purposes.
>
> If somebody asks me what feature I am missing in VMD, is the incorporation
> of IED as a standard plugin or the development of an alternative plugin
> that can be accessed through the Extensions menu in VMD ... Maybe even a
> PCA calculator would be quite nice ... I also know the answer to this
> question could be another question: why don't I develop such a tool ? I
> wish I had the time to do it ....
>
> And then movies can be created with the VMD movie maker plugin.
>
> Best,
> Vlad
>
> On 11/22/2011 01:04 PM, maria goranovic wrote:
>
> Hi Davide
>
> Thanks for the help. I was hoping to write or get help writing something
> more flexible within vmd as a script, since the eigenvectors and
> eigenvalues are already calculated. I was wondering if there were other
> suggestions?
>
> Thank you all
>
>
> On Mon, Nov 21, 2011 at 7:37 PM, Davide Provasi <davide.provasi_at_gmail.com>wrote:
>
>> Maria- I'm not sure whether this is the easiest way,
>> but you can do it using the R bio3d package
>> http://mccammon.ucsd.edu/~bgrant/bio3d/html/mktrj.pca.html
>>
>> good luck
>> Davide
>>
>>
>>
>> --
>> Davide Provasi
>> Dept. of Structural and Chemical Biology
>> Mount Sinai School of Medicine
>> Icahn Medical Institute Building
>> 1425 Madison Avenue, Box 1677
>> New York, NY 10029-6574
>> Tel.:212-659-8618
>> Fax: 212-849-2456
>>
>>
>>
>> On Mon, Nov 21, 2011 at 5:35 AM, maria goranovic
>> <mariagoranovic_at_gmail.com> wrote:
>> > Hi
>> > I used g_covar in the GROMACS utility to come up with a series of
>> > eigenvectors and eigenvalues for my protein trajectory. How does one
>> make a
>> > movie of this in vmd?
>> > --
>> > Maria G.
>> > Technical University of Denmark
>> > Copenhagen
>> >
>>
>
>
>
> --
> Maria G.
> Technical University of Denmark
> Copenhagen
>
>
> --
> Dr. Vlad Cojocaru
> Max Planck Institute for Molecular Biomedicine
> Department of Cellular and Developmental Biology
> Roentgenstrasse 20
> 48149 Muenster, Germany
> tel: +49-251-70365-324
> fax: +49-251-70365-399
> email: vlad.cojocaru[at]mpi-muenster.mpg.de
>
>

-- 
Maria G.
Technical University of Denmark
Copenhagen