VMD-L Mailing List

From: Fahimeh Baftizadeh (fahimeh.baftizadeh_at_googlemail.com)
Date: Mon Jan 10 2011 - 15:29:46 CST

thanks John for your reply.
Let me make my question more clear.
I have a grid of point which they have intensity as a function of time, they
are fixed in the space, What I would like to see is
1- their intensity change with time (like changing the colors).
2- then I would like to apply also the volume slice to have more visual
information.
I was thinking of generating a file.dx ... but maybe i need a little bit of
tcl scripting in order to generate a movie, not a single frame.

Thanks in advance
Fahimeh

On Mon, Jan 10, 2011 at 9:28 PM, John Stone <johns_at_ks.uiuc.edu> wrote:

>
> Hi,
> VMD doesn't currently allow time-varying volumetric models to be
> loaded in the same way that you can load a trajectory. That said,
> if you're willing to load each volumetric map in a separate molecule,
> you can use the "multiple molecule animation" plugin in the
> Extensions->Visualization menu to accomplish the same thing.
> Let us know if you need more assistance with this.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Mon, Jan 10, 2011 at 11:50:46AM +0100, Fahimeh Baftizadeh wrote:
> > Hello
> >
> > I want to generate a volumetric file format which can be read by VMD,
> In
> > fact I have some fixed voxel and their intensity is changing with
> time.
> > for a single fram I could generate a pdb file and simply plug it to
> vmd.
> > and then I could look at the intensity of that fram using VOLMAP tool
> > inside VMD. but for generating a trajectory of intensity, how should
> be
> > the format. I already tried to put keywork MODEL and ENDMDL like a
> normal
> > trajectory with a pdb fromat but it doesn't work.
> > Can you help me?!
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> WWW: http://www.ks.uiuc.edu/~johns/ <http://www.ks.uiuc.edu/%7Ejohns/>
> Fax: 217-244-6078
> 

-- 
--------------------------------------------------------------------------------------------------------------
Fahimeh Baftizadeh
SISSA, via Bonomea, 265
34136 Trieste, ITALY
email : fbafti_at_sissa.it
           fahimeh.baftizadeh_at_gmail.com
phone : +39-040-3787-302