VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Nov 02 2006 - 11:27:52 CST

Hi,
  If you're willing to modify the IED source code, you could
just add a few lines of code that renders the current display
each time it redraws. You could name the filenames by the eigenvector
values so you don't end up with any duplicate frames. To give it
a try, just something like these in an appropriate place in the code:
import render
...
value = get slider value...
fname = 'iedvec%03d.tga' % value;
render.render('snapshot', fname);

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Nov 02, 2006 at 12:40:08PM +0100, Vlad Cojocaru wrote:
> Dear Nadia,
>
> I am not aware of any automated way to do that but you can do it
> manually in case you dont have hundreds of movies to make.
>
> 1. Select from the IED menu the eigenvector that you are interested in.
> 2. Render images by moving the eigenvector cursor from minimum to
> maximum (lets say if your minimum is -45 and maximum +45, you can
> render at -45 -35 -25 ... +35 +45)
> 3. Convert those images to ppm by "convert file.tga file.ppm"
> 4. Use ppmtompeg to convert your ppm images to mpeg movie. ppmtompeg
> requires a parameter file..(see "man ppmtompeg" for details) An example
> of parameter file that works is given below.
>
> If somebody has a better way, I am also interested in it.
>
> Best wishes
> vlad
>
> parameter file:
>
> PATTERN I
> IQSCALE 4
> PQSCALE 5
> BQSCALE 12
> SLICES_PER_FRAME 1
> PIXEL FULL
> OUTPUT pca.mpg
> INPUT_DIR ./
> INPUT
> pca1.ppm
> pca2.ppm
> pca3.ppm
> pca4.ppm
> pca5.ppm
> pca6.ppm
> pca7.ppm
> pca8.ppm
> pca9.ppm
> pca10.ppm
> pca11.ppm
> pca12.ppm
> END_INPUT
> BASE_FILE_FORMAT PPM
> INPUT_CONVERT *
> GOP_SIZE 1
> YUV_SIZE 1278x994
> RANGE 1
> PSEARCH_ALG EXHAUSTIVE
> BSEARCH_ALG CROSS2
> REFERENCE_FRAME DECODED
>
>
>
>
> nadiav_at_soton.ac.uk wrote:
>
> >Dear VMD users,
> >
> >I am using IED to display the motions from a normal mode analysis study
> >(Amber) on a protein system (4962 atoms).
> >
> >I understand that each eigenvector is observed by selecting it manually and
> >moving the cursor manually. I am interested to know whether it is possible
> >to create movies of individual eigenvectors?! if so, how?
> >
> >Thank you in advance to your help.
> >
> >Kind regards,
> >
> >Nadia Vadahti
> >
> >
> >
> >
> >
> >
> >
> >
> >
>
> --
> Dr. Vlad Cojocaru
> EML Research gGmbH
> Molecular and Cellular Modeling Group
> Schloss-Wolfsbrunnenweg 33
> 69118 Heidelberg, Germany
> Phone: +49-6221-533266
> Fax: +49-6221-533298
> e-mail: Vlad.Cojocaru_at_eml-r.villa-bosch.de
> http://projects.villa-bosch.de/mcm/people/cojocaru/
> 

-- 
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/      Fax: 217-244-6078