VMD-L Mailing List

From: Vlad Cojocaru (Vlad.Cojocaru_at_eml-r.villa-bosch.de)
Date: Thu Nov 02 2006 - 05:40:08 CST

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/