VMD-L Mailing List

From: Prof. Y. U. Sasidhar (sasidhar_at_chem.iitb.ac.in)
Date: Thu May 04 2006 - 07:12:57 CDT

Axel Kohlmeyer wrote:

> On Thu, 4 May 2006, Prof. Y. U. Sasidhar wrote:
>
>
>>I have a set of x y z data. I want to see these points in 3D to locate
>>regions where the points are more dense etc. I am also interested in iso
>>surface plots of point density. Can this be done in VMD ?
>
>
> you can probably do this by a some smart scripting.
> first you have to do a histogram on a regular grid
> (equally spaced in x-,y-, and z-direction) and then
> you can try to display iso-surfaces of that data.
> this can be best done with some external program, but
> of course since VMD embeds the full tcl and python
> language interpreter, you could use those as programming
> languages as well. see e.g.:
> http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/mk3drama/
> which computes a 2d-histogram.
>
> do you need to display a molecule along this data?

Actually my purpose is to display eigen vectors 1,2,3 following
covariance analysis of c-alpha coordinates ( PCA ). Ultimate objective
is to get free energies from densities of points.
regards, 

-- 
  Sasidhar