Subject: Re: MESP visualization

From: "Victor Anisimov" <[email-masked]>
Date: Thu, 11 Apr 2002 11:21:15 +0200

Dear Colleagues,

In my latest question to the list I guess I wanted too much with 8 million
MESP points
on 120 000 atom's protein as I could collect no responses. Actually
complexity of
the task could be in principle reduced by switching to visualization of only
some part
of the large MESP map. Having let's say only part of the whole Connolly
surface near
to a centre of my interest would it be possible to visualize this partial
surface? As
before I have coordinates of dots corresponding to this partial Connolly
surface of my
interest with MESP potentials calculated elsewhere. What visualization tool
one can
use to draw this partial MESP surface?

The question is actually in special format of MESP surface, when GUI obtains
a ready
surface for visualization rather trying to reconstruct it from a cube grid.
Is it implemented
in some package? Perhaps, displaying a ready surface would be an extremely
economic
way when MESP of 120 000 atoms protein is a subject of study, i.e. if there
is no way
to display the whole surface at once, it would be good to display at least a
part.
If it is necessary any density of dots (0.1-0.001A) can be prepared in the
MESP file
to eliminate extra spline interpolation work within GUI.

Is there any idea how this partial surface data could be feeded to a
visualization program?

Thank you for your input.
Sincerely,
Victor.

----- Original Message -----
From: "Victor Anisimov" <[email-masked]>
To: <[email-masked]>
Sent: Friday, April 05, 2002 3:53 PM
Subject: CCL:MESP visualization

> Dear CCLers,
>
> I'd like to make nice 3D visualization of a molecular electrostatic
> potential calculated
> for 120 000 atoms protein system on Connolly surface. My MESP file is a
> textual file
> with three columns corresponding to Cartesian coordinates of a point and
> fourth
> column containing MESP value, i.e. each line corresponds to a separate
point
> on
> the Connolly surface. Number of points on one Connolly surface is about
one
> million.
> No cube format is possible I guess by size of the molecule and number of
the
> mesh
> points one would need to store in the cube file.
>
> Can someone suggest me a free software that can read this file and draw
nice
> 3D
> map with colours corresponding to MESP value? My hardware limitation is
1GB
> RAM and Windows/Linux single Athlon CPU machine. I'd greatly appreciate
any
> hints.
> Thank you in advance,
> Victor.