VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Apr 06 2000 - 10:42:51 CDT

Hi,
  I can think of two ways you can increase the level of tesselation
of your molecular surface:

1) For Surf:
   Write a wrapper script that calls Surf with some special parameters,
   and set the environment variable SURF_BIN before you run VMD, so
   that VMD will use your wrapper script instead of the real surf binary.
   We'll probably be adding this to the GUI so that people don't have
   to use this trick anymore, but this method will work for you for now...

   The flag you're wanting to modify is the "-E" flag, as per the Surf
   README file:
  
   -E flpt This is the maximum edge length of any output triangle. The
                triangles are first generated and then recursively subdivided
                till all their edge lengths are less than or equal to this
                threshold length. This default length is MAX_TESS_LEN == 1.2
                (in surf.h)

   You'll want to write a script (on unix) like this:

  ---------------cut here--------------
#!/bin/csh

# change the value of ELEN below to be whatever you want...
setenv ELEN 0.4

echo "Hacking Surf default edge length..."
echo "Using edge length $ELEN"
/usr/local/lib/vmd/surf_SOLARIS2 -E $ELEN $*
  ---------------cut here--------------

  Then do this (but edit directory name appropriately):
  chmod 755 /Home/h2/johns/surfhack
  setenv SURF_BIN /Home/h2/johns/surfhack
  vmd (run vmd in that shell after setting the SURF_BIN variable..)

2) Use MSMS to generate the surface, using a high "density" value in
   the graphics form.

Let us know how these suggestions worked out for you.

  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Apr 06, 2000 at 01:18:30PM +0100, Dr Nicolas Le Novere wrote:
> Hello,
>
> I am using raster3d to output the final version of my figures.
> They contain transparent surfaces over tubes and vdw. The surfaces
> are nice in the vmd window. However the raster3d file output from
> vmd gives me rough polygonal surfaces, far to exhibit the quality
> found at
> http://www.bmsc.washington.edu/raster3d/examples/transparent.jpeg
>
> Is there any way to decrease the size (i.e. increase the number)
> of the triangles written in the plot.r3d file?
> (I recompiled raste3d to handle huge constructs)
>
> Thank you,
>
> --
> Dr Nicolas Le Novère e-mail: nl223_at_cus.cam.ac.uk
> Dpt Zoology, Univ Cambridge, Downing street, Cambridge CB2 3EJ, UK
> http://www.pasteur.fr/recherche/unites/neubiomol/
> tel: +44 1223 336623 fax: +44 1223 336676
>
>
> 

-- 
Theoretical Biophysics Group   Email: johns_at_ks.uiuc.edu
Beckman Institute              http://www.ks.uiuc.edu/~johns/
University of Illinois         Phone:  (217) 244-3349
405 N. Mathews  Ave              FAX:  (217) 244-6078 
Urbana, IL 61801, USA          Unix Is Good For You!!!