Subject: summary: Connolly surfaces

From: "Jeff D. Saxe" <[email-masked]>
Date: Tue, 29 Jul 1997 14:16:10 -0500

I recently asked for a program which can read a pdb or xyz file and display
Connolly surfaces, preferably on an SGI, or possibly on a PC.  I received many
responses.  Some of the software listed below is free and immediately available
on the net (the ideal situation), some is available only to academic
institutions, and some is available to anyone for a price.

Thanks to everyone who responded.  I've tried a couple and they are pretty
good.

Here are the responses:

From: Patricia M Fulmer <[email-masked]>
Have you tried GRASP by Anthony Nicolls?
http://tincan.bioc.columbia.edu/Lab/grasp/

From: Dorina Kosztin <[email-masked]>
If by Connolly surface you mean solvent accessible surface, then VMD
or Grasp programs, both running on SGI, will do it for you.
For the VMD program, look at http://www.ks.uiuc.edu/Research/vmd.
It's a free software and it's very easy to install.

From: Asim Kumar Debnath <[email-masked]>
Try the MS-Connolly program from QCPE (QCPE #429).  I think it is free.
   Quantum Chemistry Program Exchange
   Creative Arts Bldg. 181
   Indiana University
   Bloomington, IN  47405
   Tel:   (812) 855-5539
   Fax:   (812) 855-4784
   email:  [email-masked]

From: [email-masked] (Jean-Luc Pellequer)
There are a couple of well known programs:
InsightII from MSI: use the user:get command (read the format for the dot file)

Turbo-Frodo can read directly an output from the MS (connolly) program as well
as read a PDB file.  Turbo-Frodo is developed at the University of Marseilles.

From: Rita Arutsian - MolSoft info <[email-masked]>
The ICM program allows to build, display Connolly surfaces.  The program uses
the fastest algorithm published recently (Totrov, M.M. & Abagyan, R.A. (1996).
The contour-buildup algorithm to calculate the analytical molecular surface.
J. Struct. Biol., 116, 138-143.) and is about an order of magnitude faster than
the alternative program.  Note that ICM creates a true analytical molecular
surface rather than a rough numerical one (usually built by so called
marching cubes algorithm).  Some images of the molecular surface can be found
on our site (http://molsoft.com).
ICM can do the following:
* build the analytical molecular surface (takes seconds for a protein) for any
  subset of atoms
* display and color this surface in many different ways
* combine it with other molecular representations
* write this image in a VECTORIZED postscript form (rather than a pixelized
  image)
* split it into individual shells, identify cavities and measure their
  volume and surface
* write it in a Wavefront format or in a POV format
If you are not interested in other features of the ICM program, we can offer a
truncated version of what you exactly need for a steeply discounted price.

From: Dr. Bruno Manunza <[email-masked]>
Have you tried the MSP package from M. Connolly or the M. Sanner MSMS & MSV?
Both run on SGI.  You may find links to these and other surface computing
packages on our software list page at http://antas.agraria.uniss.it
Also, have a look at our Tutorials page where a review from Connolly plus some
other tutorials on surface computing are linked.

From: Luigi Cavallo <[email-masked]>
Try Naccess v2.0 - Atomic solvent accessible areas written by Simon Hubbard,
at http://www.biochem.ucl.ac.uk/~roman/naccess/naccess.html
It computes Lee and Richards exact surface from a pdb file.  It is fast and
simple to use.  I compiled it on a DEC ultrix.  On an IBM RS/6000 it didn't
compile properly.  On the SGI no idea at all.

From: Raf Bruyndonckx <[email-masked]>
The program MOLEKEL is able to read pdb format and plot Connolly surfaces.
Have a look at: http://www.cscs.ch/Official/VisMolekel.html

From: Richard Woods (?) <[email-masked]>
I believe that Web Lab Viewer for Windows, available at the MSI web site, will
do it.
(See http://www.msi.com/weblab/index.html)

-- 
Jeff D. Saxe
[email-masked]
BioNumerik Pharmaceuticals, Inc.
Suite 1250
8122 Datapoint Dr.
San Antonio, TX  78229
210-614-1701 (phone)    210-615-8030 (fax)