Subject: VR for Molecular Modelling ...SUMMARY

From: S Parthiban <[email-masked]>
Date: Tue, 18 Mar 1997 22:57:38 -0500 (GMT)

I sent this mail yesterday. But it seems something went wrong.
So I am trying again. I apologise if u receive this mail twice.
<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<

Dear Netters: 

Last week, I have posted a question seeking info on Virtual Reality for
Molecular Modelling. Thanks to all who responded. I have summarised all
the replies after giving a small note.

For the benefit of non-VR people:
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
The field of chemistry is one of the most interesting fields for
applications in Virtual Reality.  The traditional approach to molecular
modelling is through the use of a workstation and an interactive graphics
system. The VR approach is to immerse the scientist such that he or she
can interact directly with the graphical representation of the molecule. 

You can visit my homepage for some interesting links to VR.
(http://144.16.73.100/~parthi/vrml/index.html)
This is just few days old. You may like to visit this page again after
couple of weeks. At a later date, u can find my article on "VR for
Molecular Modelling" in this page. 

But still I am searching more info on 

*  virtual prototyping of molecular structures;  this will be helpful for
 the physically handicapped (especially blind)students to learn chemistry
and
*  providing music beats to amino acids in proteins; this will help us
 to find out the sequence of amino acids based on the rhythm...!!!!!) 
 (I would appreciate to receive any info on these two aspects.)

Thank you again for the replies and I would appreciate to receive any
other info related to this topic. Thanks in advance. :-)

Sincerely 
S Parthiban
Supercomputer Education and Research Center
Indian Institute of Science, Bangalore 560 012, INDIA
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Replies:
~~~~~~~~

From: Andrew Tiller <[email-masked]>

Dear Parthi

I saw your message on the CCL list and wondered if you already know about
MSI's free WebLab Viewer.  This reads molecule and crystal structures from a
range of common file formats, and can write out VRML.

You can find full details at MSI's Web site (http://www.msi.com/) - follow
the link to download WebLab Viewer, or go directly to:
http://www.msi.com/weblab/viewer/index.htm

Best wishes

Andy

*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*
* Andrew Tiller, PhD. Director, Market Development                      *
*                     Molecular Simulations Inc                         *
*                     The Quorum, Barnwell Road, Cambridge, CB5 8RE, UK *
*                     Tel: +44 1223 413 300      Fax: +44 1223 413 301  *
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From [email-masked] Mar 14 23:06:50 1997
Date: Fri, 14 Mar 1997 10:59:29 +0100
From: Konrad Hinsen <[email-masked]>

I use VRML for visualization in my modelling code. That means I can
produce a VRML file for example from any protein in the PDB in either
wireframe or ball-and-stick model. Let me know if you want a few
examples...
-- 
-------------------------------------------------------------------------------
Konrad Hinsen                          | E-Mail: [email-masked]
Laboratoire de Dynamique Moleculaire   | Tel.: +33-4.76.88.99.28
Institut de Biologie Structurale       | Fax:  +33-4.76.88.54.94
41, av. des Martyrs                    | Deutsch/Esperanto/English/
38027 Grenoble Cedex 1, France         | Nederlands/Francais
-------------------------------------------------------------------------------

From: Csonka Gabor <[email-masked]>

Dear Parthiban,

please visit my collection at:

http://web.inc.bme.hu/~csonka/mke96.html

This is large summary for computational chemists, and it contains a
special link for a VRML. VRML is a potentially important tool for
chemists.

With best regards

 Gabor I. Csonka              e-mail: [email-masked]
 Lab.Chimie Theorique      Universite Henri Poincare
 B.P. 239                          54506 Vandoeuvre-les-Nancy FRANCE
 tel: +33-3.83.91.25.29    fax: +33-3.83.91.25.30
 http://www.ch.bme.hu/inc/csg.html

From [email-masked] Mar 14 23:07:04 1997
Date: Fri, 14 Mar 1997 13:01:52 +0000 (WET)
From: Gennady PODA <[email-masked]>

Your may wish to visit this site:

http://webspace.sgi.com/moving-worlds/spec/index.html

Best wishes,

Gennady

************************************************************
Dr. Gennady PODA

Laboratoire de Chimie theorique (UA 510 du C.N.R.S.)
Universite Henri Poincare, Nancy-I
Faculte des Sciences - Domaine scientifique Victor Grignard
B.P. 239 - 54500 Vandoeuvre-les-Nancy Cedex France

Fax : + 33 (0)3.83.91.25.30   E-mail : [email-masked]
************************************************************

From [email-masked] Mar 14 23:07:13 1997
Date: Fri, 14 Mar 1997 07:15:22 -0600 (CST)
From: "Preston J. MacDougall" <[email-masked]>

>Dear Netters:
>
>I would appreciate receiving information/ftp_sites on Virtual Reality
>for chemistry/molecular modelling.
>

A good place to visit would be the following:

http://wk122.nas.nasa.gov/~creon/nano/laplace.html

Preston J. MacDougall
Assistant Professor
Department of Chemistry, Box X-101
Middle Tennessee State University
Murfreesboro, TN 37132

ph: (615)898-2741,  FAX: (615)898-5182
e-mail: [email-masked]
Homepage: http://www.mtsu.edu/~chem/

From [email-masked] Mar 14 23:07:18 1997
Date: Fri, 14 Mar 1997 11:24:43 +0100 (NFT)
From: "Dr. Bruno Manunza" <[email-masked]>

Dear parthi,
	have a look at the VRML links on our web page
http://antas.agraria.uniss.it

regards
Bruno

Dr Bruno Manunza
DISAABA (Dept. of Agricultural Environm. Sci)
University of Sassari
V.le Italia 39
07100 Sassari, ITALY
phone: 39 79 229215
fax:   39 79 229276
e-mail: [email-masked]
e-mail: [email-masked]
e-mail: [email-masked]

http://antas.agraria.uniss.it

From [email-masked] Mar 14 23:07:27 1997
Date: Fri, 14 Mar 1997 16:08:19 +0000
From: Fabien Campagne <[email-masked]>

Hi,

Viseur (http://www.lctn.u-nancy.fr/viseur/viseur.html) is a program 
that can help G-Protein Coupled Receptor modelling.

The 3D molecular view can be written as an OpenInventor file and
translated (ivToVRML tool) to VRML with hyperlinked amino-acids.

Here is a very simple example:
http://www.lctn.u-nancy.fr/viseur/BACTER_RHODO.wrl.gz

We are working on an application of this VRML presentation
to GPCR 3d hyperlinked models (for annotations or link to 
mutant data: http://www-grap.fagmed.uit.no/GRAP/homepage.html).

hope it helps,

Fabien Campagne -- [email-masked] | Lab. de Chimie Theorique
phone: +33 (0)3 83 91 20 00 extension 3236  | Nancy, France.

From [email-masked] Mar 14 23:28:30 1997
Date: Fri, 14 Mar 1997 11:52:43 +0300
From: Igor Baskin <[email-masked]>

S Parthiban wrote:
> 
> Dear Netters:
> 
> I would appreciate receiving information/ftp_sites on Virtual Reality
> for chemistry/molecular modelling.
> 

Look at our site at URL
http://org.chem.msu.su/people/baskin/molvrml/molvrml.html

**********************************************************************
Dr. Igor I. Baskin         * Phones: (7-095)939-3557 - office
Department of Chemistry    *         (7-095)451-6997 - home
Moscow State University    * E-mail: [email-masked]
119899 Moscow, Russia      * Web: http://org.chem.msu.su/people/baskin
**********************************************************************

Date: Mon, 17 Mar 1997 11:13:50 +0100
From: Armel Le Bail <[email-masked]>

There is a semi-official IUCr small Web page on VRML, which is
part of a larger document on Internet tools for crystallographers at :
       http://fluo.univ-lemans.fr:8001/vrml/intvrml.html

Armel Le Bail, Laboratoire des Fluorures URA CNRS 449 
Faculte des Sciences, Universite du Maine, F-72017 Le Mans, France
http://fluo.univ-lemans.fr:8001/   and/or   http://pcb4122.univ-lemans.fr/

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