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From: rtab2@quios.com ("Dory Steiner")
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---




From owner-molmodel@hgmp.mrc.ac.uk  Wed Jun  7 16:02:21 2000
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From: skytop@wickedmail.com
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Subject: Adv. Master Disc 2000
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If you want to market a product or service to web site owners and
administrators, you need to read about the Master Disc 2000 database!!!

You can now access up-to-date data for over 8.5 million companies
worldwide. All of them have their own '.com','.net' or '.org' domain
name on the Internet, making them top prospects for Internet business.
(About 50% include email addresses...) Simply complete the request form
enclosed and return via fax, one of our sales persons will contact
regarding our products. We also build databases to order and carry more
than a dozen other databases from general contact info, fax, email, etc.

Master Disc 2000 allows you to sort data and choose companies according
to your preferences, Data can be imported and exported to your contact
management, spreadsheet, and broadcasting applications.

Please note this is sold compressed using WinZip on a single CDRom as
data only in text ASCII format and does not include any program to
manage the data!! You will need to provide your own software to import
and mange the data. Also you will need a minimum of 1.5 to 3.0 gigabits
of hard drive space to unpack the database. The fields that are contained
within the databases we offer are as follows;

Company Name
Address
City
State or Province
Postal Code
Country
Prefix (Dr., Mr., Mrs., etc.)
First Name
Middle Name
Last Name
Suffix (Jr., II, III, IV, etc.)
Title (CEO, Ph.D., D.M.D., D.D.S., etc.)
Phone
Extension
Fax
E-mail Address
Web Address
Web Title (title of web page)
META Description (description of website)
META Keywords (keywords pertinent to website)
BODY (first 255 characters of web site, e.g. index.html)
SIC Codes

Please note that each record does not include data for each field, if
you choose the upgrades and support option you will receive the updates
to existing records and fields, as well as additional records. However
we do guarantee that you will not find and duplicate domain or urls
within the database. For example you may find more than one contact
name for multiple domains if that contact owns or acts as an admin for
more than one domain.

Master Disc 2000 (ver 1.00 #8.5 million records) costs US $799.00**

Master Disc 2000 mini (ver 1.01 #4.5 million records) costs US $499.00**

Email addresses ONLY (ver 1.02 #3.5 million records), available for US $299.00*8

**Includes regular ground shipping for USA domestic


Semi-annual updates are available for US $199.00




To order FAX this form to (805) 980-5373 or call now for more info!!




*GENERAL INFORMATION*	*PLEASE WRITE CLEARLY!!!*

Company:

Name:

Street Address:

City:

State:

Zip:				Country:

Email:

Phone:

Fax:

[ ] YES! Send the "Master Disc 2000 (ver 1.00 8.5 million records)" for $799.00US

[ ] YES! Send the "Master Disc 2000 mini (ver 1.01 4.5 million records)" for $499.00US

[ ] YES! Send the "Master Disc 2000 (ver 1.02 4.5 million email addresses)" for $299.00US

[ ] YES! Register me for the semi-annual updates & support for one year at $199.00US

[ ] Please send more information before I order the "Master Disc 2000"


*SHIPPING INFORMATION*
(If no address is entered we will use the address listed in the section above)

Ship To:

Street Address:

City:

State:

Zip:			Country:

*Domestic Shipping Options Only*

[ ] Shipping & Handling via Ground Delivery included with purchase (Domestic Only,
See International section for shipping options)

[ ] Express Processing, and Ship Priority Over Night for an additional $29.00


*International Shipping Options Only*

[ ] International Shipping is a flat shipment fee of $49.00

Please select one of the following options for the billing of import duties
& import taxes:

[ ] Please have the import duties/taxes billing to my FedEx account #_____________________

[ ] By signing under the credit card authorization section I am authorizing the credit
card submitted to be billed within approximately 6 weeks after the original amount is
processed for the amount of the import duties and import taxes.  I acknowledge the fact
that Image Marketing Corporation does not know the amount of these duties/taxes prior
to shipment as they vary from country to country.

*PAYMENT INFORMATION*

[ ] Pay by check		AMOUNT OF CHECK $____________

Mail all payments by check to:

Image Marketing Group Online, Inc.
1440 Coral Ridge Dr. #336
Coral Springs, Florida 33071
Attn: Master Disc 2000

[ ] C.O.D.

By selecting this option customer agrees to pay by either a bank/certified check
or money order for the total amount plus shipping if any.  In addition to the
purchase price and shipping costs there will be an additional charge of $16.50US
for C.O.D. processing.

*CREDIT CARD AUTHORIZATION SECTION*

[ ] Pay by Credit Card	TOTAL CHARGE   $

Card Type:     [ ] Visa  [ ] Master Card  [ ] American Express [ ] Discover

Card Number:   	Exp. Date:

Card Holder Name:   	    	 (*This must be completed & signed by cardholder)

Address:

City:

State:

Zip Code: 		Country:

I authorize "Image Marketing Group Online, Inc." to charge my credit card for the
"Master Disc 2000" CdRom in the amount as specified above plus shipping costs if
express delivery. (If ordering with credit card, this must be returned with cardholder's signature!) I am also aware that the charge will show on my statement as either
"JT Nets Billing" or "Net Pro LLC".

Signature:_____________________________  Date:__________________



PLEASE NOTE:	WE WILL NOT PROCESS INCOMPLETE ORDERS!



To order or for more information please call or FAX this form to (805) 980-5373 now!!

Also Please, Send Additional Information on:

_____	Online Billing/Credit Card Processing
_____	Emailing Services and Databases
_____	Search Engine Positioning
_____	International Contact Lists
_____	Buying / Selling Traffic
_____	Other Databases Available
_____	Other:_______________________________


############################################################################
To discontinue receipt of further notice and to be removed from our database,
please reply with the word "Remove" in subject. Or call  (805) 980-5373 and
leave your email address for removal from the database and future mailings.

Image Marketing Group Online, Inc.
1440 Coral Ridge Dr. #336
Coral Springs, Florida 33071
############################################################################


.06060001.


---




From owner-molmodel@hgmp.mrc.ac.uk  Fri Jun  9 06:30:34 2000
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To: molmodel@hgmp.mrc.ac.uk
Sender: owner-molmodel@hgmp.mrc.ac.uk
Precedence: bulk

If you want to market a product or service to web site owners and
administrators, you need to read about the Master Disc 2000 database!!!

You can now access up-to-date data for over 8.5 million companies
worldwide. All of them have their own '.com','.net' or '.org' domain
name on the Internet, making them top prospects for Internet business.
(About 50% include email addresses...) Simply complete the request form
enclosed and return via fax, one of our sales persons will contact
regarding our products. We also build databases to order and carry more
than a dozen other databases from general contact info, fax, email, etc.

Master Disc 2000 allows you to sort data and choose companies according
to your preferences, Data can be imported and exported to your contact
management, spreadsheet, and broadcasting applications.

Please note this is sold compressed using WinZip on a single CDRom as
data only in text ASCII format and does not include any program to
manage the data!! You will need to provide your own software to import
and mange the data. Also you will need a minimum of 1.5 to 3.0 gigabits
of hard drive space to unpack the database. The fields that are contained
within the databases we offer are as follows;

Company Name
Address
City
State or Province
Postal Code
Country
Prefix (Dr., Mr., Mrs., etc.)
First Name
Middle Name
Last Name
Suffix (Jr., II, III, IV, etc.)
Title (CEO, Ph.D., D.M.D., D.D.S., etc.)
Phone
Extension
Fax
E-mail Address
Web Address
Web Title (title of web page)
META Description (description of website)
META Keywords (keywords pertinent to website)
BODY (first 255 characters of web site, e.g. index.html)
SIC Codes

Please note that each record does not include data for each field, if
you choose the upgrades and support option you will receive the updates
to existing records and fields, as well as additional records. However
we do guarantee that you will not find and duplicate domain or urls
within the database. For example you may find more than one contact
name for multiple domains if that contact owns or acts as an admin for
more than one domain.

Master Disc 2000 (ver 1.00 #8.5 million records) costs US $799.00**

Master Disc 2000 mini (ver 1.01 #4.5 million records) costs US $499.00**

Email addresses ONLY (ver 1.02 #3.5 million records), available for US $299.00*8

**Includes regular ground shipping for USA domestic


Semi-annual updates are available for US $199.00




To order FAX this form to (805) 980-5373 or call now for more info!!




*GENERAL INFORMATION*	*PLEASE WRITE CLEARLY!!!*

Company:

Name:

Street Address:

City:

State:

Zip:				Country:

Email:

Phone:

Fax:

[ ] YES! Send the "Master Disc 2000 (ver 1.00 8.5 million records)" for $799.00US

[ ] YES! Send the "Master Disc 2000 mini (ver 1.01 4.5 million records)" for $499.00US

[ ] YES! Send the "Master Disc 2000 (ver 1.02 4.5 million email addresses)" for $299.00US

[ ] YES! Register me for the semi-annual updates & support for one year at $199.00US

[ ] Please send more information before I order the "Master Disc 2000"


*SHIPPING INFORMATION*
(If no address is entered we will use the address listed in the section above)

Ship To:

Street Address:

City:

State:

Zip:			Country:

*Domestic Shipping Options Only*

[ ] Shipping & Handling via Ground Delivery included with purchase (Domestic Only,
See International section for shipping options)

[ ] Express Processing, and Ship Priority Over Night for an additional $29.00


*International Shipping Options Only*

[ ] International Shipping is a flat shipment fee of $49.00

Please select one of the following options for the billing of import duties
& import taxes:

[ ] Please have the import duties/taxes billing to my FedEx account #_____________________

[ ] By signing under the credit card authorization section I am authorizing the credit
card submitted to be billed within approximately 6 weeks after the original amount is
processed for the amount of the import duties and import taxes.  I acknowledge the fact
that Image Marketing Corporation does not know the amount of these duties/taxes prior
to shipment as they vary from country to country.

*PAYMENT INFORMATION*

[ ] Pay by check		AMOUNT OF CHECK $____________

Mail all payments by check to:

Image Marketing Group Online, Inc.
1440 Coral Ridge Dr. #336
Coral Springs, Florida 33071
Attn: Master Disc 2000

[ ] C.O.D.

By selecting this option customer agrees to pay by either a bank/certified check
or money order for the total amount plus shipping if any.  In addition to the
purchase price and shipping costs there will be an additional charge of $16.50US
for C.O.D. processing.

*CREDIT CARD AUTHORIZATION SECTION*

[ ] Pay by Credit Card	TOTAL CHARGE   $

Card Type:     [ ] Visa  [ ] Master Card  [ ] American Express [ ] Discover

Card Number:   	Exp. Date:

Card Holder Name:   	    	 (*This must be completed & signed by cardholder)

Address:

City:

State:

Zip Code: 		Country:

I authorize "Image Marketing Group Online, Inc." to charge my credit card for the
"Master Disc 2000" CdRom in the amount as specified above plus shipping costs if
express delivery. (If ordering with credit card, this must be returned with cardholder's signature!) I am also aware that the charge will show on my statement as either
"JT Nets Billing" or "Net Pro LLC".

Signature:_____________________________  Date:__________________



PLEASE NOTE:	WE WILL NOT PROCESS INCOMPLETE ORDERS!



To order or for more information please call or FAX this form to (805) 980-5373 now!!

Also Please, Send Additional Information on:

_____	Online Billing/Credit Card Processing
_____	Emailing Services and Databases
_____	Search Engine Positioning
_____	International Contact Lists
_____	Buying / Selling Traffic
_____	Other Databases Available
_____	Other:_______________________________


############################################################################
To discontinue receipt of further notice and to be removed from our database,
please reply with the word "Remove" in subject. Or call  (805) 980-5373 and
leave your email address for removal from the database and future mailings.

Image Marketing Group Online, Inc.
1440 Coral Ridge Dr. #336
Coral Springs, Florida 33071
############################################################################


06060001.


---




From owner-molmodel@hgmp.mrc.ac.uk  Sat Jun 10 12:57:07 2000
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From: 00qpaanr@kangaroomail.com
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Subject: Do You Need Intenet Sales Leads!
Date: 10 Jun 2000 12:57:03 +0100
Organization: BIOSCI/MRC Human Genome Mapping Project Resource Centre
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X-Accept-Language: en
To: molmodel@hgmp.mrc.ac.uk
Sender: owner-molmodel@hgmp.mrc.ac.uk
Precedence: bulk

If you want to market a product or service to web site owners and
administrators, you need to read about the Master Disc 2000 database!!!

You can now access up-to-date data for over 8.5 million companies
worldwide. All of them have their own '.com','.net' or '.org' domain
name on the Internet, making them top prospects for Internet business.
(About 50% include email addresses...) Simply complete the request form
enclosed and return via fax, one of our sales persons will contact
regarding our products. We also build databases to order and carry more
than a dozen other databases from general contact info, fax, email, etc.

Master Disc 2000 allows you to sort data and choose companies according
to your preferences, Data can be imported and exported to your contact
management, spreadsheet, and broadcasting applications.

Please note this is sold compressed using WinZip on a single CDRom as
data only in text ASCII format and does not include any program to
manage the data!! You will need to provide your own software to import
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Title (CEO, Ph.D., D.M.D., D.D.S., etc.)
Phone
Extension
Fax
E-mail Address
Web Address
Web Title (title of web page)
META Description (description of website)
META Keywords (keywords pertinent to website)
BODY (first 255 characters of web site, e.g. index.html)
SIC Codes

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To order FAX this form to (805) 980-5373 or call now for more info!!




*GENERAL INFORMATION*	*PLEASE WRITE CLEARLY!!!*

Company:

Name:

Street Address:

City:

State:

Zip:				Country:

Email:

Phone:

Fax:

[ ] YES! Send the "Master Disc 2000 (ver 1.00 8.5 million records)" for $799.00US

[ ] YES! Send the "Master Disc 2000 mini (ver 1.01 4.5 million records)" for $499.00US

[ ] YES! Send the "Master Disc 2000 (ver 1.02 4.5 million email addresses)" for $299.00US

[ ] YES! Register me for the semi-annual updates & support for one year at $199.00US

[ ] Please send more information before I order the "Master Disc 2000".


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Ship To:

Street Address:

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Zip:			Country:

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[ ] Shipping & Handling via Ground Delivery included with purchase (Domestic Only,
See International section for shipping options)

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Please select one of the following options for the billing of import duties
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[ ] Please have the import duties/taxes billing to my FedEx account #_____________________

[ ] By signing under the credit card authorization section I am authorizing the credit
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[ ] Pay by check		AMOUNT OF CHECK $____________

Mail all payments by check to:

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1440 Coral Ridge Dr. #336
Coral Springs, Florida 33071
Attn: Master Disc 2000

[ ] C.O.D.

By selecting this option customer agrees to pay by either a bank/certified check
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for C.O.D. processing.

*CREDIT CARD AUTHORIZATION SECTION*

[ ] Pay by Credit Card	TOTAL CHARGE   $

Card Type:     [ ] Visa  [ ] Master Card  [ ] American Express [ ] Discover

Card Number:   	Exp. Date:

Card Holder Name:   	    	 (*This must be completed & signed by cardholder)

Address:

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Zip Code: 		Country:

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Signature:_____________________________  Date:__________________



PLEASE NOTE:	WE WILL NOT PROCESS INCOMPLETE ORDERS!



To order or for more information please call or FAX this form to (805) 980-5373 now!!

Also Please, Send Additional Information on:

_____	Online Billing/Credit Card Processing
_____	Emailing Services and Databases
_____	Search Engine Positioning
_____	International Contact Lists
_____	Buying / Selling Traffic
_____	Other Databases Available
_____	Other:_______________________________


############################################################################
To discontinue receipt of further notice and to be removed from our database,
please reply with the word "Remove" in subject. Or call  (805) 980-5373 and
leave your email address for removal from the database and future mailings.

If you would like for more information on the other products and services we
have to offer related to online marketing databases / tools, please reply
with the word "Subscribe" in subject. Or call  (805) 980-5373 and leave your
email address for more information and future mailings.

IMG Online, Inc.
1440 Coral Ridge Dr. #336
Coral Springs, Florida 33071
############################################################################


.06060001.


---




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From owner-molmodel@hgmp.mrc.ac.uk  Wed Jun 14 11:12:15 2000
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From: ptitjean@ccr.jussieu.fr (Michel PETITJEAN)
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Subject: 3D align, surf/vol v.d.Waals, quantitative chir., convex hull...
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Hereafter are some freewares available on several platforms, including
DEC-alphastations (VMS and unix), RS6000 (and SP2), CRAY YMP and J90,
Linux, SGI (various architectures).
Mailto: petitjean@itodys.jussieu.fr


CSR reads the cartesian coordinates of two molecules, then optimally rotates and
translates the molecule 2 onto the molecule 1 to find the maximal common 3D motif.


ASV reads the cartesian coordinates of the molecule and the van der
Waals radii of the atoms, then performs both Monte-Carlo and analytical
calculation of the van der Waals surface and volume.


QCM reads the cartesian coordinates of a conformer.
It computes both the chiral index CHI and the direct symmetry index DSI.
The connex components of molecules are treated separately.
The isomorphisms of the graph (onto itself) associated to each connex
component are enumerated.


RADI reads the cartesian coordinates of the molecule. It extracts
the convex hull of the atomic positions, then computes the diameter
and the radius of the hull. Three shape coefficients are computed,
all related to the convex hull of the set.


Michel Petitjean,                     Email: petitjean@itodys.jussieu.fr
ITODYS (CNRS, ESA 7086)                      ptitjean@ccr.jussieu.fr




From owner-molmodel@hgmp.mrc.ac.uk  Wed Jun 14 20:25:51 2000
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http://home.ici.net/~hfevans/chempen3.htm
Molecular Mechanics for Windows,
Chemical Structure Drawing,
C-13 NMR Shift Prediction for Windows,





From owner-molmodel@hgmp.mrc.ac.uk  Wed Jun 14 20:26:30 2000
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C-13 NMR Shift Prediction for Windows,
Chemical Structure Drawing,
Molecular Mechanics for Windows,
http://home.ici.net/~hfevans/nmrpen.htm




From owner-molmodel@hgmp.mrc.ac.uk  Mon Jun 19 21:56:43 2000
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From owner-molmodel@hgmp.mrc.ac.uk  Thu Jun 22 12:55:13 2000
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From: Sue Taylor <Sue@polyhedron.com>
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Date: Thu, 22 Jun 2000 12:24:19 +0100
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We have added a trial version of DTMM to our Web Site.

Desktop Molecular Modeller (DTMM) Version 4.0 is a simple-to-use
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-- 
Sue Taylor             Sue@polyhedron.com             Sue@polyhedron.co.uk

Polyhedron Software Ltd.        
Programs for Programmers - QA, Compilers, Graphics

************ Visit our Web site on http://www.polyhedron.co.uk/ ************




From owner-molmodel@hgmp.mrc.ac.uk  Fri Jun 23 16:01:13 2000
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POSTDOCTORAL POSITIONS IN STRUCTURAL BIOLOGY

Two positions are available in the newly established
Structural Biology Center at the University of Texas.
Highly motivated individuals are sought to pursue
research in an active and collaborative environment.
One position will focus on x-ray crystallographic
studies of the proteins involved in the nitric oxide
signaling pathway (Cell 95: 939-950 [1998]).  
Another position is geared towards solving structures
of novel proteins in transcriptional silencing.
Diffraction-quality crystals and/or optimized protein
expression systems are in hand to provide a head-start 
on these projects. Both projects also present the
opportunity for pursuing biochemical and functional
studies in parallel with the structural analysis.  
The laboratory is equipped with state-of-the-art facilites
including a Rigaku generator, RAXIS IV++ detectors, Osmic
mirrors, cryo-cooling, and equipment for all aspects
of protein purification, expression, and characterization.

The applicant should have a Ph.D. in Biochemistry or 
Molecular Biophysics.  Preference will be given to those
candidates with training in macromolecular crystallography.
However, those with research expertise in protein chemistry,
molecular biology, or computational chemistry/biology are
encouraged to apply.  Interested candidates should send their
CV along with e-mail addresses of three references to 
craman@uci.edu OR Dr. C. S. Raman, Structural Biology Center,
Dept. of Biochemistry and Molecular Biology, University
of Texas - Houston Medical School, Suite 6.200, 6431 Fannin St,
Houston, TX 77030.  URL:deanweb.med.uth.tmc.edu.  The University
of Texas - Medical School in Houston is an Equal Employment/
Opportunity Employer.



---




From owner-molmodel@hgmp.mrc.ac.uk  Sun Jun 25 04:01:03 2000
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From: sudha@scripps.edu (Sudha Veeraraghavan)
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Subject: Postdoctoral Positions: Protein NMR
Date: 25 Jun 2000 04:00:58 +0100
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		 Postdoctoral Positions
		Structural Biology Center
	University of Texas-Houston Medical School

Two postdoctoral positions are available immediately to solve
protein structures using modern NMR methods.  Research focus is to 
elucidate the molecular basis for cell cycle regulation.  One project
involves studies on a novel protein that regulates oocyte 
maturation; another involves investigating a kinase that plays a key
role in cell proliferation.  Fellows will study the solution structures
and dynamics of proteins or protein fragments using hetero- and
homonuclear multidimensional gradient NMR techniques on a 600 MHz Avance
NMR spectrometer.  The projects will also incorporate proteomics
approaches to identify and characterize interacting proteins.

Candidates who are competent in macromolecular NMR methods and
solving structures or with a strong background in pulse program
development and interest in learning to solve structures are preferred.
Interested candidates should e-mail their CV with the names, addresses,
and e-mail of three references to sudha@scripps.edu or mail to

Dr. Sudha Veeraraghavan
Structural Biology Center 
Department of Biochemistry and Molecular Biology
University of  Texas-Houston Medical School
6431 Fannin Street
Houston, TX 77030

***The UT-Houston Medical School is an Equal Opportunity/Affirmative
Action Employer ***


!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
*************************************************************************


Sudha Veeraraghavan, Ph.D.              E-Mail: sudha@scripps.edu
Department of Molecular Biology TPC15
The Scripps Research Institute          Office: (858) 784-8824
10550 N. Torrey Pines Rd.		Harper Lab: (858) 784-9858
La Jolla, CA 92037                      FAX   : (858) 784-8895
							  ^^^^   

**************************************************************************
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!





---




From owner-molmodel@hgmp.mrc.ac.uk  Tue Jun 27 16:18:20 2000
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From owner-molmodel@hgmp.mrc.ac.uk  Wed Jun 28 12:20:44 2000
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From: rlm1003@cus.cam.ac.uk (Ricardo Mancera)
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Subject: UK-System Admin (De Novo Pharma, Cambridge)
Date: 28 Jun 2000 11:20:39 GMT
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De Novo Pharmaceuticals is a start-up company of the University of
Cambridge whose mission is to apply in silico drug design and other
computational chemistry techniques to the novel therapeutic targets coming
from the Human Genome Project.  De Novo works in collaboration with other
pharmaceutical and biotechnology companies to design novel, patentable
chemical leads based on their proprietary chemistries.

Due to future expansion of our research team, we are seeking a
computational facility manager to oversee the company's SGI Power
Challenge server, graphics workstations and PC network.  The manager will
have a BA/Ph.D. in chemistry, physics, computer science or a related field
and should have extensive experience in system administration.  It is
essential that the candidate have a thorough background in Unix and
Windows operating systems, HTML, Perl, Java and/or C++ and experience
developing web applications.  Experience developing database applications
and knowledge of modern computational chemistry and molecular modelling
techniques are definite advantages, as there is the possibility of
participating in the creation of web-based, database-driven software to
advance drug discovery and development efforts. 

The successful candidate will have good communication and teamwork skills,
as he/she will have to interact with research scientists and staff in
general on a regular basis to support their work, and be responsible for
system administration, computer and software maintenance. Salary will be
commensurate with experience and skills. 

Interested applicants should send their CVs to Dr. David Bailey, CEO, De
Novo Pharmaceuticals, St. Andrew's House, 59 St. Andrew's Street,
Cambridge CB2 3DD, by e-mail to David.Bailey@denovopharma.com or by fax to
01223 327392. 

-- 
*******************************
Ricardo L. Mancera, M.A., Ph.D.

Research Fellow 




From owner-molmodel@hgmp.mrc.ac.uk  Thu Jun 29 07:33:16 2000
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Subject: Get a FREE Deluxe Satellite T.V. System ...
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From owner-molmodel@hgmp.mrc.ac.uk  Thu Jun 29 19:26:09 2000
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From: johns@ks.uiuc.edu (John Stone)
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Subject: Announce: VMD 1.5 Released
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         VMD "Visual Molecular Dynamics" 1.5 Announcement
         ------------------------------------------------
The Theoretical Biophysics group at the Beckman Institute For Advanced  
Science and Technology, the University of Illinois (U-C), is proud to
announce the public release of VMD 1.5.  VMD is a package for the 
visualization and analysis of biomolecular systems.  This software is
distributed free of charge and includes source code, documentation,
and precompiled binaries for Compaq, IBM, HP, Linux, Sun, and SGI systems
systems running Unix, as well as Microsoft Windows 95/98/NT/2000.
The VMD documentation includes an installation guide, a users guide, and a 
programmers guide for interested researchers.  VMD also provides on-line 
help through the use of an external HTML viewer.  VMD development is 
supported by the NIH National Center for Research Resources.

A full description of VMD is available via the VMD WWW home page:
        http://www.ks.uiuc.edu/Research/vmd/

We are eager to hear from you, and thank you for using our software!

                                                John Stone
                                                vmd@ks.uiuc.edu
                                                June, 2000


                       README file for VMD 1.5
---------------------------------------------------------------------------

What is VMD?            See also http://www.ks.uiuc.edu/Research/vmd/
---------------------------------------------------------------------
  VMD is designed for the visualization and analysis of biological
systems such as proteins, nucleic acids, lipid bilayer assemblies,
etc.  It may be used to view more general molecules, as VMD can read
standard Protein Data Bank (PDB) files and display the contained
structure.  VMD provides a wide variety of methods for rendering and
coloring a molecule: simple points and lines, CPK spheres and
cylinders, licorice bonds, backbone tubes and ribbons, and others.
VMD can be used to animate and analyze the trajectory of a molecular
dynamics (MD) simulation.  In particular, VMD can act as a graphical
front end for an external MD program by displaying and animating a
molecule undergoing simulation on a remote computer.

The program has many features, which include:
  o No limit on the number of molecules, atoms, residues or
    number of animation frames, except available memory.

  o Many molecular rendering and coloring methods.

  o Stereoscopic display capability.

  o Extensive atom selection syntax for choosing subsets of atoms for
    display (includes boolean operators, regular expressions, and more).

  o Integration with the program 'Babel' which allows VMD to read many
    molecular data file formats.  Even without the use of Babel,
    VMD can read PDB files, as well as CHARMM- and X-PLOR compatible
    binary DCD files and X-PLOR compatible PSF files.

  o Ability to write the current image to a file  which may be 
    processed by a number of popular raytracing and image rendering
    packages, including POV-Ray, Radiance, Raster3D, Rayshade, 
    and Tachyon.

  o Extensive graphical and text-based user interfaces, which use the
    Tcl package to provide full scripting capabilities.

  o Extensions to the Tcl language which enable researchers to write
    their own routines for molecular analysis.

  o Modular, extensible source code using an object-oriented design in
    C++, with a programmer's guide outlining the source code structure.

  o Integration with the program NAMD, a fast, parallel, and scalable
    molecular dynamics program developed in conjunction with VMD
    in the Theoretical Biophysics Group at the University of Illinois.
    See the NAMD WWW home page for more info:  
      http://www.ks.uiuc.edu/Research/namd

    VMD can be used to interactively display and control an MD simulation
    using NAMD.  


What's new in VMD 1.5?
----------------------
  New Features
    o Support for several Gromacs structure and trajectory file formats:
      - Can read .gro for structure (concatenated multiple-frame .gro
        files are read automatically) (variable precision ASCII format)
      - Can read .g96 for structure (concatenated multiple-frame .g96
        files are read automatically) (fixed high precision ASCII format)
      - Can read .trr for trajectory (full precision, portable binary format)
      - Can read .xtc for trajectory (variable precision, compressed binary
        format)                                                              
      Note: Doesn't support .trj files, or combined run-input files yet, but
            Gromacs users can run trjconv to convert these into one of the 
            formats that VMD can read.
    o Windows versions of VMD now write their snapshot images as 
      24-bit color Windows Bitmaps (.bmp) files directly.
    o Added the ability to modify the name, type, resname, resid
      chain, and segname of a selection of atoms.
    o Entirely new rendering capabilities implementing "material" 
      properties, for user control of ambient, diffuse, and specular
      reflectivity, as well as surface shininess.

  General Improvements and Bug Fixes
    o Improved the rendering output for Raster3D and Tachyon 
    o General improvements to all renderer output.
    o Major revision of IMD (Interactive MD) features in VMD.
    o The Unix versions of VMD are now built with FLTK instead of XForms,
      this brings both the Unix and Windows versions of VMD to using exactly
      the same GUI, and decreases VMD's code/binary size noticably.
    o New OpenGL code to allow SGI O2s to support stereoscopic display 
      with 16-bit depth buffering and and 12-bit color.
    o Fixed quite a few of the outstanding problem reports (bugs)
      that were sent in on previous versions of VMD.
      PRs fixed: 5, 7, 10, 19, 23, 29, 58, 64, 68, 75, 76, 78, 79, 81, 
                 83, 87, 88, 89, 90, 94, 95, 96, 97, 98, 100, 104, 105
    o Rewrote large parts of the VMD display command system, yielding
      some significant performance increases.
    o Improvements to VMD's built-in help for various commands, better
      help topic listings.

  User Interface Changes
    o New GUI color scheme, using lighter colors which are easier on most
      people's eyes, particularly with laptops, projectors, etc.
    o New "Mouse" form which supercedes the old "popup menu" found in
      all of the previous Unix versions of VMD.  The Mouse menu is 
      identical on both Windows and Unix, unlike the previous versions of
      VMD where the Windows version had no analog to the popup menu.
    o New "Materials" form which provides controls over rendering
      properties for representations.  (controls for shininess,
      diffuse, ambient and specular reflectivity etc)
    o Renamed the "Mol" and "Sim" forms to their longer names for increased
      intuitiveness to new users.
    o New "Cancel" button on the Molecule form providing the ability to
      cancel loading of very large trajectory files.

  User Documentation Updates
    o Improved HTML version of documentation (new rev of latex2html)
    o Improved PDF version of documentation, now uses better scalable fonts
    o Updated the VMD tutorial to cover new GUI features 
    o The user guide does more to cover issues specific to the Windows
      versions of VMD in better detail.
    o Updated docs on rendering to snapshots and to external renderers
    o Many updates to sections explaining the VMD GUI, particularly
      the new GUI features.

Known bugs
----------
  Please visit the VMD web site for information on known bugs, 
  workarounds, and fixes:
      http://www.ks.uiuc.edu/Research/vmd/


Cost and Availability
---------------------
  VMD, NAMD, and BioCoRE represent the broad efforts of the 
Theoretical Biophysics group, an NIH Resource for Macromolecular 
Modeling and Bioinformatics, designed to develop and distribute free,
effective tools (with source code) for molecular dynamics studies in
structural biology.  For more information, see:

  http://www.ks.uiuc.edu/Research/VMD/
  http://www.ks.uiuc.edu/Research/NAMD/
  http://www.ks.uiuc.edu/Research/biocore/

The VMD project is funded by the National Institutes of Health
(grant number PHS 5 P41 RR05969).


Disclaimer and Copyright
------------------------
  VMD is Copyright (c) 1995-2000 the Board of Trustees of the 
University of Illinois and others.

The terms for using, copying, modifying, and distributing VMD are
specified in the file LICENSE. If you use VMD in a way you think is
interesting or novel, we would like to know about it.

The authors request that any published work which utilizes VMD 
includes a reference to the VMD web page:

  http://www.ks.uiuc.edu/Research/vmd/

and/or the following reference:

  Humphrey, W., Dalke, A. and Schulten, K., "VMD - Visual Molecular
  Dynamics", J. Molec. Graphics, 1996, vol. 14, pp. 33-38.


Documentation
-------------
  Three VMD manuals are available which describe how to install, 
use, and modify VMD.  The VMD installation guide, is contained in 
the VMD distribution in the file "doc/ig.ps". 
The User's Guide and Programmer's Guide are available separately 
(due to size) from the VMD web site.  Quick help may be accessed
by pressing the "Help" button on the main VMD form, or by typing
help in the VMD command window.  This will bring up the VMD
quick help page, and will lead you to several other VMD help files
and manuals. 


Quick Installation Instructions
-------------------------------
  Detailed instructions for compiling this version of VMD can be found
in the installation guide, ig.ps.  For quick installation of the
binary distribution for Unix do the following:

  1) uncompress and untar the distribution into a working directory.
     In this working directory, there are several subdirectories such 
     as bin, src, doc, data, as well as this README and a configure script.  
     Change to this working directory after the unpacking is complete.

  2) Edit the file 'configure'; change the values for
     the $install_library_dir and $install_bin_dir to a directory in 
     which vmd data files and executables should be installed:

     $install_bin_dir is the location of the startup script 'vmd'.  
     It should be located in the path of users interested in running VMD.

     $install_library_dir is the location of all other VMD files.  
     This included the binary and helper scripts.  It should not be 
     in the path.

  3) A Makefile must be generated based on these configuration variables
     by running "./configure". 

  4) After configuration is complete, cd to the src directory,
     and type "make install".  This will install VMD in the two
     directories listed above.  Note that running "make install" 
     twice will print error messages because you are attempting to 
     overwrite some read-only files.  This should be fine.

  5) When installed, type 'vmd' to start (make sure the
     $install_bin_dir directory is in your path).


Required Libraries
------------------
  VMD requires several libraries and programs for various of its functions.
In particular, it uses GL or OpenGL based 3-D rendering, and will require
that you have the appropriate GL or OpenGL libraries on your system.  
Other programs are required by some of VMD's optional features.
Please visit the VMD web site for more information:
  http://www.ks.uiuc.edu/Research/vmd/

For problems, questions, or suggestions, send e-mail to 'vmd@ks.uiuc.edu'.

  VMD Development Team
  Theoretical Biophysics Group
  University of Illinois and Beckman Institute
  405 N. Matthews
  Urbana, IL  61801
  TBG: http://www.ks.uiuc.edu/
  VMD: http://www.ks.uiuc.edu/Research/vmd/


README for VMD; last modified June 28, 2000 by John Stone
-- 

Theoretical Biophysics Group   Email: johns@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!!!


-- 

Theoretical Biophysics Group   Email: johns@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!!!