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+--------------------------------------------------------------------+
|                                                                    |
|                   NAMD 2.3 Release Announcement                    |
|                                                                    |
+--------------------------------------------------------------------+

                                                      August 2, 2001

The Theoretical Biophysics Group at the University of Illinois is
proud to announce the public release of a new version of NAMD, a
parallel, object-oriented molecular dynamics code designed for
high-performance simulation of large biomolecular systems.  NAMD is
distributed free of charge and includes source code.  NAMD development
is supported by the NIH National Center for Research Resources.

NAMD 2.3 has several advantages over NAMD 2.2:

- AMBER file compatibility (parm and coordinate input only).

- The new psfgen tool for building PSF structure files.

- Simpler to run on a single workstation.  (No more rsh!)

- New ports to the Compaq AlphaServer SC, Scyld Beowulf, and Mac OS X.

- Improved serial performance, particularly with PME on Alpha.

NAMD is available from http://www.ks.uiuc.edu/Research/namd/.

For your convenience, NAMD has been ported to and will be installed on
both the PSC TCS1 Alpha cluster and the NCSA Platinum Linux cluster.
Please consider the performance advantages of running NAMD when you
apply for time on these new resources.  Benchmarks for your proposal
are available at http://www.ks.uiuc.edu/Research/namd/performance.html

The Theoretical Biophysics Group encourages NAMD users to be closely
involved in the development process through reporting bugs, contributing
fixes, periodical surveys and via other means.  Questions or comments
may be directed to namd@ks.uiuc.edu.

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


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From owner-molmodel@hgmp.mrc.ac.uk  Mon Aug  6 07:08:47 2001
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From: qs_tong@hotmail.com ("Tong Qiangsong")
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                              CURRICULUM VITAE

NAME IN FULL : Qiangsong Tong     SEX: Male

MAILING ADDRESS :
Department of Urology, Union Hospital, Tongji Medical University,
Wuhan 430022, P.R. China
TEL: (L) 86-27-85726303  (H) 86-27-86843149
Email address: qs_tong@hotmail.com

OBJECTIVE:
To obtain a postdoctoral position in molecular genetics, molecular biology 
or biochemistry.

EDUCATION :
M.D. in Tongji Medical University. (September 1997 to present).
Bachelor of science in Medicine. (September 1992 to September 1997).

RESEARCH EXPERIENCE:
1.Sep.1997‘ͺAug.1998    Virology Laboratory of Union Hospital, Wuhan, China.
  Study of the therapeutic effects and its molecular mechanisms of arsenic 
trioxide on human  bladder cancer ( supported by grant form Tongji Medical 
University)
2.Sep.1998‘ͺJuly.2000   Virology institute of Wuhan University & Cancer 
research institute of Chinese Academy of Medicine Science
The regulation effects on biological behavior of bladder cancer by antisense 
RNA targeting proliferating cell nuclear antigen gene ( supported by grant 
from National Natural Science Fund of China )
3.Sep.2000-present   Urology Laboratory of Union Hospital, Wuhan, China.
Study of the therapeutic effects on prostate diseases by hammered ribozyme 
targeting androgen receptor ( supported by grant from National Natural 
Science Fund of China )

TECHNICAL EXPERIENCE :
1.Cell Biology
Preparation and primary culture of tumor cells
Cell line culture
Nude mice model for tumor
3H-TdR incorporation
MTT colorimetry
Flow cytometry
DNA Ladder detection
Cloning formation assay
TUNEL detection

2. Molecular biology
Gene cloning and expression
Plasmid and genomic DNA extraction
mRNA isolation and RT-PCR
Adenovirus and retrovirus packaging
Polymerase chain reaction
Western blotting and colony
Northern blotting
Hybridization in situ
DNA sequencing

3. Histopathology
Histochemistry
Immunocytochemistry & immunofluorescence
Electron microscopy

PUBLICATIONS:
1. Tong QS, Zeng FQ, Lu GC, et al. Experiment study of the growth inhibition 
effects of arsenic trioxide on human bladder cancer cell line BIU-87. J Clin 
Urol, 2000,15(2):72-74.
2. Tong QS, Zeng FQ, LU GC, et al. Primary study of the effects and 
mechanisms of arsenic trioxide on the growth of human bladder cancer line 
BIU-87. Acta Univ Med Tongji, 2000,29(2): 25-27.
3. Tong QS, Zeng FQ, Zheng LD,et al. Experiment study of the inducing 
apoptosis effects of arsenic trioxide on human bladder cancer. Chin Med J 
,2001: 114(4):402-406.‘‘
4. Tong QS, Zeng FQ, Zhu ZH, et al. Construction of the antisense eukaryotic 
vector for proliferating cell nuclear antigen gene and its expression in 
bladder cancer EJ cell line. Chin J Exp Surg, 2001, 17: in press.
5. Zeng FQ, Tong QS, Zhu ZH, et al. Study of the proliferation inhibition 
effects on human bladder cancer cells by gene transduction of antisense cDNA 
targeting  proliferating cell nuclear antigen. Chin J Urol, 
2000,21(6):216-219.
6. Tong QS, Zeng FQ, Zheng LD, et al. Experiment study of the inducing 
apoptosis effects on human bladder cancer cell by recombinant BAK gene 
transfer.  Chin J Exp Surg, 2001, in press.
7. Zeng FQ, Tong QS, Lin Chen, et al.  Growth inhibition effects on nude 
mice model of human bladder cancer by antisense cDNA targeting proliferating 
cell nuclear antigen gene . Chin J Urol, 2001,in press.
8.Tong QS, Zeng FQ, Lin Chen, et al.  The regulation effects on the in vitro 
biological behavior of human bladder cancer EJ cells by stable antisense 
PCNA gene transfer. Chin J oncol, 2001: submitted.
9. Tong QS, Zhao Jun, Zeng FQ, et al. The construction of Androgen 
receptor(AR)-specific hammered ribozyme vector and its expression in human 
prostate cancer cell line. Chin J oncol, 2001: submitted.
10.Tong QS, Zhao Jun, Zeng FQ, et al. The growth inhibition effects of 
Androgen receptor(AR)-specific hammered ribozyme on human prostate cell 
line. Chin J Urol, 2001: submitted.
11.Tong QS, Zhao Jun, Zeng FQ, et al. The insulin-induced androgen receptor 
activation of  androgen-independent human prostate cancer cell line. Chin J 
Urol, 2001: submitted.

REFERENCES
1. Fuqing ZENG, professor of Urology, Department of Urology, Union Hospital 
of Tongji Medical University, Wuhan, China. Email: fuqing_zeng@yahoo.com
2. Jun ZHAO, associate professor of Urology, College of Physicians & 
Surgeons, Columbia University, New York, USA. Email: zhaojun21@yahoo.com
3. Chen LIN, professor of Cell Biology, Cancer Research Institute, Chinese 
Academy of Medical Sciences, Beijing , China. Email: chenlin_cams@263.net









_________________________________________________________________
Get your FREE download of MSN Explorer at http://explorer.msn.com/intl.asp

---


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sold for 10 times earnings. Just based on simple interest<BR>
an associate with 5 million in real estate liens could sell<BR>
their business for approximately 2.5 million dollars.<BR>
<BR>
</FONT>
<FONT color=3D"#0000A0"> 92% of all of our associates work out of their ho=
me; 43%<BR>
are women and 36% are part time</FONT>
<FONT color=3D"#000000">  .<BR>
<BR>
One of the benefits of working in this field is that you are<BR>
not under any kind of time frame. If you decide to take off<BR>
for a month on vacation then go. The Judgments you are<BR>
working on will be there when you return. The Judgments<BR>
are still in force, they do not disappear.<BR>
<BR>
The way we train you is non-confrontational. You use your<BR>
computer and telephone to do most of the processing. You<BR>
never confront the debtor. The debtor doesn't know who you<BR>
are. You are not a collection agency.<BR>
<BR>
Simply stated the steps to successful Money Processing<BR>
are as follows:<BR>
<BR>
Mail our recommended letter to companies and individuals<BR>
with Money Judgments. (We train you how to find out who<BR>
to write to)<BR>
<BR>
8% to 11% of the firms and people you write will call you<BR>
and ask for your help. They call you, you don't call them<BR>
unless you want to.<BR>
<BR>
You send them an agreement (supplied in the course) to<BR>
sign which splits every dollar you collect 50% to you and<BR>
50% to them. This applies no matter if the judgment is for<BR>
$2,000.00 or $2,000,000.00.<BR>
<BR>
You then go on-line to our computers to find the debtor<BR>
and their assets. We offer over 120 powerful reports to<BR>
assist you. They range from credit reports from all three<BR>
credit bureaus, to bank account locates, employment<BR>
locates, skip traces and locating stocks and bonds, etc.<BR>
The prices of our reports are very low. Typically 1/2 to<BR>
1/3 of what other firms charge. For example we charge<BR>
$6.00 for an individuals credit report when some other<BR>
companies charge $25.00.<BR>
<BR>
Once you find the debtor and their assets you file<BR>
garnishments and liens on the assets you have located.<BR>
(Standard fill in the blanks forms are included in the<BR>
course)<BR>
<BR>
When you receive the assets you keep 50% and send 50% to<BR>
the original Judgment holder.<BR>
<BR>
Once the Judgment is fully paid you mail a Satisfaction of<BR>
Judgment to the court. (Included in the course)<BR>
<BR>
Quote's from several of our students:<BR>
<BR>
Thomas in area code 516 writes us: "I just wanted to drop<BR>
you a short note thanking you for your excellent course. </FONT>
<FONT color=3D"#0000A0"> My<BR>
first week, part time, will net me 3,700.00 dollars</FONT>
<FONT color=3D"#000000">  . Your<BR>
professionalism in both the manual and the video opened<BR>
doors for me in the future. There's no stopping me now.<BR>
Recently Thomas states he has over $8,500,000 worth of<BR>
judgments he is working on.<BR>
<BR>
After only having this course for four months, Larry S. in<BR>
area code 314 stated to us: " </FONT>
<FONT color=3D"#0000A0"> I am now making $2,000.00 per<BR>
week </FONT>
<FONT color=3D"#000000"> and expect this to grow to twice this amount with=
in the<BR>
next year. I am having a ball. I have over $250,000 in<BR>
judgments I am collecting on now."<BR>
<BR>
After having our course for 7 months Larry S. in 314 stated<BR>
" </FONT>
<FONT color=3D"#0000A0"> I am now making $12,000.00</FONT>
<FONT color=3D"#000000">  per month and have approximately<BR>
$500,000.00 in judgments I am collecting on. Looks like I<BR>
will have to hire someone to help out"<BR>
<BR>
Marshal in area code 407 states to us "I feel bad, you only<BR>
charged me $259.00 for this course and it is a goldmine. I<BR>
have added 3 full time people to help me after only having<BR>
your course for 5 months"<BR>
<BR>
>From the above information and actual results you can see<BR>
why we can state the following:<BR>
<BR>
With our course you can own your own successful business.<BR>
A business which earns you substantial income now and one<BR>
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<BR>
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<BR>
If the above sounds interesting to you then its time for you<BR>
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<BR>
</FONT>
<FONT color=3D"#800040"> Please call us at  1--4 0 6 --6 5 2 --0 1 9 4 </F=
ONT>
<FONT color=3D"#000000"> ..<BR>
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We have Service Support</FONT>
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<FONT color=3D"#000000">  . If you call this number<BR>
you can talk to one of our experienced Customer Support personnel.<BR>
They can answer any questions you may have - with no obligation.<BR>
Sometimes we run special pricing on our courses and combinations<BR>
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Thank you for your time and interest.<BR>
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To be deleted from our mailing list please email us at <BR>
becky_adminsupport@freeze.com with not interested in the sub-line or<BR>
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Subject: Get  The  4 1 1  On  Anyone.
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From owner-molmodel@hgmp.mrc.ac.uk  Thu Aug  9 22:24:21 2001
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From: Anthony Park <park2@indiana.edu>
X-Newsgroups: sci.bio.microbiology,bionet.info-theory,bionet.jobs.ofered,biont.cellbiol,bionet.microbiology,bionet.molec-model
Subject: postdoc/grad. student post for cell modelling
Date: Thu, 09 Aug 2001 16:08:48 -0500
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Postdoctoral and Graduate Student Research positions available in the
Department of Chemistry at Indiana University for those with experience
in chemical physics, bioinformatics, cell biology, or numerical
simulation to further develop our unique genomic, proteomic, and
metabolic cell simulator, Cyber-Cell.

If interested, please send CV, a brief note of your interests, and the
names (include email and phone numbers) of three persons familiar with
your professional activities to ortoleva@indiana.edu.

Indiana University is an equal opportunity employer.



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Subject: Do you owe the IRS money?                                                   [2q3u1]
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Subject: virtual conference
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         First Virtual Conference in Genomics and Bioinformatics

October 15 & 16, 2001

At World-Wide Access Grid Locations

Sequencing projects and genomics research has led to an explosive rate of 
data accumulation and to a shift in the way biological research is 
conducted. Bioinformatic tools of the post-genome era are providing new 
insights about gene expression patterns, intron/exon structure, 
post-translational changes and protein interactions as well as phylogenetic 
relationships.  Parallel analysis of thousands of genes using microarray 
technology has become a multi-disciplinary endeavor in which unsupervised 
and supervised learning is applied for gene expression clustering and/or 
classification.  Although genomic technologies offer an enormous scientific 
potential to understand organisms at the molecular level, new challenges on 
the horizon are envisioned.  There is a need for improvement of microarray 
technology, data standardization, and tools for integration of multiple 
databases and data mining.  Other necessary needs include the improvement 
of bioinformatic tools and statistical approaches for sequence analysis, 
gene annotation, categorization of protein families, protein-protein 
interactions, and phylogenetic studies.

The goal for the First Virtual Conference in Genomics and Bioinformatics is 
to increase the exchange of ideas and establish new ways of interaction and 
collaboration among scientists around the world.

For the 2001 Virtual Conference, topics include:

Functional Genomics

Structural Genomics

Computational Approaches for Gene Expression Analysis

Metabolic Profiling

Genomic Data Standardization and Management

Implications of Genomic Research

Proteomics

Invited speakers and Participation:

For the First Conference, invited speakers and reviewers represent 
institutions including:

Argonne National Laboratory

Brookhaven National Laboratory

Cold Spring Harbor Laboratory

First Genetic Trust, Inc.

Massachusetts Institute of Technology

National Center for Genome Resources

National Institute of Standars and Technology

North Dakota State University

Ohio State University

Stanford University

UC Berkeley

Although registration is required, there are no required registration fees 
to participate in the conference.  To participate at the Fargo Access Grid 
Node or one of several other Nodes around the world, please register 
through our web page

http://www.ndsu.nodak.edu/virtual-genomics/registration.htm

 Abstract and Papers:

In addition to the invited presentations, we invite participants to 
consider additional participation through abstracts and papers.  This is a 
fully refereed meeting and each submitted abstract will be peer-reviewed. 
Abstracts should describe unpublished research that is not under review. 
Abstracts describing novel applications and theoretical contributions are 
also requested.  An abstract of no more than 250 words should be submitted 
by August 31, 2001. Please submit your abstract through our web page 
http://www.ndsu.nodak.edu/virtual-genomics/abstract.htm

Accepted abstracts will be invited for a complete paper to be submitted by 
September 21, 2001.  Papers should not be more than 20 pages long using 11 
point font times new roman, 1.5 line spacing, and 3 cm margins on all four 
sides on letter size paper.  An electronic document session will be 
scheduled following the conference to allow the maximum participation 
between the attendees and the authors. Accepted documents as well documents 
submitted by invited speakers will be available in electronic version in 
the "Proceedings of the Virtual Conferences of Genomics and 
Bioinformatics."

Deadline: August 31, 2001 for abstracts

Deadline: September 21, 2001 complete documents

Useful links:

Access Grid locations in the US and around the world:

http://www-fp.mcs.anl.gov/fl/accessgrid/ag-nodes.htm


Registration to attend the meeting in Fargo, North Dakota

http://www.ndsu.nodak.edu/virtual-genomics/registration.htm

Link to submit your abstract

http://www.ndsu.nodak.edu/virtual-genomics/abstract.htm

Susbcribe to our e-mail list

http://listserv.nodak.edu/scripts/wa.exe?SUBED1=virtual-genomics&A=1

E-mail your questions to

Edward_Deckard@ndsu.nodak.edu

Willy_Valdivia@ndsu.nodak.edu

 

---


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Subject: Best way to pay your taxes                                                   [6wck9]
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                       CALL FOR POSTERS

    ------------------------------------------------------
                      *** ICSB 2001 ***

    The Second International Conference on Systems Biology
    ------------------------------------------------------

            The California Institute of Technology
                      Pasadena, CA, USA

                      November 4-7, 2001

                   http://www.icsb2001.org

    Poster abstract submission deadline: September 2, 2001

Systems Biology is the synergistic application of experiment,
theory and modeling towards understanding biological processes as
whole systems instead of isolated parts.  Understanding
biological processes from the systems perspective is an essential
cornerstone of a true understanding of biological function.

The Second International Conference on Systems Biology (ICSB2001)
will bring together researchers working in systems biology and
related areas to present the current status of their research and
to discuss future directions for the field.  This year, ICSB2001
will be held during November 4-7, 2001, at the California
Institute of Technology in Pasadena, California, USA.

The conference will begin with tutorials and workshops on the
morning of Sunday, November 4.  The formal scientific sessions
will begin on Monday, November 5, at 8:30 AM and end at noon on
Wednesday, November 7.  The sessions will feature keynote
speeches and invited presentations by world-renowned researchers,
along with afternoon poster sessions and evening social
activities.

KEYNOTE SPEAKERS
----------------

Dr. Alfred G. Gilman -- Nobel laureate and head of the Alliance
                        for Cellular Signaling

Dr. David Botstein   -- Chair of the Dept. of Genetics at Stanford

Dr. Adam Arkin       -- Assistant Professor of Biophysical Chemistry 
                        and Bioengineering at LBL/UCBerkeley

IMPORTANT DATES
---------------

Poster submission deadline:     Sep.   2, 2001
Tutorials                       Nov.   4, 2001
Technical sessions              Nov. 5-7, 2001

SUBMISSION INFORMATION
----------------------

With this announcement we solicit submissions of POSTER ABSTRACTS to
the meeting.  Relevant topics include (but are certainly not limited
to) the following:

  Experiment: 
    Quantitative behavioral measurements for systems biology 
    Quantitative microscopy and imaging methods 
    Metabolomic arrays 
    Gene expression arrays 
    Mass spectrometry 
    Pharmacological methods 
    In vitro reconstituted systems 
   
  Theory: 
    Metabolic control theory & biochemical systems theory 
    Biological engineering control theory 
    Stochastic and multiscale simulation 
    Robustness, modularity and evolvability 
    Network structure and dynamics 
    Spatiotemporal systems 
    Optimization methods 
    Bifurcation analysis 
  
  Modeling: 
    Modeling of gene, signal and metabolic networks 
    Novel computational algorithms 
    Software for system biology 
    Standards for systems biology 
    Databases for systems biology 
    Visualisation of networks and dynamics 
    Application of modeling to drug targeting 

Poster abstracts submitted by the deadline (September 2, 2001) to
the conference will be accepted and published in the proceedings
volume distributed at the conference.  The abstracts will also be
made available online at http://www.icsb2001.org prior the
conference.

Please visit the web site (http://www.icsb2001.org) or contact us
directly (icsb2001@caltech.edu) for information about format
requirements and submission procedure.

PROGRAM COMMITTEE
-----------------

John Doyle      -- California Institute of Technology
Mel Simon       -- California Institute of Technology
Hiroaki Kitano  -- ERATO Kitano Symbiotic Systems Project, JST, 
                   and The Systems Biology Institute

LOCAL ORGANIZING COMMITTEE
--------------------------

Tau-Mu Yi       -- Division of Biology, Caltech
Michael Hucka   -- Control and Dynamical Systems, Caltech
Herbert Sauro   -- Control and Dynamical Systems, Caltech
Mineo Morohashi -- ERATO Kitano Symbiotic Systems Project, JST

mailto:icsb2001@caltech.edu


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                       CALL FOR POSTERS

    ------------------------------------------------------
                      *** ICSB 2001 ***

    The Second International Conference on Systems Biology
    ------------------------------------------------------

            The California Institute of Technology
                      Pasadena, CA, USA

                      November 4-7, 2001

                   http://www.icsb2001.org

    Poster abstract submission deadline: September 2, 2001

Systems Biology is the synergistic application of experiment,
theory and modeling towards understanding biological processes as
whole systems instead of isolated parts.  Understanding
biological processes from the systems perspective is an essential
cornerstone of a true understanding of biological function.

The Second International Conference on Systems Biology (ICSB2001)
will bring together researchers working in systems biology and
related areas to present the current status of their research and
to discuss future directions for the field.  This year, ICSB2001
will be held during November 4-7, 2001, at the California
Institute of Technology in Pasadena, California, USA.

The conference will begin with tutorials and workshops on the
morning of Sunday, November 4.  Technical sessions will beginn
on Monday morning.  The sessions will feature keynote
speeches and invited presentations by world-renowned researchers,
along with afternoon poster sessions and evening social
activities.

KEYNOTE SPEAKERS
----------------

Dr. Alfred G. Gilman -- Nobel laureate and head of the Alliance
                        for Cellular Signaling

Dr. David Botstein   -- Chair of the Dept. of Genetics at Stanford

Dr. Adam Arkin       -- Assistant Professor of Biophysical Chemistry 
                        and Bioengineering at LBL/UCBerkeley

IMPORTANT DATES
---------------

Poster submission deadline:     Sep.   2, 2001
Tutorials                       Nov.   4, 2001
Technical sessions              Nov. 5-7, 2001

SUBMISSION INFORMATION
----------------------

With this announcement we solicit submissions of POSTER ABSTRACTS to
the meeting.  Relevant topics include (but are certainly not limited
to) the following:

  Experiment: 
    Quantitative behavioral measurements for systems biology 
    Quantitative microscopy and imaging methods 
    Metabolomic arrays 
    Gene expression arrays 
    Mass spectrometry 
    Pharmacological methods 
    In vitro reconstituted systems 
   
  Theory: 
    Metabolic control theory & biochemical systems theory 
    Biological engineering control theory 
    Stochastic and multiscale simulation 
    Robustness, modularity and evolvability 
    Network structure and dynamics 
    Spatiotemporal systems 
    Optimization methods 
    Bifurcation analysis 
  
  Modeling: 
    Modeling of gene, signal and metabolic networks 
    Novel computational algorithms 
    Software for system biology 
    Standards for systems biology 
    Databases for systems biology 
    Visualisation of networks and dynamics 
    Application of modeling to drug targeting 

Poster abstracts submitted by the deadline (September 2, 2001) to
the conference will be accepted and published in the proceedings
volume distributed at the conference.  The abstracts will also be
made available online at http://www.icsb2001.org prior the
conference.

Please visit the web site (http://www.icsb2001.org) or contact us
directly (icsb2001@caltech.edu) for information about format
requirements and submission procedure.

PROGRAM COMMITTEE
-----------------

John Doyle      -- California Institute of Technology
Mel Simon       -- California Institute of Technology
Hiroaki Kitano  -- ERATO Kitano Symbiotic Systems Project, JST, 
                   and The Systems Biology Institute

LOCAL ORGANIZING COMMITTEE
--------------------------

Tau-Mu Yi       -- Division of Biology, Caltech
Michael Hucka   -- Control and Dynamical Systems, Caltech
Herbert Sauro   -- Control and Dynamical Systems, Caltech
Mineo Morohashi -- ERATO Kitano Symbiotic Systems Project, JST

mailto:icsb2001@caltech.edu


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---


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Subject: GET RID OF YOUR DEBT - NOW and FOREVER!                                                   [97cxe]
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I would like a fast, simple and effective 3D molecular visualisation program for the PC, preferably
freeware. It's to help me visualise the molecules I am encountering in A-Level biology.

Any recommendations?

Thanks

Ben



From owner-molmodel@hgmp.mrc.ac.uk  Thu Aug 16 16:24:08 2001
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Ben Tristem wrote:
> 
> I would like a fast, simple and effective 3D molecular visualisation 
> program for the PC, preferably freeware. It's to help me visualise 
> the molecules I am encountering in A-Level biology.

A few choices;

Swiss PDB Viewer: 	Comprehensive package, with every viewing 
			option you could want (including stereo!), but a 
			bit of a steep learning curve;

			http://www.expasy.ch/spdbv/


Rasmol:			Very simple, very quick, easy to use for basic 
			visualisation.  No real accommodation for multiple
			structures, and many advanced features are through
			a command line interface.

			http://www.openrasmol.org/


Protein Explorer:	Web-based protein visualisation.  Simple interface
with 
			good basic viewing features.  Can load any file from the PDB
			and also from a load disk.  Requires the Chime plugin and 
			Netscape 4.x.

			http://www.umass.edu/microbio/chime/explorer/


Weblab Lite:		Free cut down version of Weblab viewer Pro.  Very pretty 
			graphics in real time, but only basic viualisation options.
			Needs you to register to download, but it's free once you've
			done that.
								http://www.accelrys.com/viewer/register/lite/viewerlite_reg.php


I'm sure that one of these should meet your needs!

	TTFN

	Simon.


From owner-molmodel@hgmp.mrc.ac.uk  Thu Aug 16 18:09:06 2001
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From: "Andrew Dalke" <dalke@acm.org>
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To add to Simon's list, here's two more structure visulization
programs that run under Windows (they also run under Unix).

VMD http://www.ks.uiuc.edu/Research/vmd/ - requires registration
MolMol http://www.mol.biol.ethz.ch/wuthrich/software/molmol/

                    Andrew




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Thanks guys, much appreciated.


"Andrew Dalke" <dalke@acm.org> wrote in message news:9lgtpv$410$1@slb7.atl.mindspring.net...
> To add to Simon's list, here's two more structure visulization
> programs that run under Windows (they also run under Unix).
>
> VMD http://www.ks.uiuc.edu/Research/vmd/ - requires registration
> MolMol http://www.mol.biol.ethz.ch/wuthrich/software/molmol/
>
>                     Andrew
>
>
>



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From owner-molmodel@hgmp.mrc.ac.uk  Thu Aug 16 23:53:52 2001
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As far as the viewing is concerned I'm very happy with WebLab ViewerLite. What would be the most
similar product for construction of the models?

Thanks

Ben


"Simon Andrews" <simon.andrews@bbsrc.ac.uk> wrote in message news:3B7BE304.B676E484@bbsrc.ac.uk...
> Ben Tristem wrote:
> >
> > I would like a fast, simple and effective 3D molecular visualisation
> > program for the PC, preferably freeware. It's to help me visualise
> > the molecules I am encountering in A-Level biology.
>
> A few choices;
>
> Swiss PDB Viewer: Comprehensive package, with every viewing
> option you could want (including stereo!), but a
> bit of a steep learning curve;
>
> http://www.expasy.ch/spdbv/
>
>
> Rasmol: Very simple, very quick, easy to use for basic
> visualisation.  No real accommodation for multiple
> structures, and many advanced features are through
> a command line interface.
>
> http://www.openrasmol.org/
>
>
> Protein Explorer: Web-based protein visualisation.  Simple interface
> with
> good basic viewing features.  Can load any file from the PDB
> and also from a load disk.  Requires the Chime plugin and
> Netscape 4.x.
>
> http://www.umass.edu/microbio/chime/explorer/
>
>
> Weblab Lite: Free cut down version of Weblab viewer Pro.  Very pretty
> graphics in real time, but only basic viualisation options.
> Needs you to register to download, but it's free once you've
> done that.
> http://www.accelrys.com/viewer/register/lite/viewerlite_reg.php
>
>
> I'm sure that one of these should meet your needs!
>
> TTFN
>
> Simon.



From owner-molmodel@hgmp.mrc.ac.uk  Fri Aug 17 01:38:54 2001
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On Thu, 16 Aug 2001 23:46:04 +0100, "Ben Tristem" <news@tristem.net>
wrote:

>As far as the viewing is concerned I'm very happy with WebLab ViewerLite. What would be the most
>similar product for construction of the models?

Are you talking about "small" organic molecules (not proteins)? If so,
use ChemSketch, from ACD Labs, which let's you draw a structure, and
convert it to the 3D. Don't need WebLab Viewer anymore.

Many many small molecules are available as pdb files. the Okanagan
collection is one excellent source, and probably includes much of what
you want for biol.

I have introductory pages for RasMol and ChemSketch (as well as Isis),
for my students. Suggest you start with the RasMol page, especially
the section on making your own structure files. The RasMol page also
contains the Okanagan address.

http://www.geocities.com/Athens/Thebes/5118/rasmol.htm

bob

posted/emailed


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Ben Tristem wrote:
> 
> As far as the viewing is concerned I'm very happy with WebLab ViewerLite. 
> What would be the most similar product for construction of the models?

Frankly, for the sort of molecules you're likely to come across in
A-level biology you shouldn't need to construct models.  Most common
biological small molecules have already been solved, along with most of
the common globular proteins (don't even bother looking for
transmembrane proteins though!).

A scout around some of the larger structure databases should get you all
the molecules you need.

Protein Database (contains all the released protein structures);
	http://www.rcsb.org/pdb/
	http://pdb-browsers.ebi.ac.uk//index.shtml

Small molecule databases
	http://triton.ps.toyaku.ac.jp/~dobashi/database/indexe.html
	http://alpha2.bmc.uu.se/hicup/
	http://www.ibc.wustl.edu/moirai/klotho/compound_list.html

I think you should find most of what you want in one of those.

	TTFN

	Simon.


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http://digilander.iol.it/biomed/



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From: =?iso-8859-1?Q?Rapha=EBl?= Chaleil <r.chaleil@icrf.icnet.uk>
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Subject: Re: Visualisation program
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There's no doubt, Rasmol is the one you need, providing you have the structures coordinates like PDB.
It is fast effective, very easy to use, totally free and available on most platforms.
Of course, there are hundreds different programs to visualise molecules but this one is the most
simple.

--
Raphael Chaleil
Biomolecular Modelling Laboratory
Imperial Cancer Research Fund
44, Lincoln's Inn Fields
WC2A3PX London
http://www.bmm.icnet.uk



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From owner-molmodel@hgmp.mrc.ac.uk  Mon Aug 20 09:54:30 2001
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From: Simon Andrews <simon.andrews@bbsrc.ac.uk>
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Subject: Re: Visualisation program
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Raphaλl Chaleil wrote:
> 
> There's no doubt, Rasmol is the one you need, providing you 
> have the structures coordinates like PDB.
> It is fast effective, very easy to use, totally free and 
> available on most platforms.
> Of course, there are hundreds different programs to visualise 
> molecules but this one is the most simple.

I think this is overstating the case for Rasmol a bit!  Whilst it has
its good points it also has it's limitations.  It has very poor support
for multiple structures (though some extension patches have been made to
partially fix this), and many of its more advanced functions are only
available through a command line interface - not the most user friendly
thing to use.  Also, it's graphics, whilst very quick and smooth even on
slow machines, are not particularly pretty in comparison to many more
recent programs.

Rasmol certainly used to be the automatic choice for this kind of
viewing a few years back, but there are several other strong competitors
in that field now. (Several of which have already been mentioned in this
thread).

	TTFN

	Simon.


From owner-molmodel@hgmp.mrc.ac.uk  Mon Aug 20 20:24:51 2001
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From: =?iso-8859-1?Q?Rapha=EBl?= Chaleil <r.chaleil@icrf.icnet.uk>
X-Newsgroups: bionet.molec-model
Subject: Re: Visualisation program
Date: Mon, 20 Aug 2001 21:11:06 +0200
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The question was about a freeware program to show biological molecules for A
level students. For sure Rasmol has a lot of limitations but frankly i'm
using it daily in my work when i want quick visualisation of structures, for
more advanced functions i use some other softwares, like SPDBV, Molmol, VMD,
Prepi or and some commercial softwares; but Rasmol is the best for basic
functions, i know many people hate the command line but it's really good and
in most cases the menu is sufficient.
May i suggest a program of my own for PC under win at
http://perso.infonie.fr/sphinx05/Resources/Telecharg/mv131.zip
it is not as fast as Rasmol, but is OpenGL based, and unfortunately the menu
options are in French.
I think Rasmol is really the best for basic use.
--
Raphael Chaleil
Biomolecular Modelling Laboratory
Imperial Cancer Research Fund
44, Lincoln's Inn Fields
WC2A3PX London
http://www.bmm.icnet.uk



From owner-molmodel@hgmp.mrc.ac.uk  Tue Aug 21 05:54:12 2001
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From: rathore@bloch.utmb.edu (Ravindranath Singh Rathore)
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I am trying to display molecular surface of a protein and color 
its hydrophobic residues on the surface.
does any one have an  idea, how to do it in GRASP or in any other surface 
representation program. Thanks.

Rathore, RNS 
Univ. Texas Medical Branch,    
Galveston, Texas

---


From owner-molmodel@hgmp.mrc.ac.uk  Tue Aug 21 18:39:09 2001
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From owner-molmodel@hgmp.mrc.ac.uk  Tue Aug 21 19:24:09 2001
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From: "Ben Tristem" <news@tristem.net>
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References: <997969098.663838@dionysos> <3B7E4EAA.302F9D6A@icrf.icnet.uk> <3B80CCC6.A91A3756@bbsrc.ac.uk> <3B8160C9.CA3AADC@icrf.icnet.uk>
Subject: Re: Visualisation program
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I'm probably being stupid here, but I can't see a stand-alone version of Protein explorer that I can
use on my PC without installing Netscape Navigator?

Thanks

Ben


"Raphaλl Chaleil" <r.chaleil@icrf.icnet.uk> wrote in message news:3B8160C9.CA3AADC@icrf.icnet.uk...
> The question was about a freeware program to show biological molecules for A
> level students. For sure Rasmol has a lot of limitations but frankly i'm
> using it daily in my work when i want quick visualisation of structures, for
> more advanced functions i use some other softwares, like SPDBV, Molmol, VMD,
> Prepi or and some commercial softwares; but Rasmol is the best for basic
> functions, i know many people hate the command line but it's really good and
> in most cases the menu is sufficient.
> May i suggest a program of my own for PC under win at
> http://perso.infonie.fr/sphinx05/Resources/Telecharg/mv131.zip
> it is not as fast as Rasmol, but is OpenGL based, and unfortunately the menu
> options are in French.
> I think Rasmol is really the best for basic use.
> --
> Raphael Chaleil
> Biomolecular Modelling Laboratory
> Imperial Cancer Research Fund
> 44, Lincoln's Inn Fields
> WC2A3PX London
> http://www.bmm.icnet.uk
>
>



From owner-molmodel@hgmp.mrc.ac.uk  Tue Aug 21 19:24:10 2001
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From: "Ben Tristem" <news@tristem.net>
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Subject: Re: Visualisation program
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I also should have made it clear that I need to be able to create simple structures (water to
glucose and the like) and preferably view them in one package.


"Ben Tristem" <news@tristem.net> wrote in message news:jAxg7.303456$Do6.12692145@nnrp4.clara.net...
> I'm probably being stupid here, but I can't see a stand-alone version of Protein explorer that I
can
> use on my PC without installing Netscape Navigator?
>
> Thanks
>
> Ben
>
>
> "Raphaλl Chaleil" <r.chaleil@icrf.icnet.uk> wrote in message
news:3B8160C9.CA3AADC@icrf.icnet.uk...
> > The question was about a freeware program to show biological molecules for A
> > level students. For sure Rasmol has a lot of limitations but frankly i'm
> > using it daily in my work when i want quick visualisation of structures, for
> > more advanced functions i use some other softwares, like SPDBV, Molmol, VMD,
> > Prepi or and some commercial softwares; but Rasmol is the best for basic
> > functions, i know many people hate the command line but it's really good and
> > in most cases the menu is sufficient.
> > May i suggest a program of my own for PC under win at
> > http://perso.infonie.fr/sphinx05/Resources/Telecharg/mv131.zip
> > it is not as fast as Rasmol, but is OpenGL based, and unfortunately the menu
> > options are in French.
> > I think Rasmol is really the best for basic use.
> > --
> > Raphael Chaleil
> > Biomolecular Modelling Laboratory
> > Imperial Cancer Research Fund
> > 44, Lincoln's Inn Fields
> > WC2A3PX London
> > http://www.bmm.icnet.uk
> >
> >
>
>



From owner-molmodel@hgmp.mrc.ac.uk  Wed Aug 22 08:54:06 2001
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From: Simon Andrews <simon.andrews@bbsrc.ac.uk>
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Subject: Re: Visualisation program
Date: Wed, 22 Aug 2001 08:38:56 +0100
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Ben Tristem wrote:
> 
> I'm probably being stupid here, but I can't see a stand-alone version of Protein > explorer that I can use on my PC without installing Netscape Navigator?

There's a good reason for that ;-)

There is a "stand alone" version of protein explorer, but it still runs
through Netscape.  It's a bit like downloading an html page to view
offline.  The downloaded version will be quicker, and means you don't
need to be online to use it.

If you don't have Netscape and Chime, you would need to install them
too.  This is because of the limited communications which are possible
between plug-ins (ie Chime) and Internet Explorer.

Simon.


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