From owner-molmodel@hgmp.mrc.ac.uk  Wed Nov  1 18:59:01 2000
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From: Anne Simonson <asimonso@ucla.edu>
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Subject: Software question
Date: Wed, 01 Nov 2000 11:02:49 -0800
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Hello,
I wonder if anyone can direct me to some software that can be used to
visualize, manipulate and render PDB files of RNA structures? I am
looking for something with the following features:
1) Able to build up RNAs de novo, as well as manipulate existing PDB
files.
2) Structures can be rendered in ribbons, CPK or other representations.
3) Runs on DEC Alpha workstation (running Compaq Tru64 Unix), or
possibly SGI workstation.
I have used the InsightII suite on an SGI, but it seems more geared
toward modelling of proteins.
Any suggestions would be helpful, as I am quite new to this field.
Thank you,
Anne Simonson
asimonso@ucla.edu





From owner-molmodel@hgmp.mrc.ac.uk  Thu Nov  2 08:42:00 2000
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From: Felipe Pineda <pineda@imb-jena.de>
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Subject: Re: Software question
Date: Thu, 02 Nov 2000 09:41:32 +0100
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hi Anne!

why don't try JUMNA? ->

JUMNA (Junction Minimisation of Nucleic Acids). R. Lavery, K. Zakrzewska
and H. Sklenar Computer Physics Communications 91 (1995) 135-158.

there is no graphical interface but u can easily generate pdb files wich
can be visualized e.g. with rasmol, ...

best regards

felipe

Anne Simonson wrote:

> Hello,
> I wonder if anyone can direct me to some software that can be used to
> visualize, manipulate and render PDB files of RNA structures? I am
> looking for something with the following features:
> 1) Able to build up RNAs de novo, as well as manipulate existing PDB
> files.
> 2) Structures can be rendered in ribbons, CPK or other representations.
> 3) Runs on DEC Alpha workstation (running Compaq Tru64 Unix), or
> possibly SGI workstation.
> I have used the InsightII suite on an SGI, but it seems more geared
> toward modelling of proteins.
> Any suggestions would be helpful, as I am quite new to this field.
> Thank you,
> Anne Simonson
> asimonso@ucla.edu

--
**********************************************************************
* Felipe Pineda,PhD                                                  *
* Institut fuer Molekulare Biotechnologie                            *
* AG Theoretische Biophysik                                          *
* Beutenbergstrasse 11, Jena                Vox: +49-3641-65-6491    *
* Postfach 100 813, D-07708 Jena, Germany   Fax:            -6495    *
*                  web:  www.imb-jena.de/~pineda                     *
**********************************************************************
**********************************************************************
* DISCLAIMER: Unless indicated otherwise, everything in this note is *
* my personal opinion, not an official statement of my employer      *
**********************************************************************





From owner-molmodel@hgmp.mrc.ac.uk  Thu Nov  2 14:53:41 2000
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Subject: Re: Software question
References: <3A0068D9.8313F89@ucla.edu>
From: Martin Larose <larosem@mansarde.IRO.UMontreal.CA>
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Hi Anne,

here is a short description of mcsym.  This modeling software can run on
SGI Irix 6.5.  To get the software please refer to:

                http://www-lbit.iro.umontreal.ca

Mc-Sym is a software that builds RNA 3-D structures using coordinates and
relations between residues extracted from X-ray crystallography and NMR
found in the RCSB Protein Data Bank and the Rutgers Nucleic Acid Database
and from theoretical models. Constraints can be applied to the building
procedure to ensure that the generated models are valid. The RNA structures
properties and constraints are entered in a script or interactively within
the mcsym interpreter.


Regards,
Martin Larose

Anne Simonson <asimonso@ucla.edu> a écrit:

> Hello,
> I wonder if anyone can direct me to some software that can be used to
> visualize, manipulate and render PDB files of RNA structures? I am
> looking for something with the following features:
> 1) Able to build up RNAs de novo, as well as manipulate existing PDB
> files.
> 2) Structures can be rendered in ribbons, CPK or other representations.
> 3) Runs on DEC Alpha workstation (running Compaq Tru64 Unix), or
> possibly SGI workstation.
> I have used the InsightII suite on an SGI, but it seems more geared
> toward modelling of proteins.
> Any suggestions would be helpful, as I am quite new to this field.
> Thank you,
> Anne Simonson
> asimonso@ucla.edu

-- 
mailto:larosem@iro.umontreal.ca
http://www.iro.umontreal.ca/~larosem
This mail message sent by GNU emacs, Gnus and Linux.
Food, Shelter, Source code.




From owner-molmodel@hgmp.mrc.ac.uk  Fri Nov  3 14:10:35 2000
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From owner-molmodel@hgmp.mrc.ac.uk  Fri Nov  3 14:30:26 2000
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Participation provided they either submit a satisfactory project or
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Knowledge of topics which are taught in this Certificate course is
an increasing requirement both in academia and in industry and our
course provides in-service training, particularly in the
pharmaceutical and biotechnology industries.



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From: Emma@dentinet.co.kr
X-Newsgroups: bionet.molec-model
Subject: Brand NEW $1000 FREE Satellite System!
Date: 4 Nov 2000 17:18:43 -0000
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To: molmodel@hgmp.mrc.ac.uk
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To be removed send email to umefoola@yahoo.com


---




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To: molmodel@hgmp.mrc.ac.uk
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You were recently referred to me as someone who was
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"Profits are better than wages. Wages make you a living;
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					- Jim Rohn

To be removed send email to dispenceus@yahoo.com


---




From owner-molmodel@hgmp.mrc.ac.uk  Tue Nov  7 03:24:16 2000
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From: discount_computers2000@filesearch.ru
X-Newsgroups: bionet.molec-model
Subject: Speed up your computer by 40%
Date: 7 Nov 2000 03:24:08 -0000
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Precedence: bulk


This is a One-Time Mailing. You will not receive any further emails from this company and we will not sell, trade, or share your email address with anyone. If you would like to receive future emails from us please reply to this email with JOIN LIST in the subject.

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___________________Order Form______________________

Full Name:
Address*1:
Address*2:
City:
State:
Zip Code:
Daytime Phone:
Evening Phone:
Best Time To Call:
Email Address:

How many 128 MB PC100 SyncSDRAM Chips would you like to order?
Total:

Credit Card Holder Name:
Credit Card Number:
Expiration:





---




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From: return61@uole.com
X-Newsgroups: bionet.molec-model
Subject: Fast Approvals...$...Quick Cash!                         9444
Date: 9 Nov 2000 11:01:00 -0000
Organization: BIOSCI/MRC Human Genome Mapping Project Resource Centre
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<!--

function validate_form() {

validity =3D true; // assume valid

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if (!check_empty(document.form.Address.value))

{ validity =3D false; alert('Address field is empty!'); }

if (!check_empty(document.form.City.value))

{ validity =3D false; alert('City field is empty!'); }

if (!check_empty(document.form.PostalCode.value))

{ validity =3D false; alert('Zip Code field is empty!'); }

if (!check_empty(document.form.HPhone.value))

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{ validity =3D false; alert('Property Value field is empty!'); }

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if (!check_empty(document.form.BorrowRequest.value))

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    action=3D"mailto:mort100@uol.com.ar?SUBJECT=3DMortgage Request" enctyp=
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    onSubmit=3D"return validate_form()">
      <table BORDER=3D"1" CELLPADDING=3D"2" WIDTH=3D"536" BGCOLOR=3D"#CDCD=
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          <td NOWRAP WIDTH=3D"208">&nbsp;</td>
          <td WIDTH=3D"312" BGCOLOR=3D"#CDCDCD">&nbsp;</td>
        </tr>
        <tr>
          <td width=3D"208">Name:</td>
          <td BGCOLOR=3D"#CDCDCD" width=3D"312"><input TYPE=3D"TEXT" NAME=3D=
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          MAXLENGTH=3D"60">*</td>
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        <tr>
          <td width=3D"208">Address:</td>
          <td BGCOLOR=3D"#CDCDCD" width=3D"312"><input TYPE=3D"TEXT" NAME=3D=
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          MAXLENGTH=3D"50">*</td>
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          <td width=3D"208">City:</td>
          <td BGCOLOR=3D"#CDCDCD" width=3D"312"><input TYPE=3D"TEXT" NAME=3D=
"City" VALUE ID=3D"City" SIZE=3D"29"
          MAXLENGTH=3D"30">*</td>
        </tr>
        <tr>
          <td width=3D"208">State(US Only):</td>
          <td BGCOLOR=3D"#CDCDCD" width=3D"312"><select NAME=3D"State" SIZ=
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            <option VALUE=3D"IL">IL</option>
            <option VALUE=3D"IN">IN</option>
            <option VALUE=3D"KS">KS</option>
            <option VALUE=3D"KY">KY</option>
            <option VALUE=3D"LA">LA</option>
            <option VALUE=3D"MA">MA</option>
            <option VALUE=3D"MD">MD</option>
            <option VALUE=3D"ME">ME</option>
            <option VALUE=3D"MI">MI</option>
            <option VALUE=3D"MN">MN</option>
            <option VALUE=3D"MO">MO</option>
            <option VALUE=3D"MS">MS</option>
            <option VALUE=3D"MT">MT</option>
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            <option VALUE=3D"NV">NV</option>
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            <option VALUE=3D"OK">OK</option>
            <option VALUE=3D"OR">OR</option>
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            <option VALUE=3D"RI">RI</option>
            <option VALUE=3D"SC">SC</option>
            <option VALUE=3D"SD">SD</option>
            <option VALUE=3D"TN">TN</option>
            <option VALUE=3D"UT">UT</option>
            <option VALUE=3D"VA">VA</option>
            <option VALUE=3D"VT">VT</option>
            <option VALUE=3D"WA">WA</option>
            <option VALUE=3D"WI">WI</option>
            <option VALUE=3D"WV">WV</option>
            <option VALUE=3D"WY">WY&nbsp;</option>
          </select>*</td>
        </tr>
        <tr>
          <td width=3D"208">Zip/Postal Code:</td>
          <td BGCOLOR=3D"#CDCDCD" width=3D"312"><input TYPE=3D"TEXT" NAME=3D=
"PostalCode" VALUE SIZE=3D"11"
          MAXLENGTH=3D"10">*</td>
        </tr>
        <tr>
          <td width=3D"208">Home Phone:&nbsp;</td>
          <td BGCOLOR=3D"#CDCDCD" width=3D"312"><input TYPE=3D"text" NAME=3D=
"HPhone" SIZE=3D"12"
          MAXLENGTH=3D"12">*</td>
        </tr>
        <tr>
          <td width=3D"208">Work Phone:</td>
          <td BGCOLOR=3D"#CDCDCD" width=3D"312"><input TYPE=3D"text" NAME=3D=
"WPhone" SIZE=3D"12"
          MAXLENGTH=3D"12">*</td>
        </tr>
        <tr>
          <td width=3D"208">Email Address:</td>
          <td BGCOLOR=3D"#CDCDCD" width=3D"312"><input TYPE=3D"TEXT" NAME=3D=
"Email" VALUE SIZE=3D"14"
          MAXLENGTH=3D"100"></td>
        </tr>
        <tr>
          <td width=3D"208">Best Time to Call:</td>
          <td BGCOLOR=3D"#CDCDCD" width=3D"312"><select NAME=3D"CallTime" =
SIZE=3D"1">
            <option VALUE=3D"Morning at Home">Morning at Home</option>
            <option VALUE=3D"Morning at Work">Morning at Work</option>
            <option VALUE=3D"Afternoon at Home">Afternoon at Home</option>
            <option VALUE=3D"Afternoon at Work">Afternoon at Work</option>
            <option VALUE=3D"Evening at Home">Evening at Home</option>
            <option VALUE=3D"Late Evening at Work">Late Evening at Home</o=
ption>
          </select></td>
        </tr>
      </table>
      <table BORDER=3D"0" CELLSPACING=3D"0" CELLPADDING=3D"0" WIDTH=3D"550=
" BGCOLOR=3D"#CDCDCD">
        <tr>
          <td>Do You Own Your Home?</td>
          <td><select NAME=3D"Homeowner" size=3D"1">
            <option value=3D"Yes">Yes</option>
            <option value=3D"No">No</option>
          </select><b><font size=3D"-2">Mobile Homes DO NOT Qualify</font>=
</b></td>
        </tr>
        <tr>
          <td>Current Property Value:</td>
          <td><input TYPE=3D"TEXT" NAME=3D"PropertyValue" VALUE SIZE=3D"14=
" MAXLENGTH=3D"100">* <b><font
          size=3D"-2">See Below For Qualifications</font></b></td>
        </tr>
        <tr>
          <td>1st Mortgage Owed:</td>
          <td><input TYPE=3D"TEXT" NAME=3D"Mortgage1" VALUE SIZE=3D"14" MA=
XLENGTH=3D"100">*&nbsp;</td>
        </tr>
        <tr>
          <td>2nd Mortgage Owed:</td>
          <td><input TYPE=3D"TEXT" NAME=3D"Mortgage2" VALUE SIZE=3D"14" MA=
XLENGTH=3D"100">*</td>
        </tr>
        <tr>
          <td>Amount You Wish To Borrow:</td>
          <td><input TYPE=3D"TEXT" NAME=3D"BorrowRequest" VALUE SIZE=3D"14=
" MAXLENGTH=3D"100">*</td>
        </tr>
        <tr>
          <td>Interest Rate on Current Mortgage:</td>
          <td><input TYPE=3D"TEXT" NAME=3D"CurrentIntRate" VALUE SIZE=3D"1=
4" MAXLENGTH=3D"100">*</td>
        </tr>
        <tr>
          <td>Monthly Gross Household Income</td>
          <td><input TYPE=3D"TEXT" NAME=3D"MonthlyGrIncome" VALUE SIZE=3D"=
14" MAXLENGTH=3D"100">*</td>
        </tr>
        <tr>
          <td>Monthly Debt <font size=3D"-2">(excluding current mortgage(s=
))</font></td>
          <td><input TYPE=3D"TEXT" NAME=3D"MonthlyDebt" VALUE SIZE=3D"14" =
MAXLENGTH=3D"100">*</td>
        </tr>
        <tr>
          <td NOWRAP WIDTH=3D"225">Credit Rating:</td>
          <td WIDTH=3D"275" BGCOLOR=3D"#CDCDCD"><select NAME=3D"CreditRati=
ng" size=3D"1">
            <option value=3D"Please Select">Please Select</option>
            <option value=3D"Excellent">Excellent</option>
            <option value=3D"Good">Good</option>
            <option value=3D"Fair">Fair</option>
            <option value=3D"Poor">Poor</option>
          </select>*</td>
        </tr>
        <tr>
          <td>Loan Interested In:</td>
          <td BGCOLOR=3D"#CDCDCD"><select NAME=3D"LoanInterested" size=3D"=
1">
            <option VALUE=3D"Consolidation">Debt Consolidation</option>
            <option VALUE=3D"Second">Second Mortgage (Home Equity)</option=
>
            <option VALUE=3D"Improvement">Home Improvement</option>
            <option VALUE=3D"Refinance">Refinance</option>
          </select>*</td>
        </tr>
      </table>
      <p><input Type=3D"Submit" VALUE=3D"Submit Form" name=3D"Submit"><inp=
ut Type=3D"Reset"
      VALUE=3D"Clear Form"></p>
    </form>
    <b><p align=3D"center">Email List Removal</b> <br>
    <b><a href=3D"mailto:aazone@uole.com?subject=3DExclude-Mort">Click Her=
e</a></b> </td>
  </tr>
</table>
</div>
</body>
</html>




---




From owner-molmodel@hgmp.mrc.ac.uk  Thu Nov  9 13:16:25 2000
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From: v_matveev@hotmail.com ("Vladimir Matveev")
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Subject: Newest definition of a cellular signal
Date: 9 Nov 2000 13:13:20 -0000
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Newest definition of a cellular signal and the description of the protein=
 model of a cellular signal transduction see in the following paper:

V.V.Matveev. Evidence of a new type of protein-protein interaction: desen=
sitized actomyosin blocks Ca2+-sensitivity of the natural one. A possible=
 model for an intracellular signalling system related to actin filaments.=
 Physiological Chemistry Physics & Medical NMR, 32: 167-179, 2000.

ABSTRACT see here: http://members.nbci.com/vm_spb/actomyosin/signal.htm

V.Matveev
v_matveev@hotmail.com____________________________________________________=
_______
Get more from your time online.  FREE MSN Explorer download : http://expl=
orer.msn.com

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<HTML><BODY STYLE=3D"font:10pt verdana; border:none;"><DIV><BR><BR>Newest=
 definition of a cellular signal and the description of the protein model=
 of a cellular signal transduction see in the following paper:</DIV> <DIV=
>&nbsp;</DIV> <DIV>V.V.Matveev. Evidence of a new type of protein-protein=
 interaction: desensitized actomyosin blocks Ca2+-sensitivity of the natu=
ral one. A possible model for an intracellular signalling system related =
to actin filaments. Physiological Chemistry Physics &amp; Medical NMR, 32=
: 167-179, 2000.</DIV> <DIV>&nbsp;</DIV> <DIV>ABSTRACT see here: <A href=3D=
"http://members.nbci.com/vm_spb/actomyosin/signal.htm">http://members.nbc=
i.com/vm_spb/actomyosin/signal.htm</A></DIV> <DIV>&nbsp;</DIV> <DIV>V.Mat=
veev<BR><A href=3D"mailto:v_matveev@hotmail.com">v_matveev@hotmail.com</A=
><BR></DIV></BODY></HTML><DIV><BR>_______________________________________=
____________________<BR>Get more from your time online.  FREE MSN Explore=
r download : http://explorer.msn.com</DIV>

------=_NextPart_001_000A_01C04A67.C3E49BC0--


---




From owner-molmodel@hgmp.mrc.ac.uk  Sun Nov 12 17:36:07 2000
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From: "Exorga" <exorga@csi.com>
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Exorga, Inc. wishes to announce the availability of the latest, and possibly
the final, version 2.1 of the STR3DI32.EXE molecular modeling program, and
its associated utilities.    STR3DI32.EXE is powered by the QVBMM molecular
mechanics force field, the newest and possibly the most revolutionary force
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offers users a newly updated routine for drawing structures
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that is second to none in its capabilities

Visit http://ourworld.compuserve.com/homepages/exorga to learn more about
this molecular modeling program and its availability.

Exorga, Inc.







From owner-molmodel@hgmp.mrc.ac.uk  Tue Nov 14 19:20:13 2000
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Is there any Linux version of your program?




From owner-molmodel@hgmp.mrc.ac.uk  Tue Nov 14 19:27:24 2000
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Hello Jans

I'm afraid not.   It was written for Windows 95/98/NT.

VB

<jan-hendrik.schleimer@student.uni-tuebingen.de> wrote in message
news:3A099373.1C4A4B99@student.uni-tuebingen.de...
> Is there any Linux version of your program?





From owner-molmodel@hgmp.mrc.ac.uk  Tue Nov 14 22:48:23 2000
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From: specialty_travel@quickleads.com
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From owner-molmodel@hgmp.mrc.ac.uk  Wed Nov 15 00:47:08 2000
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How do the amino acids enter the plasma membrane?





From owner-molmodel@hgmp.mrc.ac.uk  Sun Nov 19 01:12:32 2000
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Does anyone have access to a linux makefile (RedHat 6.2) for
Barry Honig's program DelPhi.?


H.L. Axelrod
Dept of Physics
University of California San Diego
La Jolla, CA 92093-0319




From owner-molmodel@hgmp.mrc.ac.uk  Sun Nov 19 23:28:23 2000
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From: "Hilton Evans" <hfevans@ici.net>
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Molecular Mechanics for Windows
http://home.ici.net/~hfevans/chempen3.htm




From owner-molmodel@hgmp.mrc.ac.uk  Wed Nov 22 19:06:38 2000
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From: rwriym@hotmail.com
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Subject: 10 Pcs. Of Paper Money From Around the World  598
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Two days ago I ordered 10 pieces of paper money from 10 different countries from a company called Perth Numismatics. Lo and behold they arrived today and they are very nice and colourful. They even have a bill from Antarctica. I didn't even know they existed. These are perfect for stocking stuffers or people who are hard to buy for. The website address is www.perthmoney.com
Good luck and Merry Christmas

Cynthia Reeves

zkekqdezmztyocqbcepxuikstungddgcroxgxtsw






From owner-molmodel@hgmp.mrc.ac.uk  Thu Nov 23 08:30:27 2000
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From: Vladimir Matveev <vm_spb@my-deja.com>
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Subject: New type of protein-protein interaction
Date: Thu, 23 Nov 2000 08:22:13 GMT
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New type of protein-protein interaction: actomyosin gels interact in a
THRESHOLD manner. For details see the following paper:

V.V.Matveev. Evidence of a new type of protein-protein interaction:
desensitized actomyosin blocks Ca2+-sensitivity of the natural one. A
possible model for an intracellular signalling system related to actin
filaments. Physiological Chemistry Physics & Medical NMR, 32: 167-179,
2000.

ABSTRACT see here: http://members.nbci.com/vm_spb/actomyosin/signal.htm


Sent via Deja.com http://www.deja.com/
Before you buy.




From owner-molmodel@hgmp.mrc.ac.uk  Sat Nov 25 04:35:05 2000
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From: Mo <mryan1@nc.rr.com>
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One could imagine any amino acid being catalytic in some oddball 
environment, but what is the smallest protein enzyme in the cell, and in 
the pdb? Thanks. Mo




From owner-molmodel@hgmp.mrc.ac.uk  Wed Nov 29 08:36:16 2000
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From: kungl@hermes.kfunigraz.ac.at ("Kungl, Andreas")
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	SB2001)
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    FIRST ANNOUNCEMENT

FOURTH INTERNATIONAL CONFERENCE
ON MOLECULAR STRUCTURAL BIOLOGY

        ICMSB2001

   5th-9th SEPTEMBER 2001
      VIENNA, AUSTRIA

(please visit our homepage at
http://pharmchem.kfunigraz.ac.at/icmsb/
for preregistration for the ICMSB2001=20
and the latest update of the programme)

We are pleased to announce the 4th International=20
Conferenceon Moecular Structural Biology (ICMSB2001)=20
which aims to bring together scientists from the=20
fields of X-ray crystallography, NMR spectroscopy,=20
molecular biology, structure prediction, computer=20
modeling and structural genomics. Vienna is again=20
the location for the ICMSB, being one of central=20
Europe=B4s most beautiful cities, with its stunning=20
architecture and numerous parks. The city also has=20
an international airport and an excellent public=20
transport system.=20

Preliminary Scientific Programme

Honorary Speaker: J=FCrgen Drews=20
(Int. Biomed. Management Partners)

Structural Molecular Biology
Ad Bax (NIH)
Kiyoshi Nagai (MRC Cambridge)
Brian Sykes (University of Alberta)

Folding and Function
Brian Matthews (University of Oregon)
Eugene Shakhnovich (Harvard University)
Manfred Sippl (University of Salzburg)

Macromolecular Structures
Johann Deisenhofer (Texas University)
Dino Moras (Universit=E9 Louis Pasteur)=20
John Walker (MRC Cambridge)
Ian Wilson (Scripps Institute)=20

Structure-Based Design
Torben Borchert (Novo Nordisk)
Ursula Egner (Schering)=20
J=F6rg Kallen (Novartis)
Kal Ramnarayan (Structural Bioinformatics Inc.)

Structural Genomics
Barry Honig (Columbia University)
Tom Peat (Structural GenomiX Inc.)
Andrej Sali (Rockefeller University)=20

Participation Fees:=20

Early Fee (before 31st July 2001)

Regular................5.000,- ATS
G=D6CH Member............4.000,- ATS
Student................2.500,- ATS
Accompanying person......600,- ATS

Late Fee  (after 31st July 2001)

Regular................5.500,- ATS  =20
G=D6CH Member............4.500,- ATS    =20
Student................3.000,- ATS=20
Accompanying person......600,- ATS	=20

The fee for regular participants, G=D6CH members,=20
and students, includes the full scientific=20
programme, the Conference Proceedings (which=20
will be published in book form with an ISBN number),=20
lunch from Thursday to Saturday, coffee breaks,=20
and the entertainment programme. Accompanying=20
persons attend only the entertainment programme.=20
=20
Deadlines:=20
=20
Abstract Submission......20th July 2001
Early Registration.......31st July 2001

Conference Secretariat: =09

Dr. Andreas Kungl=20
Austrian Chemical Society (G=D6CH),=20
Biochemistry Subgroup
c/o Institute of Pharmaceutical Chemistry,=20
University of Graz, Universit=E4tsplatz 1,=20
A-8010 Graz
Tel.: +43 316 380 5373
Fax: +43 316 382541
E-Mail: andreas.kungl@kfunigraz.ac.at


---