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Dear all:
We have 3 superimposed protein conformations and we would need to
calculate the RMS deviation between pairs of residues. Any idea?
Thank you so much in advance for the reply.
Regards,

-------------------------------------------------------------------------
   Mario Garcia de Lacoba, PhD.       Phone   : +341 915611800 (ext.4334)
                                      Fax     : +341 915627518
Centro de Investigaciones Biologicas  E-mail  : mario@cib.csic.es
              C.S.I.C.
          c/ Velazquez, 144                 BIOINFORMATIC UNIT
         28006-Madrid. SPAIN.      
-------------------------------------------------------------------------



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From owner-molmodel@hgmp.mrc.ac.uk  Mon Aug  7 12:23:33 2000
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Mario Garcia wrote:
> 
> Dear all:
> We have 3 superimposed protein conformations and we would need to
> calculate the RMS deviation between pairs of residues. Any idea?
> Thank you so much in advance for the reply.

Swiss PDB viewer (www.expasy.ch/spdbv) can certainly do this.  Simply
select the residues you wish to compare, then use Tools -> Calculate
RMS.  I imagine most modelling programs have a similar facility.

Simon.




From owner-molmodel@hgmp.mrc.ac.uk  Tue Aug  8 23:32:31 2000
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From: Anne Simonson <asimonso@ucla.edu>
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I am new to the field of molecular modeling, and would like some
advice.  Does anyone have recommendations for software that can be used
to model RNA-RNA interactions as well as protein-nucleic acid
interactions?  I appreciate any help you can give.
Thank you,
asimonso@ucla.edu

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From owner-molmodel@hgmp.mrc.ac.uk  Wed Aug  9 17:07:34 2000
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Hi Anne,
	you'll probably want to have a look at NAMOT  (http://namot.lanl.gov/)
and NAB (http://www.scripps.edu/case/casegr-sh-2.2.html) for building
and visualising and there are a load of programs aorund for calculating
interaction energies (CHARMm, AMBER, NAMD. Just do a 'net search on
these terms and you'll find the relevent sites easily).
	RNA isn't an easy system to work with computationally due to the large
charge associated with these systems (also DNA) and the high flexibility
of the structures. You should read up on energy calculations and
simulations using solvent and counter-ions and also on techniques
involving 'particle mesh Ewald summations' (sounds horrid, I know...!).
	Have fun,

Mike




From owner-molmodel@hgmp.mrc.ac.uk  Wed Aug  9 19:10:33 2000
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THanks, Mike!  I appreciate your input.
--Anne

Mike Tennant wrote:

> Hi Anne,
>         you'll probably want to have a look at NAMOT  (http://namot.lanl.gov/)
> and NAB (http://www.scripps.edu/case/casegr-sh-2.2.html) for building
> and visualising and there are a load of programs aorund for calculating
> interaction energies (CHARMm, AMBER, NAMD. Just do a 'net search on
> these terms and you'll find the relevent sites easily).
>         RNA isn't an easy system to work with computationally due to the large
> charge associated with these systems (also DNA) and the high flexibility
> of the structures. You should read up on energy calculations and
> simulations using solvent and counter-ions and also on techniques
> involving 'particle mesh Ewald summations' (sounds horrid, I know...!).
>         Have fun,
>
> Mike




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From owner-molmodel@hgmp.mrc.ac.uk  Fri Aug 11 22:23:01 2000
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Mike Tennant <tennant@mh.uk.sbphrd.com> writes:

> Hi Anne, you'll probably want to have a look at NAMOT
> (http://namot.lanl.gov/) and NAB
> (http://www.scripps.edu/case/casegr-sh-2.2.html) for building

I am totally biased in that suggestion, but depending on the specific
project (i missed the initial post!), I would strongly recommand to
give MCSYM a try.

Web site for 3.0 beta version: 
  http://www-lbit.iro.umontreal.ca/mcsym/mcsym-3.0.shtml

Information about obtaining the current release:
  mailto:larosem@iro.umontreal.ca

I'd be happy to discuss any problem/question about the program or
general approach...

-- 
------------------ Sebastien Lemieux, Microbio/CS -------------------
	     Breaking the Second Half of the Genetic Code

  cggacacaca aaaagaaaga agaattttta ggatcttttg tgtgcgaata actatgagga




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From owner-molmodel@hgmp.mrc.ac.uk  Wed Aug 16 23:20:43 2000
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From: Anne Simonson <asimonso@ucla.edu>
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References: <39907E7F.811E9C01@ucla.edu> <3991668F.DF430DCF@mh.uk.sbphrd.com> <yatvgx75w7k.fsf@inox.IRO.UMontreal.CA>
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Thank you for your suggestion, also, Sebastian.
--Anne Simonson
asimonso@ucla.edu





From owner-molmodel@hgmp.mrc.ac.uk  Tue Aug 22 18:33:42 2000
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From: Lothar Esser <esser@chop.swmed.edu>
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Lothar Esser wrote:

> Dear Colleagues,
>
>    a new version of glr is now available via anonymous ftp:
> ftp://hhmi.swmed.edu/glr/glr.tar.gz
>

    Sorry that is :
ftp://hhmi.swmed.edu/pub/glr/glr.tar.gz

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Lothar Esser wrote:
<blockquote TYPE=CITE>Dear Colleagues,
<p>&nbsp;&nbsp; a new version of glr is now available via anonymous ftp:
<br><a href="ftp://hhmi.swmed.edu/glr/glr.tar.gz">ftp://hhmi.swmed.edu/glr/glr.tar.gz</a>
<br>&nbsp;</blockquote>
&nbsp;&nbsp;&nbsp; Sorry that is :
<br><a href="ftp://hhmi.swmed.edu/glr/glr.tar.gz">ftp://hhmi.swmed.edu/pub/glr/glr.tar.gz</a></html>

--------------2C0C84D6FF14BD04CD82F80C--




From owner-molmodel@hgmp.mrc.ac.uk  Tue Aug 22 18:33:42 2000
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From: Lothar Esser <esser@chop.swmed.edu>
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Dear Colleagues,

   a new version of glr is now available via anonymous ftp:
ftp://hhmi.swmed.edu/glr/glr.tar.gz

 glr is the successor of gl_render.

  Please feel free to contact me  if you have any problems
(installation, use etc.) at
  esser@chop.swmed.edu

   Lothar Esser




From owner-molmodel@hgmp.mrc.ac.uk  Tue Aug 29 18:13:21 2000
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Reply-To: "Larry \"Harris\" Taylor" <divegeek@earthlink.net>
From: "Larry \"Harris\" Taylor" <divegeek@earthlink.net>
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Subject: Need Help with WHATIF in WIndows 98
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I am trying to run WHATIF under a windows 98 SE environment using Exceed 6.2
as an interface. Windows and Exceed have latest updates according to
vendor's web sites.


Both programs reside on the same computer.

Exceed is in c:\program files\exceed

Whatif is in c:\whatif



Both programs report successful install.

Exceed is functioning with respect to running remote hosts.


Setting exceed to local host:


If I run DO_WHATIF

the program appears to start, but stays within a DOS window ...

execution terminates with a c:> WHATIF prompt, but also

has the following error messages directly above the prompt

c-inittext could not open message file '/dbdata/messages.txt
possible configuration error in DO_WHATIF.com, whatif.fig or configf1.fig



If I attempt to run Whatif

I get the error message:

cannot find cygwin1.dll


The files that WHATIF cannot find are present in default installed
locations.


I have tried adding c:\whatif and c:\whatif\cgyusr  to the path command in
the autoexec.bat file and it has had no effect.


There appears to be a problem in getting WHATIF to export its output to
xterminal display
(Display has been set to localhost by vendor install config files)

Any thoughts on configuring WHATIF to find cgywin1.dll ? and to run via
Exceed under Windows98?


Thanks

Larry Taylor

lpt@umich.edu