°¤ø,¸¸,ø¤°`´°¤ø,¸¸,ø¤°`´°¤ø,¸¸,ø¤°`´°¤ø,¸¸,ø¤°`´°¤ø,¸¸,ø¤°`
//=\Mr. Lee R. Cooper Bsc(Hons) MSc, Parallel, Emergent//=\evolution,
\=//& Distributed Architechture Laboratory, Dept. of \=//creationists
//=\Comp. Science, University of Reading, Whiteknights //=\have argued,
\=//PoBox 225, Reading, Berkshire. RG6 6AY (UK) \=/was as likely
//=\Tel +44 (0)118 987 5123 x7645 (0915-1700)|Fax //=to have made
\=//Tel +44 (0)118 931 8188 x7817 (1900-2300)|0118 975 \=//man as a
//=\http://www.rdg.ac.uk/~ssr97lrc/ 1994 //=\monkey...,
°¤ø,¸¸,ø¤°`´°¤ø,¸¸,ø¤°`´°¤ø,¸¸,ø¤°`´°¤ø,¸¸,ø¤°`´°¤ø,¸¸,ø¤°`
randomly typing the bible without error. with natural selection acting
as an eraser of mistakes; assuming thirteen mistakes for every correct
character & a rate of 1 keystroke per second, the 6 million characters
of the holy script could be typed in 13x6e6 s, or <3 yrs.
-------------- next part --------------
From l.r.cooper at reading.ac.uk Fri May 14 11:35:18 1999
Date: Fri, 14 May 1999 11:36:20 +0100
From: "l.r.cooper" <l.r.cooper at reading.ac.uk>
To: CHEMISTRY at ccl.net
Cc: ssr97lrc at reading.ac.uk
Subject: Summary PDB superposition and RMS
[The following text is in the "iso-8859-1" character set]
[Your display is set for the "US-ASCII" character set]
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Dear Lee,
This question had also been posted several years
ago, and I enclose the response received in that
time, together with a useful piece of software.
Regards.
Jose I. Garcia
From:
"Rino Ragno (uniroma1.it)" <ragno at uniroma1.it>
To:
"l.r.cooper" <ssr97lrc at reading.ac.uk>
Hi,
PROFIT 17 does what you are looking for, have a look at:
www.biochem.ucl.ac.uk/~martin/programs/index.html
Ciao
From:
Paul at pdchem.demon.co.uk (Paul Davis)
To:
ssr97lrc at reading.ac.uk
Dear Lee,
Unless you are looking at different conformations of the
same molecule, this is not a trivial problem because you
have to decide which atoms in each molecule have to be
equivalenced.
Here are two suggestions.
1) ProFit by Andrew Martin is an excellent, flexible program.
http://www.biochem.ucl.ac.uk/~martin/programs/index.html#profit
2) The 'Motif' routine in WhatIf (by Gert Vriend) is
especially worth looking at; it offers automatic alignment
of molecules in three dimensions. The program suggests which
atoms should be equivalenced. WhatIf is a large and complex
modelling and structural analysis package, and so may not be
exactly what you were asking for; however you can write scripts
to routinely perform a given set of tasks.
http://www.sander.embl-heidelberg.de/whatif/
ProFit probably fits the bill.
http://www.biochem.ucl.ac.uk/~martin/programs/index.html
cheers,
Malcolm
--
Malcolm Gillies <M.B.Gillies at pharm.uu.nl>
PhD student, computational medicinal chemistry
Dept Medicinal Chemistry, Faculty of Pharmacy,
Utrecht University, The Netherlands
There are many programs try
http://www.biochem.ucl.ac.uk/~martin/swreg.html = FroFit v1.8
Miri
From:
"Mauro A. Cremonini" <mauro at foodsci.unibo.it>
To:
"l.r.cooper" <ssr97lrc at reading.ac.uk>
Hi!
I did it once in fortran. I used the orthogonal procrustes algorithm by
Golub and Pereira.
Unfortunately I haven't the code anymore, but it was some 30 lines of
fortran code and one call to the lapack library.
If you want I can fax you 4 pages with the original reference.
Hope it helps,
Mauro
Try SwissPDB viewer
Claude Aflalo ######################## Phones: Office 972-7-6472118 ####
Dept. of Life Sciences Lab 972-7-6472119
Ben Gurion University of the Negev Fax 972-7-6472890
P.O.Box 653 email: aflaloc at bgumail.bgu.ac.il
Beer Sheva 84105 Israel URL: http://www.bgu.ac.il/life/aflalo.html
Hi Lee,
I suggest you use my ProFit program:
http://www.biochem.ucl.ac.uk/~martin/programs/
Hi, I recommand you use:
(1) the superpose module in Sybly
(2) TINKER
(3) Modeller
both tinker and modeller are public available without any
charge for academic coummunity, and Tinker also offers the
F77 (?) source codes, and the c codes translated by f2c.
Good luck.
Dayong
I don't know of any c code that will do that
but I know that you can do it with MSI's Cerius.
Nathalie Godbout |
| University of Illinois at Urbana-Champaign |
| 600 S. Goodwin Av. Box 23.6 |
| Urbana, IL 61801
--
°¤ø,¸¸,ø¤°`´°¤ø,¸¸,ø¤°`´°¤ø,¸¸,ø¤°`´°¤ø,¸¸,ø¤°`´°¤ø,¸¸,ø¤°`
//=\Mr. Lee R. Cooper Bsc(Hons) MSc, Parallel, Emergent//=\evolution,
\=//& Distributed Architechture Laboratory, Dept. of \=//creationists
//=\Comp. Science, University of Reading, Whiteknights //=\have
argued,
\=//PoBox 225, Reading, Berkshire. RG6 6AY (UK) \=/was as likely
//=\Tel +44 (0)118 987 5123 x7645 (0915-1700)|Fax //=to have made
\=//Tel +44 (0)118 931 8188 x7817 (1900-2300)|0118 975 \=//man as a
//=\http://www.rdg.ac.uk/~ssr97lrc/ 1994 //=\monkey...,
°¤ø,¸¸,ø¤°`´°¤ø,¸¸,ø¤°`´°¤ø,¸¸,ø¤°`´°¤ø,¸¸,ø¤°`´°¤ø,¸¸,ø¤°`
randomly typing the bible without error. with natural selection acting
as an eraser of mistakes; assuming thirteen mistakes for every correct
character & a rate of 1 keystroke per second, the 6 million characters
of the holy script could be typed in 13x6e6 s, or <3 yrs.
[Part 2, Text/PLAIN 621 lines]
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