Subject: Summary :Superimposition Program

From: Sangeeta Sawant <[email-masked]>
Date: Thu, 9 Jul 1998 02:43:05 +0500 (GMT-5)

Hi all,
Thanks to everyone who sent a reply to my query regarding superimposition 
of several structures of peptides in batch mode. The suggestions are 
extremely useful. Here is the summary of the replies along with the query:

+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+  Mrs. Sangeeta Sawant                                                   +
+  Research Fellow                     email : [email-masked]  +
+  Bioinformatics Centre               phone : +91-212-355039             +
+  University of Pune                  fax   : +91-212-350087             +
+  Ganeshkhind                                                            +
+  Pune - 411007                                                          +
+  India.                                                                 +
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-----Original Query-------
>Hi all!
>I would like to know if there is any software/program (preferably 
>shareware/public-domain) which allows to superimpose several 
>protein/peptide conformations onto one (say, template confo.) in a batch 
>mode. The program may be for either IRIX or OS2 (DEC-ALPHA) or SOLARIS or 
>LINUX or DOS (No Mac-OS please). Any help will be appreciated.

-----------Responses---------
I am not sure if this helps; but did you take a look at swisspdb viewer
http://www.expasy.ch
Sasidhar

- Sasidhar
____________________________________________________________________________

Dr. Y. U. Sasidhar, Associate Professor, Department of Chemistry
Indian Institute of Technology, Powai, Mumbai 400 076, INDIA
____________________________________________________________________________
e-mail : [email-masked]
Fax    : (+91-22 ) 578 3480 (IIT Main ), (+91-22 ) 576 7152 ( Chemistry )
_____________________________________________________________________________
Tel    : (+91-22 ) 578 2545 Ext.7179(O), 8198(Lab), 7151(Message), 8179(R)
       : (+91-22 ) 576-Ext. Number          
____________________________________________________________________________

---------- 
Hi Sangeeta,
  You can use the CCP4 program PolyPose for the purpose. If you don't have
CCP4 (which, I believe you don't). You can use Gerard's program LSQMAN
which is the most versatile superimposition program I've seen, but
requires some inspired script writing. Lastly I've got a fast
superimposer, which is a debugged and improved version of the one I wrote
in Pune.
  For more info. see the following:

LSQMAN http://alpha2.bmc.uu.se/~gerard/manuals/lsqman_man.html

CCP4 (PolyPose and many other useful programs)
http://www/dl.ac.uk/CCP/CCP4/main.html

super_duper.c  (That's mine)
Can superimpose using the whole molecule or any sub-set which you
define. The algo. is the same as the one I wrote in Pune, but now
re-written and de-bugged. I can send you OSF1 Version 4.0 (DEC-ALPHA)
executable, or the C-sources. Finally if you want any special things
to be done, it may be possible to incorporate them. 
Hope this helps.

deva

----------------------------------------------------------------------------
Devapriya Choudhury

Office:                           Home:
Deptt. of Molecular Biology       Oskar Arpis Vag 2,2
Box 590, BMC,                     S75650, Uppsala
S75124, Uppsala                   Sweden
Sweden

Tel: +46 18 4714524               +46 18 400314
FAX: +46 18 536971
e-mail [email-masked]
-----------------------------------------------------------------------------

---------- 
it's called profit and does exactly what ou want!

	cheers,
	gerald

----------------------------------------------------------------------
Gerald Loeffler - Bioinformatics Scientist
Boehringer Ingelheim R&D Vienna, Molecular Biology Department
Email: [email-masked]
Phone: +43 676 3289588 (and +43 1 80105 634)
Fax:   +43 1 80105 683
Smail: Bender+Co, Dr. Boehringer-Gasse 5-11, A-1121 Vienna, Austria

---------- 
You may try the molecular modelling package MOLMOL from ETH Zuerich.

It is a graphical program which can also be run in batch-mode (without
graphics-display.

It can be controlled from shellscripts or directly at the commandline.

It is able to superimpose as many molecules as you wish in several modes
(to first, to mean, circular), and you can choose, which atoms or
residues to consider for superposition.

And!!!!

It is freeware!

Take a look at http://www.mol.biol.ethz.ch/wuthrich/software/molmol/

There are versions for UNIX (IRIX, DEC OSF, SOLARIS, LINUX), VMS, and
Windows95/NT. You can also get the source and adapt it to whatever you
want.

-- 
Bye,

Marc Saric

Lehrstuhl fuer Biophysik
Projektgruppe Theoretische Biophysik
http://www.bph.ruhr-uni-bochum.de/

Ruhr-Universitaet Bochum
Germany

---------- 
Dear Sangeeta,

Try MOLMOL:
There is a nice way to run it in batch as well.
http://www.mol.biol.ethz.ch/wuthrich/software/molmol

Hope it helps,
Jurgen
-- 
    Drs Jurgen F. Doreleijers
    NMR spectroscopy, Utrecht University,  The Netherlands
    mailto:[email-masked]
    http://www-nmr.chem.uu.nl/~jurgen

---------- 
Hi ,

make a search in the web for a programm Profit, it is a powerfull unix
programm that allow you to make a protein superimposition also in batch
mode.

Maybe you can find it at http://www.biochem.ucl.ac.uk/~martin/swreg.html

Hope this helps.

-- Rino Ragno

++----------------------------------------------------------------------++
++----------------------------------------------------------------------++
||                                                                      ||
||  Dr. Rino Ragno                      E-mail: [email-masked]       ||
||  Institute for Biomedical Computing      or: [email-masked]      ||
||  Center for Molecular Design             or: [email-masked]  ||
||  Box8036, Washington University      Phone : 314-362-2272            ||
||  700 South Euclid Avenue             FAX   : 314-362-0234            ||
||  St. Louis, Missouri 63110                                           ||
||  U. S. A.                                                            ||
||                                                                      ||
||       WEB PAGE   : www.ibc.wustl.edu/cmd/people/rino/rino.html       ||
||                                                                      ||
++----------------------------------------------------------------------++
++----------------------------------------------------------------------++
---------- 
Have a look at the Molecular Modelling toolkit at:

  http://starship.skyport.net/crew/hinsen/mmtk.html

It contains the necessary superposition code, and making a batch mode
program that uses it is a simple matter (maybe 10 lines of code).
I could even write you that small piece of code, if I knew
what exactly you want the program to do with the superposed
structure!
-- 
-------------------------------------------------------------------------------
Konrad Hinsen                            | E-Mail: [email-masked]
Centre de Biophysique Moleculaire (CNRS) | Tel.: +33-2.38.25.55.69
Rue Charles Sadron                       | Fax:  +33-2.38.63.15.17
45071 Orleans Cedex 2                    | Deutsch/Esperanto/English/
France                                   | Nederlands/Francais
-------------------------------------------------------------------------------
--------------
Sangeeta,
  You might look into a program called MOE, by the Chemical Computing
Group.  It has very nice 3D homology modeling capabilities and will run in
batch mode.

_____________________________________________________________________
                                              
                    Abby Parrill, Ph.D.

Currently:         Chemistry Department
                 Michigan State University
                East Lansing, MI  48824-1322
                 [email-masked]
          
Soon:               Chemistry Department
                   University of Memphis                                 
                    Memphis, TN  38152
Computational Research on Materials Institute at University of Memphis
                         (CROMIUM)         
______________________________________________________________________

---------- 
Hi Sangeeta, 

I'd highly recommend VMD. It's available for many platforms (SGI, Linux,
AIX, HPUX), it's free and very flexible due to a (TCL-like?) scripting
language. Check http://www.ks.uiuc.edu/Research/vmd/ for more. 

Cheers,

Chris
-- 
Dr. Christoph Steinbeck (mailto:[email-masked] -
http://seneca.ice.mpg.de/~stein)
Max-Planck-Institute of Chemical Ecology (http://www.ice.mpg.de)
Tatzendpromenade 1a, 07745 Jena, Germany
Tel: int + (49) 3641 643644 --- Fax: int + (49) 3641 643665

What is man but that lofty spirit -- that sense of enterprise. 
 ... Kirk, "I, Mudd," stardate 4513.3..