There was a posting that I found in the modeller archives about this. I took the liberty of reposting it (thanks to Roberto Sanchez I think!) :
------------- re-posted message Date: Wed, 13 Jun 2001 10:36:15 -0400 From: Roberto Sanchez roberto.sanchez@physbio.mssm.edu Organization: Mount Sinai School of Medicine X-Mailer: Mozilla 4.77 [en] (Windows NT 5.0; U) X-Accept-Language: en,pdf MIME-Version: 1.0 To: Kim Vilbour Andersen kva@maxygen.dk, Modeller List <modeller_usage> Subject: Re: Modeling homotrimer References: 20010613122759.36494.qmail@web10107.mail.yahoo.com Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Sender: owner-modeller_usage Precedence: bulk
Hi,
You can have more than one pair of segments defined trough the DEFINE_SYMMETRY command, so you can restrict the three molecules to be identical by defining, for example, three pairs. If you have three monomers A, B, and C you would define pairs A-B, B-C, and C-A, that should make all three identical.
The 'defsym' routine in the TOP file would look something like this (note the values for the ADD_SYMMETRY option):
SUBROUTINE ROUTINE = 'defsym'
SET RES_TYPES = 'ALL' SET ATOM_TYPES = 'MNCH' SET SELECTION_STATUS = 'INITIALIZE' SET SELECTION_SEARCH = 'SEGMENT'
SET SYMMETRY_WEIGHT = 0.5 PICK_ATOMS PICK_ATOMS_SET = 2, SELECTION_SEGMENT = '1:' '102:' PICK_ATOMS PICK_ATOMS_SET = 3, SELECTION_SEGMENT = '103:' '204:' DEFINE_SYMMETRY ADD_SYMMETRY = on off PICK_ATOMS PICK_ATOMS_SET = 2, SELECTION_SEGMENT = '103:' '204:' PICK_ATOMS PICK_ATOMS_SET = 3, SELECTION_SEGMENT = '205:' '306:' DEFINE_SYMMETRY ADD_SYMMETRY = on off PICK_ATOMS PICK_ATOMS_SET = 2, SELECTION_SEGMENT = '205:' '306:' PICK_ATOMS PICK_ATOMS_SET = 3, SELECTION_SEGMENT = '1:' '102:' DEFINE_SYMMETRY ADD_SYMMETRY = on off
RETURN
END_SUBROUTINE
I hope this helps.
Best,
Roberto
-- Roberto Sanchez, Assistant Professor Structural Biology Program, Department of Physiology & Biophysics and Institute for Computational Biomedicine, Mount Sinai School of Medicine Box 1677, 1425 Madison Avenue, New York, NY 10029 phone +1 (212) 659 8648, fax +1 (212) 849 2456 http://physbio.mssm.edu/~sanchez/ --------------- End of re-posted messsage