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/

> ------------------------------------------------------------------------ > > Subject: Modeling homotrimer > Date: Tue, 12 Jun 2001 15:09:54 +0200 > From: "KVA (Kim Vilbour Andersen)" kva@maxygen.dk > To: "'modeller_usage@salilab.org'" modeller_usage@guitar > > Hello Modeller users > > I'm trying to model a homotrimeric molecule. > > The template is a trimer with speudosymmetry making the three molecules > identical. > > I would like to include this pseudosymmetry in the model forcing the three > molecules to be identical. > > In the manual I found the DEFINE_SYMMETRY command, but this seems to me > mainly to be for dimers. > > Any ideas will be greatly appreciated > > Best regards > > Kim Vilbour Andersen > > ------------------------------------------------------------------------ > Kim Vilbour Andersen, PhD > Principal Scientist > Maxygen > Agern Allé 1 > DK-2970 Hørsholm > Denmark > > NB! Maxygen Denmark was previously known as ProFound Pharma A/S > > Tel: +45 7020 5550 > Direct: +45 4517 8473 > Fax: +45 7020 5530 > > E-mail: kva@maxygen.dk > http://www.maxygen.dk/ > ------------------------------------------------------------------------