Re: [modeller_usage] symmetrisation of models

[J B Procter <>]

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!) :

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Date: Wed, 13 Jun 2001 10:36:15 -0400
From: Roberto Sanchez <>
Organization: Mount Sinai School of Medicine
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To: Kim Vilbour Andersen <>, Modeller List
<modeller_usage> Subject: Re: Modeling homotrimer
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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