Re: Modeling homotrimer

[Roberto Sanchez <>]

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)" <>
> To: "''" <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
> 
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> 
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