Hi Roberto
I think I have the answer to the symmetry problem. With a more detailed
log file I found that that RES_TYPE it was searching was BLK, a hangover
from some previous step. If I insert
SET RES_TYPES = 'ALL'
I get
defsym___> New number of symmetry segments, atom pairs: 1 686
and then at the end
Value of the symmetry term within -Ln(Mpdf) : 17.403
So it worked, but I was surprised to find that the stereochemical quality
of the constrained model is dreadful compared to that calculated without
symmetry.
Anyway, another small question. At the moment my two monomers come out as
residues 1-89 and 90-178, no chain ID. Is there any way to get them as
1-89 of chains A and B, say?
Thanks
Daniel Rigden
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On Mon, 7 Dec 1998, Roberto Sanchez wrote:
> Hi,
>
> Your TOP file looks fine to me. If the symmetry is operating you should
> get a value that is different from 0.0000 in the following line in the
> log file:
>
> Value of the symmetry term within -Ln(Mpdf) : 0.0000
>
> just grep for "symmetry" and you will get the line.
>
> By the way, you don't need to (and maybe you shouldn't) edit the
> __special.top script. It is enough to redefine a subroutine in your main
> TOP file. You can just add the code you show to your main TOP file and
> the new 'special_restraints' routine will be used by MODELLER.
>
> I hope this helps.
>
> Best Wishes,
>
> Roberto
>
> --
> Roberto Sanchez | phone : (212) 327 7206
> The Rockefeller University | fax : (212) 327 7540
> 1230 York Avenue, Box 38 | e-mail:
> New York, NY 10021-6399 | http://salilab.org
>
>
> Daniel John Rigden wrote:
> >
> > Dear Modellers
> >
> > I'm trying to build a dimer, constraining the two monomers to be
> > identical. From the manual this seems reasonably straightforward but I
> > can't get it to work.
> >
> > My current idea is to include the commands in the 'special_restraints'
> > subroutine (in __special.top), which gets called by __homscr.top after the
> > other restraints subroutines, thus
> >
> > SUBROUTINE ROUTINE = 'special_restraints'
> >
> > # Try to put symmetry restraints here
> > # This is called from __homcsr after other restraints set up
> >
> > SET ATOM_TYPES = 'ALL'
> > SET SELECTION_STATUS = 'INITIALIZE'
> > SET SELECTION_SEARCH = 'SEGMENT'
> >
> > SET SYMMETRY_WEIGHT = 5.0
> > PICK_ATOMS PICK_ATOMS_SET = 2, SELECTION_SEGMENT = '1:' '89:'
> > PICK_ATOMS PICK_ATOMS_SET = 3, SELECTION_SEGMENT = '90:' '178:'
> > DEFINE_SYMMETRY ADD_SYMMETRY = on off
> >
> > RETURN END_SUBROUTINE
> >
> > I know that this subroutine is read but I never see any indication of
> > symmetry having been set up when I read the logfile.
> >
> > What am I doing wrong?
> >
> > Thanks in advance
> >
> > Daniel Rigden
>