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Re: How to define symmetry?



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