Re: [modeller_usage] problem with modelling a non-template helix

[Modeller Caretaker <>]

Renée Vancraenenbroeck wrote:
> I've come to the problem where I have to elongate a helix but the 
> template is absent, I've tried to restrain it into a helixconformation 
> using the following script wich I found in the archive, however it 
> doesn't seem to make any difference. What am I doing wrong?
>
> renée vancraenenbroeck
>
>  
>
> from modeller.automodel import *
>
> # Redefine the special_restraints routine to include the secondary
> # structure restraints (this routine is empty by default):
> class mymodel(automodel):
>     def special_restraints(self, aln):
>         rsr = self.restraints
>         # An alpha-helix:
>         rsr.make(aln, restraint_type='ALPHA', residue_ids=
> ('133', '139'),
>                  spline_on_site=False)
>         
>
> # This is as usual:
> log.verbose()
> env = environ()
> a = automodel(env, alnfile='Lrrk2-mult5.ali',
>               knowns=('2aedA','1byuA'), sequence='Lrrk2roc')
> a.starting_model = 1
> a.ending_model = 5
> a.make()

Simply replace 'a=automodel' with 'a=mymodel'.

	Ben Webb, Modeller Caretaker
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