Re: [modeller_usage] loop refinement with disulfide patch

[Modeller Caretaker <>]

M. Seigneuret wrote:
> A previous case of using restraints or patches in loop refinement 
> already appeared in the discussion  list but there, loopmodel was used 
> on the fly after automodel so that the redefined patches and restraints 
> automodel subclasses were active during loop refinement.
> What happens when one uses only loopmodel or dope_loopmodel to refine an 
> existing model ? I suppose it is possible to import patches subclasses 
> from automodel. I tried to fiddle but got nowhere. Could somebody help me ?

It works in just the same way. loopmodel is a derived class of 
automodel, so everything you can do in automodel can also be done in 
loopmodel (it doesn't make any difference whether you build models and 
refine the loops in one go, or just use loopmodel to refine the loops of 
an existing model). See the example at
http://salilab.org/modeller/9v3/manual/node34.html

It should be straightforward to modify this example to also override the 
special_patches routine. In your case, your TOP script would translate 
to something like:

from modeller import *
from modeller.automodel import *

env = environ()

class MyLoop(loopmodel):
    def select_loop_atoms(self):
        return selection(self.residue_range('59:', '61:'))
    def special_patches(self):
        self.patch(residue_type='DISU',
                   residues=(self.residues['41'],
                             self.residues['60']))

m = MyLoop(env,
           inimodel='mod2f.B99990002.pdb',
           sequence='mod2134')
m.loop.starting_model = 20
m.loop.ending_model = 30
m.loop.md_level = refine.very_fast
m.make()


	Ben Webb, Modeller Caretaker
--
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