Re: [modeller_usage] How to set starting residue number in modeling

[Modeller Caretaker <modeller-care@ucsf.edu>]

On 5/27/10 9:17 AM, Keehyoung Joo wrote:
> Today, I tried it by using rename_segments method.
> But, I did not make model that I want.
> The following is my script to model.
> I add MyModel class and function rename_segments.
> I want to build model that have chain id ='A' and starting residue number=5.

To use rename_segments in combination with automodel, use the 
special_patches() method, as detailed at
http://salilab.org/archives/modeller_usage/2009/msg00245.html

A minimal script which should do what you want is:

from modeller import *
from modeller.automodel import *

class MyModel(automodel):
    def special_patches(self, aln):
        self.rename_segments(segment_ids='A', renumber_residues=5)

log.verbose()
env = environ()

a = MyModel(env, alnfile='alignment.ali',
            knowns='5fd1', sequence='1fdx')
a.make()


	Ben Webb, Modeller Caretaker
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