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