[modeller_usage] Loop redefine on tetramer

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    Date: Wed, 23 Nov 2005 12:06:42 +0000
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 Subject: Loop redefine of tetramer
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Dear Modellers,

I have a tetramer model generated by MODELLER 8v1. I want to redefine one
10-residue long loop on all four subunit. Unfortunately MODLLER only worked on
one of the chaines. My question is how I can model the identical-residue loop
on all chains at one calculation?

Here is the script I used.

# Loop refinement of an existing model (RCK4S56-65.pdb)

from modeller.automodel import *

log.verbose()
env = environ()

# directories for input atom files
env.io.atom_files_directory = '.'

# Create a new class based on 'loopmodel' so that we can redefine
# select_loop_atoms (necessary)
class myloop(loopmodel):
    # This routine picks the residues to be refined by loop modeling
    def select_loop_atoms(self):
        # 10 residue insertion
        self.pick_atoms(selection_segment=('39:', '49:'),
                        selection_status='INITIALIZE')

        self.pick_atoms(selection_segment=('149:', '159:'),
                        selection_status='INITIALIZE')
        self.pick_atoms(selection_segment=('259:', '269:'),
                        selection_status='INITIALIZE')
        self.pick_atoms(selection_segment=('369:', '379:'),
                        selection_status='INITIALIZE')

m = myloop(env,
           inimodel='sample.pdb', # initial model of the target
           sequence='sample')          # code of the target

m.loop.starting_model= 1           # index of the first loop model
m.loop.ending_model  = 100          # index of the last loop model
m.loop.md_level = refine.very_fast  # loop refinement method

m.make()

Thank you for any hints.


Binbin


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