----- Forwarded message from bmbbl@leeds.ac.uk ----- Date: Wed, 23 Nov 2005 12:06:42 +0000 From: bmbbl@leeds.ac.uk Reply-To: bmbbl@leeds.ac.uk Subject: Loop redefine of tetramer To: modeller_usage@salilab.org

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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