Hi, I am new to modeller and I have trouble creating a homology model of a protein using model-loop-refine. I modified the model-loop-refine.py script as shown below and I got error messages. About an hour before, I got your repaly of the 'using model-loop-refine in Modeller9v1', you sent me a URL 'http://salilab.org/archives/modeller_usage/attachments/20070417/32969431/att...'. But I can not understand it. Could you explain it again for me?

from modeller import * from modeller.automodel import *

log.verbose() env = environ()

env.io.atom_files_directory = './:../atom_files'

# Create a new class based on 'loopmodel' so that we can redefine # select_loop_atoms class myloop(loopmodel): # This routine picks the residues to be refined by loop modeling def select_loop_atoms(self): return selection(self.residue_range('53:', '67:') (self.residue_range('89:', '96:') (self.residue_range('118:', '144:') (self.residue_range('166:', '177:') (self.residue_range('199:', '221:') (self.residue_range('243:', '254:'))

a = myloop(env, alnfile = 'seg.ali', # alignment filename knowns = '1u19A', # codes of the templates sequence = 'mrg1', # code of the target loop_assess_methods=assess.DOPE) # assess each loop with DOPE a.starting_model= 1 # index of the first model a.ending_model = 1 # index of the last model

a.loop.starting_model = 1 # First loop model a.loop.ending_model = 2 # Last loop model

a.make() # do modeling and loop refinement

This is the error: File "model-loop-refine.py", line 21 a = myloop(env, ^ SyntaxError: invalid syntax

This is the .log contents: MODELLER 9v1, 2007/01/19, r4822

PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS

Copyright(c) 1989-2007 Andrej Sali All Rights Reserved

Written by A. Sali with help from B. Webb, M.S. Madhusudhan, M-Y. Shen, M.A. Marti-Renom, N. Eswar, F. Alber, M. Topf, B. Oliva, A. Fiser, R. Sanchez, B. Yerkovich, A. Badretdinov, F. Melo, J.P. Overington, E. Feyfant University of California, San Francisco, USA Rockefeller University, New York, USA Harvard University, Cambridge, USA Imperial Cancer Research Fund, London, UK Birkbeck College, University of London, London, UK

Kind, OS, HostName, Kernel, Processor: 4, Linux linux 2.6.11.4-21.7-default i686 Date and time of compilation : 2007/01/19 13:47:34 MODELLER executable type : i386-intel8 Job starting time (YY/MM/DD HH:MM:SS): 2007/04/17 19:12:02