Re: [modeller_usage] using model-loop-refine in Modeller9v1 - modeller_usage

17 Apr 2007


      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