[modeller_usage] Make model containing alpha-helix in addition to template

[Iain Aspley <>]

Hello Modellers,
I am having difficulty getting modeller to produce a model for my sequence containing a region which has no template which I wish to be an alpha-helix, the rest of the sequence should be modelled according to the template.

I used the following script

from modeller.automodel import*
from modeller import*

# Set up environment
log.verbose()
env=environ()
env.libs.topology.read('${LIB}/top_heav.lib')
env.libs.parameters.read('${LIB}/par.lib')
env.io.atom_files_directory='./:../3BO9.pdb'
a=automodel(env,
alnfile='target2.ali',
knowns='3BO9',
sequence='query')
a.restraints.add(secondary_structure.alpha(a.residue_range('129:A', '154:A')))
a.starting_model=1
a.ending_model=5
a.make()


and I receive the following error messages

Could not find platform independent libraries <prefix>
Could not find platform dependent libraries <exec_prefix>
Consider setting $PYTHONHOME to <prefix>[:<exec_prefix>]
'import site' failed; use -v for traceback
Traceback (most recent call last):
  File "target2.py", line 14, in ?
    a.restraints.add(secondary_structure.alpha(a.residue_range('129:A', '154:A')))
  File "/usr/lib/modeller9.10/modlib/modeller/coordinates.py", line 304, in residue_range
    start = self.residues[start]._num
  File "/usr/lib/modeller9.10/modlib/modeller/coordinates.py", line 234, in __getitem__
    (self.offset, self.length, self.suffix))
  File "/usr/lib/modeller9.10/modlib/modeller/util/modutil.py", line 23, in handle_seq_indx
    int_indx = lookup_func(*args)
  File "/usr/lib/modeller9.10/modlib/modeller/coordinates.py", line 298, in _indxres
    raise KeyError("No such residue: %s" % indx)
KeyError: 'No such residue: 129:A'

I have checked the pdb file and the residues do indeed exist!

The log file reads as follows


                         MODELLER 9.10, 2011/09/28, r8346

     PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS


                     Copyright(c) 1989-2011 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 bio-haw-pc10 2.6.32-43-generic x86_64
Date and time of compilation         : 2011/09/28 18:39:17
MODELLER executable type             : x86_64-intel8
Job starting time (YY/MM/DD HH:MM:SS): 2012/10/10 11:28:47

openf___224_> Open           $(LIB)/restyp.lib
openf___224_> Open           ${MODINSTALL9v10}/modlib/resgrp.lib
rdresgr_266_> Number of residue groups:        2
openf___224_> Open           ${MODINSTALL9v10}/modlib/sstruc.lib

Dynamically allocated memory at   amaxlibraries [B,KiB,MiB]:      3234076    3158.277     3.084

Dynamically allocated memory at   amaxlibraries [B,KiB,MiB]:      3234604    3158.793     3.085
openf___224_> Open           ${MODINSTALL9v10}/modlib/resdih.lib

Dynamically allocated memory at   amaxlibraries [B,KiB,MiB]:      3283204    3206.254     3.131
rdrdih__263_> Number of dihedral angle types         :        9
              Maximal number of dihedral angle optima:        3
              Dihedral angle names                   :  Alph Phi Psi Omeg chi1 chi2 chi3 chi4 chi5
openf___224_> Open           ${MODINSTALL9v10}/modlib/radii.lib

Dynamically allocated memory at   amaxlibraries [B,KiB,MiB]:      3292444    3215.277     3.140
openf___224_> Open           ${MODINSTALL9v10}/modlib/radii14.lib
openf___224_> Open           ${MODINSTALL9v10}/modlib/af_mnchdef.lib
rdwilmo_274_> Mainchain residue conformation classes:  APBLE
openf___224_> Open           ${MODINSTALL9v10}/modlib/mnch.lib
rdclass_257_> Number of classes:        5
openf___224_> Open           ${MODINSTALL9v10}/modlib/mnch1.lib
openf___224_> Open           ${MODINSTALL9v10}/modlib/mnch2.lib
openf___224_> Open           ${MODINSTALL9v10}/modlib/mnch3.lib
openf___224_> Open           ${MODINSTALL9v10}/modlib/xs4.mat
rdrrwgh_268_> Number of residue types:       21
openf___224_> Open           ${LIB}/top_heav.lib
read_to_681_> topology.submodel read from topology file:        3
openf___224_> Open           ${MODINSTALL9v10}/modlib/models.lib
openf___224_> Open           ${LIB}/par.lib

Dynamically allocated memory at  amaxparameters [B,KiB,MiB]:      4241404    4141.996     4.045
openf___224_> Open           ${LIB}/par.lib
read_pa_232_> parameters    BONDS   ANGLS  DIHEDS IMPROPS    MODE
                              227     561     661     112       0
io_data____W> Setting io.atom_files_directory to a colon-delimited string is
              deprecated, as it is not robust on Windows systems. Set it to
              a list of directories instead. For example:
              env.io.atom_files_directory = ['./', '../3BO9.pdb']
automodel__W> Topology and/or parameter libraries already in memory. These will
                be used instead of the automodel defaults. If this is not what you
                want, clear them before creating the automodel object with
                env.libs.topology.clear() and env.libs.parameters.clear()

Can anybody help me please?

Thanks in advance

Iain Aspley