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