Thanks so much for the quick response. I've tried the suggestions & get similar results to before: [newhoir@hals cpt6short]$ python cps6.py

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 hals 2.6.32-220.4.1.el6.x86_64 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): 2012/03/07 06:52:00

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______E> Cannot open file cp6s.ali: No such file or directory

Traceback (most recent call last): File "cps6.py", line 42, in <module> a.make() # do the actual homology modeling File "/usr/lib64/python2.6/site-packages/modeller/automodel/automodel.py", line 96, in make self.homcsr(exit_stage) File "/usr/lib64/python2.6/site-packages/modeller/automodel/automodel.py", line 408, in homcsr aln = self.read_alignment() File "/usr/lib64/python2.6/site-packages/modeller/automodel/automodel.py", line 398, in read_alignment aln.append(file=self.alnfile, align_codes=self.knowns+[self.sequence]) File "/usr/lib64/python2.6/site-packages/modeller/alignment.py", line 78, in append allow_alternates) IOError: openf______E> Cannot open file cp6s.ali: No such file or directory

Yes, the ali file is there: [newhoir@hals cpt6short]$ ls *ali

My .py file is:

cps6.alifrom modeller import * from modeller.automodel import *

# build 20 copies of a dimer from a single template

log.verbose() # request verbose output # Override the 'special_restraints' and 'user_after_single_model' methods: class MyModel(automodel): def special_restraints(self, aln): # Constrain the A and B chains to be identical (but only restrain # the C-alpha atoms, to reduce the number of interatomic distances # that need to be calculated): s1 = selection(self.chains['A']).only_atom_types('CA') s2 = selection(self.chains['B']).only_atom_types('CA') self.restraints.symmetry.append(symmetry(s1, s2, 1.0)) def user_after_single_model(self): # Report on symmetry violations greater than 1A after building # each model: self.restraints.symmetry.report(1.0)

env = environ() # create a new MODELLER environment to build this model in

# directories for input atom files env.io.atom_files_directory = ['.', '/home/newhoir/rub-atfiles/']

#read HETATMS in template env.io.hetatm = True

# Be sure to use 'MyModel' rather than 'automodel' here! a = MyModel(env, alnfile = 'cp6s.ali' , # alignment filename knowns = ('2x06'), # codes of the templates sequence = 'cps6', # code of the target assess_methods=assess.GA341) # request model assessment a.starting_model= 1 # index of the first model a.ending_model = 20 # index of the last model # (determines how many models to calculate) a.library_schedule = autosched.slow # thorough VTFM opt a.max_var_iterations = 300 a.md_level = refine.very_slow a.make() # do the actual homology modeling

It makes no difference if I insert a first line #!/usr/bin/python or not.

Thanks again! Irene

----- Original Message ----- From: Modeller Caretaker modeller-care@salilab.org Date: Tuesday, March 6, 2012 12:03 pm Subject: Re: [modeller_usage] Modeller9.10 on Centos 6.2 To: Irene Newhouse irenenew@hawaii.edu Cc: modeller_usage@salilab.org

> On 3/6/12 1:31 PM, Irene Newhouse wrote: > > I've installed Modeller9.10 on my Centos 62. linux station. I > had an > > earlier version working under Centos 5.x. Now I find that if I > set an > > alias I call mod9v10 to point to modeller9.10_x86_64-intel8 in > > analogy to the alias I successfully set to its analog previously > > There's no need to do that - there's already a script called > mod9.10 > which does basically that, which ships as part of Modeller. But > we > generally recommend to use Python instead if you can. > > > Furthermore, I get an error indicating that my > > .ali file can't be found& I've triple-checked to make > sure I've > > entered the name correctly. > > Are you sure it's complaining about the .ali file and not > something > else? Or maybe you're running in the wrong directory. > > > There is no modpy.sh in the directory to which the web pages point. > > If you installed the RPM, there is no modpy.sh because it isn't > necessary. You can just run your regular system Python, e.g. > "python > foo.py". > > > it cannot find the equivalent of foo.py unless I give the full > path to foo.py > > If you're trying to run "foo.py" in the current directory by > just typing > "foo.py", that typically won't work on a Unix system since the > current > directory isn't usually in your path. Try "./foo.py" instead. > > > When I specify the full path, I get error > > messages such as "from: command not found"& > a crash, indicative of > > a massive failure to access python. > > This sounds like you have tried to run the Python script as a > shell > script. Either prefix it with "python", as above, or add > "#!/usr/bin/python" to the first line of your Python script to > tell the > system to use Python to run it. > > Ben Webb, Modeller Caretaker > -- > modeller- > care@salilab.org http://www.salilab.org/modeller/ > Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage