Thanks so much for the quick response. I've tried the suggestions &amp; get similar results to before:<br>[newhoir@hals cpt6short]$ python cps6.py<br><br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; MODELLER 9.10, 2011/09/28, r8346<br><br>&nbsp;&nbsp;&nbsp;&nbsp; PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS<br><br><br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Copyright(c) 1989-2011 Andrej Sali<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; All Rights Reserved<br><br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Written by A. Sali<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; with help from<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; B. Webb, M.S. Madhusudhan, M-Y. Shen, M.A. Marti-Renom,<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; N. Eswar, F. Alber, M. Topf, B. Oliva, A. Fiser,<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; R. Sanchez, B. Yerkovich, A. Badretdinov,<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; F. Melo, J.P. Overington, E. Feyfant<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; University of California, San Francisco, USA<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Rockefeller University, New York, USA<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Harvard University, Cambridge, USA<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Imperial Cancer Research Fund, London, UK<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Birkbeck College, University of London, London, UK<br><br><br>Kind, OS, HostName, Kernel, Processor: 4, Linux hals 2.6.32-220.4.1.el6.x86_64 x86_64<br>Date and time of compilation&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; : 2011/09/28 18:39:17<br>MODELLER executable type&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; : x86_64-intel8<br>Job starting time (YY/MM/DD HH:MM:SS): 2012/03/07 06:52:00<br><br>openf___224_&gt; Open&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; $(LIB)/restyp.lib<br>openf___224_&gt; Open&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; ${MODINSTALL9v10}/modlib/resgrp.lib<br>rdresgr_266_&gt; Number of residue groups:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2<br>openf___224_&gt; Open&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; ${MODINSTALL9v10}/modlib/sstruc.lib<br><br>Dynamically allocated memory at&nbsp;&nbsp; amaxlibraries [B,KiB,MiB]:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 3234076&nbsp;&nbsp;&nbsp; 3158.277&nbsp;&nbsp;&nbsp;&nbsp; 3.084<br><br>Dynamically allocated memory at&nbsp;&nbsp; amaxlibraries [B,KiB,MiB]:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 3234604&nbsp;&nbsp;&nbsp; 3158.793&nbsp;&nbsp;&nbsp;&nbsp; 3.085<br>openf___224_&gt; Open&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; ${MODINSTALL9v10}/modlib/resdih.lib<br><br>Dynamically allocated memory at&nbsp;&nbsp; amaxlibraries [B,KiB,MiB]:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 3283204&nbsp;&nbsp;&nbsp; 3206.254&nbsp;&nbsp;&nbsp;&nbsp; 3.131<br>rdrdih__263_&gt; Number of dihedral angle types&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; :&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 9<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Maximal number of dihedral angle optima:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 3<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Dihedral angle names&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; :&nbsp; Alph Phi Psi Omeg chi1 chi2 chi3 chi4 chi5<br>openf___224_&gt; Open&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; ${MODINSTALL9v10}/modlib/radii.lib<br><br>Dynamically allocated memory at&nbsp;&nbsp; amaxlibraries [B,KiB,MiB]:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 3292444&nbsp;&nbsp;&nbsp; 3215.277&nbsp;&nbsp;&nbsp;&nbsp; 3.140<br>openf___224_&gt; Open&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; ${MODINSTALL9v10}/modlib/radii14.lib<br>openf___224_&gt; Open&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; ${MODINSTALL9v10}/modlib/af_mnchdef.lib<br>rdwilmo_274_&gt; Mainchain residue conformation classes:&nbsp; APBLE<br>openf___224_&gt; Open&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; ${MODINSTALL9v10}/modlib/mnch.lib<br>rdclass_257_&gt; Number of classes:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 5<br>openf___224_&gt; Open&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; ${MODINSTALL9v10}/modlib/mnch1.lib<br>openf___224_&gt; Open&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; ${MODINSTALL9v10}/modlib/mnch2.lib<br>openf___224_&gt; Open&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; ${MODINSTALL9v10}/modlib/mnch3.lib<br>openf___224_&gt; Open&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; ${MODINSTALL9v10}/modlib/xs4.mat<br>rdrrwgh_268_&gt; Number of residue types:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 21<br>openf______E&gt; Cannot open file cp6s.ali: No such file or directory<br><br>Traceback (most recent call last):<br>&nbsp; File "cps6.py", line 42, in &lt;module&gt;<br>&nbsp;&nbsp;&nbsp; a.make()&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; # do the actual homology modeling<br>&nbsp; File "/usr/lib64/python2.6/site-packages/modeller/automodel/automodel.py", line 96, in make<br>&nbsp;&nbsp;&nbsp; self.homcsr(exit_stage)<br>&nbsp; File "/usr/lib64/python2.6/site-packages/modeller/automodel/automodel.py", line 408, in homcsr<br>&nbsp;&nbsp;&nbsp; aln = self.read_alignment()<br>&nbsp; File "/usr/lib64/python2.6/site-packages/modeller/automodel/automodel.py", line 398, in read_alignment<br>&nbsp;&nbsp;&nbsp; aln.append(file=self.alnfile, align_codes=self.knowns+[self.sequence])<br>&nbsp; File "/usr/lib64/python2.6/site-packages/modeller/alignment.py", line 78, in append<br>&nbsp;&nbsp;&nbsp; allow_alternates)<br>IOError: openf______E&gt; Cannot open file cp6s.ali: No such file or directory<br><br>Yes, the ali file is there:<br>[newhoir@hals cpt6short]$ ls *ali<br><br>My .py file is: <br><br>cps6.alifrom modeller import *&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <br>from modeller.automodel import *&nbsp;&nbsp; <br><br># build 20 copies of a dimer from a single template<br><br>log.verbose()&nbsp;&nbsp;&nbsp; # request verbose output<br># Override the 'special_restraints' and 'user_after_single_model' methods:<br>class MyModel(automodel):<br>&nbsp;&nbsp;&nbsp; def special_restraints(self, aln):<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; # Constrain the A and B chains to be identical (but only restrain<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; # the C-alpha atoms, to reduce the number of interatomic distances<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; # that need to be calculated):<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; s1 = selection(self.chains['A']).only_atom_types('CA')<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; s2 = selection(self.chains['B']).only_atom_types('CA')<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; self.restraints.symmetry.append(symmetry(s1, s2, 1.0))<br>&nbsp;&nbsp;&nbsp; def user_after_single_model(self):<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; # Report on symmetry violations greater than 1A after building<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; # each model:<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; self.restraints.symmetry.report(1.0) <br><br>env = environ()&nbsp; # create a new MODELLER environment to build this model in<br><br># directories for input atom files<br>env.io.atom_files_directory = ['.', '/home/newhoir/rub-atfiles/']<br><br>#read HETATMS in template<br>env.io.hetatm = True<br><br># Be sure to use 'MyModel' rather than 'automodel' here!<br>a = MyModel(env,<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; alnfile&nbsp; = 'cp6s.ali' ,&nbsp;&nbsp;&nbsp;&nbsp; # alignment filename<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; knowns&nbsp;&nbsp; = ('2x06'),&nbsp;&nbsp; # codes of the templates<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; sequence = 'cps6',&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; # code of the target<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; assess_methods=assess.GA341)&nbsp;&nbsp;&nbsp;&nbsp; # request model assessment<br>a.starting_model= 1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; # index of the first model<br>a.ending_model&nbsp; = 20&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; # index of the last model<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; # (determines how many models to calculate)<br>a.library_schedule = autosched.slow # thorough VTFM opt<br>a.max_var_iterations = 300<br>a.md_level = refine.very_slow<br>a.make()&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; # do the actual homology modeling<br><br>It makes no difference if I insert a first line&nbsp; #!/usr/bin/python or not.<br><br>Thanks again!<br>Irene<br><br>----- Original Message -----<br>From: Modeller Caretaker &lt;modeller-care@salilab.org&gt;<br>Date: Tuesday, March 6, 2012 12:03 pm<br>Subject: Re: [modeller_usage] Modeller9.10 on Centos 6.2<br>To: Irene Newhouse &lt;irenenew@hawaii.edu&gt;<br>Cc: modeller_usage@salilab.org<br><br>&gt; On 3/6/12 1:31 PM, Irene Newhouse wrote:<br>&gt; &gt; I've installed Modeller9.10 on my Centos 62. linux station. I <br>&gt; had an<br>&gt; &gt; earlier version working under Centos 5.x. Now I find that if I <br>&gt; set an<br>&gt; &gt; alias I call mod9v10 to point to modeller9.10_x86_64-intel8 in<br>&gt; &gt; analogy to the alias I successfully set to its analog previously<br>&gt; <br>&gt; There's no need to do that - there's already a script called <br>&gt; mod9.10 <br>&gt; which does basically that, which ships as part of Modeller. But <br>&gt; we <br>&gt; generally recommend to use Python instead if you can.<br>&gt; <br>&gt; &gt; Furthermore, I get an error indicating that my<br>&gt; &gt; .ali file can't be found&amp;&nbsp; I've triple-checked to make <br>&gt; sure I've<br>&gt; &gt; entered the name correctly.<br>&gt; <br>&gt; Are you sure it's complaining about the .ali file and not <br>&gt; something <br>&gt; else? Or maybe you're running in the wrong directory.<br>&gt; <br>&gt; &gt; There is no modpy.sh in the directory to which the web pages point.<br>&gt; <br>&gt; If you installed the RPM, there is no modpy.sh because it isn't <br>&gt; necessary. You can just run your regular system Python, e.g. <br>&gt; "python <br>&gt; foo.py".<br>&gt; <br>&gt; &gt; it cannot find the equivalent of foo.py unless I give the full <br>&gt; path to foo.py<br>&gt; <br>&gt; If you're trying to run "foo.py" in the current directory by <br>&gt; just typing <br>&gt; "foo.py", that typically won't work on a Unix system since the <br>&gt; current <br>&gt; directory isn't usually in your path. Try "./foo.py" instead.<br>&gt; <br>&gt; &gt; When I specify the full path, I get error<br>&gt; &gt; messages such as "from:&nbsp; command not found"&amp;&nbsp;&nbsp; <br>&gt; a crash, indicative of<br>&gt; &gt; a massive failure to access python.<br>&gt; <br>&gt; This sounds like you have tried to run the Python script as a <br>&gt; shell <br>&gt; script. Either prefix it with "python", as above, or add <br>&gt; "#!/usr/bin/python" to the first line of your Python script to <br>&gt; tell the <br>&gt; system to use Python to run it.<br>&gt; <br>&gt; 	Ben Webb, Modeller Caretaker<br>&gt; -- <br>&gt; modeller-<br>&gt; care@salilab.org&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; http://www.salilab.org/modeller/<br>&gt; Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage