Hi I got this output when I ran the script. Is there any python library that I have not installed. I am using python 2.6 in ubuntu 2.6 with all numpy,scipy and scitools installed. I tried to use inheritance to get my class to also import parallel.

Knut J

                         MODELLER 9v7, 2009/06/12, r6923


                     Copyright(c) 1989-2009 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 Human-Naa50p 2.6.31-17-generic x86_64
Date and time of compilation         : 2009/06/12 12:23:44
MODELLER executable type             : x86_64-intel8
Job starting time (YY/MM/DD HH:MM:SS): 2010/01/21 09:51:09

read_to_681_> topology.submodel read from topology file:        3
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()

check_ali___> Checking the sequence-structure alignment.

Implied target CA(i)-CA(i+1) distances longer than  8.0 angstroms:


getf_______W> RTF restraint not found in the atoms list:
              residue type, indices:    16   235
              atom names           : C     +N
              atom indices         :  1851     0

getf_______W> RTF restraint not found in the atoms list:
              residue type, indices:    16   235
              atom names           : C     CA    +N    O
              atom indices         :  1851  1848     0  1852
mdtrsr__446W> A potential that relies on one protein is used, yet you have at
              least one known structure available. MDT, not library, potential is used.
0 atoms in HETATM residues constrained
to protein atoms within 2.30 angstroms
and protein CA atoms within 10.00 angstroms
0 atoms in residues without defined topology
constrained to be rigid bodies
condens_443_> Restraints marked for deletion were removed.
              Total number of restraints before, now:    16251    14565
1468 (of 1853 total) atoms selected for optimization
Running 20 tasks on 3 slaves
/usr/bin/python2.6 /usr/lib/modeller9v7/bin/modslave.py -slave >& build_model_single.slave0
/usr/bin/python2.6 /usr/lib/modeller9v7/bin/modslave.py -slave >& build_model_single.slave1
/usr/bin/python2.6 /usr/lib/modeller9v7/bin/modslave.py -slave >& build_model_single.slave2
Identified slave <Slave on localhost>
Identified slave <Slave on localhost>
Identified slave <Slave on localhost>
Traceback (most recent call last):
  File "/home/knut/workspace/natAhnaa10/src/build_model_single.py", line 38, in <module>
  File "/usr/lib/python2.6/dist-packages/modeller/automodel/automodel.py", line 109, in make
  File "/usr/lib/python2.6/dist-packages/modeller/automodel/automodel.py", line 212, in multiple_models
  File "/usr/lib/python2.6/dist-packages/modeller/automodel/automodel.py", line 232, in parallel_multiple_models
  File "/usr/lib/python2.6/dist-packages/modeller/parallel/job.py", line 127, in run_all_tasks
    for task in self._finish_all_tasks():
  File "/usr/lib/python2.6/dist-packages/modeller/parallel/job.py", line 160, in _finish_all_tasks
    task = self._process_event(obj, s)
  File "/usr/lib/python2.6/dist-packages/modeller/parallel/job.py", line 176, in _process_event
    task = obj.task_results()
  File "/usr/lib/python2.6/dist-packages/modeller/parallel/slave.py", line 61, in task_results
    r = self.get_data(allow_heartbeat=True)
  File "/usr/lib/python2.6/dist-packages/modeller/parallel/communicator.py", line 84, in get_data
    (cmdtype, obj) = self._recv()
  File "/usr/lib/python2.6/dist-packages/modeller/parallel/communicator.py", line 125, in _recv
    raise RemoteError(obj.exc, self)
modeller.parallel.communicator.RemoteError: <type 'AttributeError'>: 'module' object has no attribute 'KJ' from <Slave on localhost>

> Date: Wed, 20 Jan 2010 14:26:01 -0800
> From: modeller-care@salilab.org
> To: knutjbj@hotmail.com
> CC: modeller_usage@salilab.org
> Subject: Re: [modeller_usage] muliplay cpu
> On 01/20/2010 01:14 PM, Knut J Bjuland wrote:
> > How do I use multiple cpu when doing loop which I have shown in a script
> > below. I am trying to use several cpus to get a faster build of a model.
> Your script looks fine to me, and should run in parallel, except that
> you're using the automodel class (not loopmodel) so you're doing regular
> homology modeling, not loop modeling.
> Ben Webb, Modeller Caretaker
> --
> modeller-care@salilab.org http://www.salilab.org/modeller/
> Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage

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