Hi,
Check this link:
http://www.salilab.org/archives/modeller_usage/2009/msg00222.html
Hope this helps,
Rui Rodrigues
On Wed, 7 Jul 2010 15:13:03 +0800 (CST), albert wrote
> Hello:
> I try to do loop refinement by loop.py using mutiple CPU, but it doesn't work.
> Here is the scrips and log file. Could anybody give me some advices?
>
> scrips:
> ------------------------------------------------------------
> from modeller import *
> from modeller.automodel import *
> from modeller.parallel import *
>
> j = job()
> j.append(local_slave())
> j.append(local_slave())
> j.append(local_slave())
> j.append(local_slave())
>
> env = environ()
> log.verbose()
>
> # directories for input atom files
> env.io.atom_files_directory = ['.', '../atom_files']
>
> # Create a new class based on 'loopmodel' so that we can redefine
> # select_loop_atoms (necessary)
> class dope_loopmodel(loopmodel):
> # This routine picks the residues to be refined by loop modeling
> def select_loop_atoms(self):
> # One loop from residue 19 to 28 inclusive
> return selection(self.residue_range('238:', '241:'))
>
> m = dope_loopmodel(env,
> inimodel='backbone', # initial model of the target
> sequence='a8') # code of the target
>
> m.loop.starting_model= 1 # index of the first loop model
> m.loop.ending_model = 100 # index of the last loop model
> m.loop.md_level = refine.slow # loop refinement method
>
> m.use_parallel_job(j)
> m.make()
>
> logfile
> --------------------------------------------------------------------------------------
-------------
> Traceback (most recent call last):
> File "loop.py", line 34, in ?
> m.make()
> File "/usr/lib64/python2.4/site-packages/modeller/automodel/loopmodel.py",
> line 34, in make self.build_seq(self.inimodel, 1) File
> "/usr/lib64/python2.4/site-packages/modeller/automodel/loopmodel.py", line 146,
> in build_seq self.parallel_loop_models(atmsel, ini_model, num, sched)
> File "/usr/lib64/python2.4/site-packages/modeller/automodel/loopmodel.py",
> line 164, in parallel_loop_models
> self.loop.outputs.extend(job.run_all_tasks()) File "/usr/lib64/python2.4/site-
> packages/modeller/parallel/job.py", line 130, in run_all_tasks for task in
> self._finish_all_tasks(): File "/usr/lib64/python2.4/site-
> packages/modeller/parallel/job.py", line 163, in _finish_all_tasks task =
> self._process_event(obj, s) File "/usr/lib64/python2.4/site-
> packages/modeller/parallel/job.py", line 179, in _process_event task =
> obj.task_results() File "/usr/lib64/python2.4/site-
> packages/modeller/parallel/slave.py", line 61, in task_results r =
> self.get_data(allow_heartbeat=True) File "/usr/lib64/python2.4/site-
> packages/modeller/parallel/communicator.py", line 84, in get_data
> (cmdtype, obj) = self._recv() File "/usr/lib64/python2.4/site-
> packages/modeller/parallel/communicator.py", line 125, in _recv raise
> RemoteError(obj.exc, self) modeller.parallel.communicator.RemoteError:
> AttributeError: 'module' object has no attribute 'MyLoop' from <Slave on localhost>
--
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