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>