Hello: I am trying to generate loop models with loop protocol in the latest Modeller verison. It only produced 8 models and stopped, and it said the following:
File "loop.py", line 41, in <module> a.make() File "/usr/lib64/python2.7/site-packages/modeller/automodel/loopmodel.py", line 36, in make self.build_seq(self.inimodel, 1) File "/usr/lib64/python2.7/site-packages/modeller/automodel/loopmodel.py", line 190, in build_seq self.parallel_loop_models(atmsel, ini_model, num, sched) File "/usr/lib64/python2.7/site-packages/modeller/automodel/loopmodel.py", line 208, in parallel_loop_models self.loop.outputs.extend(job.run_all_tasks()) File "/usr/lib64/python2.7/site-packages/modeller/parallel/job.py", line 131, in run_all_tasks for task in self._finish_all_tasks(): File "/usr/lib64/python2.7/site-packages/modeller/parallel/job.py", line 164, in _finish_all_tasks task = self._process_event(obj, s) File "/usr/lib64/python2.7/site-packages/modeller/parallel/job.py", line 180, in _process_event task = obj.task_results() File "/usr/lib64/python2.7/site-packages/modeller/parallel/slave.py", line 61, in task_results r = self.get_data(allow_heartbeat=True) File "/usr/lib64/python2.7/site-packages/modeller/parallel/communicator.py", line 89, in get_data (cmdtype, obj) = self._recv() File "/usr/lib64/python2.7/site-packages/modeller/parallel/communicator.py", line 130, in _recv raise RemoteError(obj.exc, self) modeller.parallel.communicator.RemoteError: <type 'ValueError'>: GA341______E> Sequence identity -999.000 out of range - must be between 0 and 100. Seq. ID is read from the model.seq_id variable, which is obtained automatically from the REMARK lines of MODELLER-produced PDB files from <Slave on localhost>
On 2/19/12 11:59 AM, albert wrote: > I am trying to generate loop models with loop protocol in the latest > Modeller verison. It only produced 8 models and stopped, and it said the > following: ... > modeller.parallel.communicator.RemoteError: <type 'ValueError'>: > GA341______E> Sequence identity -999.000 out of range - must be between > 0 and 100. > Seq. ID is read from the model.seq_id variable, which > is obtained automatically from the REMARK lines of > MODELLER-produced PDB files
GA341 takes the sequence identity of the template as a parameter. Are you trying to refine a regular PDB file? If so, you can't use GA341, because Modeller doesn't know the sequence identity. If you're trying to refine a model produced by Modeller, it should work, because that information should be present in the PDB file as a REMARK record.
Ben Webb, Modeller Caretaker