June 2008 - modeller_usage

question about mutate_model
by Anna Marabotti 30 Jun '08

30 Jun '08

I would like to use the script mutate_model to evaluate different conformations of the same mutant side chain inserted in a protein. Therefore I used the script "mutate model" as suggested in the Wiki section, and repeated the procedure 5 times, expecting to obtain 5 different conformations of the mutant side chain. Instead, I obtained 5 identical proteins with side chains perfectly superimposable between each others. How can I manage myself in order to obtain 5 different models of the same mutation? Moreover, this is probably a naive question, but since repeated MD cycles generally do not produce identical results, why this protocol did not work in such a way? Many thanks and best regards Anna Marabotti ______________________________________________ Anna Marabotti, Ph.D. Laboratorio di Bioinformatica e Biologia Computazionale Istituto di Scienze dell'Alimentazione, CNR Via Roma 52 A/C 83100 Avellino (Italy) Tel: +39 0825 299651 Fax: +39 0825 781585 Skype: annam1972 E-mail: amarabotti(a)isa.cnr.it Web page: http://bioinformatica.isa.cnr.it/anna.htm Funded by RNBIO: http://www.rnbio.it/ ____________________________________________________ "If you think you are too small to make a difference, try sleeping with a mosquito"

2 1

Parallel job (part 2)
by Francesco Musiani 17 Jun '08

17 Jun '08

Ok, I modified my script as in the example. ---- (script) from modeller import * from modeller.automodel import * from modeller.scripts import complete_pdb from modeller.parallel import * j = job() j.append(local_slave()) j.append(local_slave()) log.verbose() class mymodel(allhmodel): def special_restraints(self, aln): s1 = selection(self.chains['A']) s2 = selection(self.chains['B']) self.restraints.symmetry.append(symmetry(s1, s2, 1.0)) def user_after_single_model(self): self.restraints.symmetry.report(1.0) env = environ() env.io_atom_files_directory = './' a = mymodel(env, alnfile = 'HpUreE.ali', knowns = 'dimerBp', sequence = 'HpUreE', assess_methods=(assess.DOPE, assess.GA341)) a.starting_model = 1 a.ending_model = 25 a.use_parallel_job(j) a.make() # Output data ok_models = filter(lambda x: x['failure'] is None, a.outputs) key = 'DOPE score' ok_models.sort(lambda a,b: cmp(a[key], b[key])) m = ok_models[0] print "Top model: %s (DOPE score %.3f)" % (m['name'], m[key]) env.libs.topology.read(file='$(LIB)/top_heav.lib') env.libs.parameters.read(file='$(LIB)/par.lib') # read model file mdl = complete_pdb(env, m['name']) # Assess with DOPE: s = selection(mdl) s.assess_dope(output='ENERGY_PROFILE NO_REPORT', file='HpUreE.best.profile', normalize_profile=True, smoothing_window=15) ---- (end) i obtained this error: ---- (log) Traceback (most recent call last): File "HpUreE.py", line 40, in ? a.make() File "/work/programs/MODELLER/modlib/modeller/automodel/automodel.py", line 109, in make self.multiple_models(atmsel) File "/work/programs/MODELLER/modlib/modeller/automodel/automodel.py", line 213, in multiple_models self.parallel_multiple_models(atmsel) File "/work/programs/MODELLER/modlib/modeller/automodel/automodel.py", line 233, in parallel_multiple_models self.outputs.extend(job.run_all_tasks()) File "/work/programs/MODELLER/modlib/modeller/parallel/job.py", line 110, in run_all_tasks self.finish_next_task() File "/work/programs/MODELLER/modlib/modeller/parallel/job.py", line 127, in finish_next_task self.process_event(obj, s) File "/work/programs/MODELLER/modlib/modeller/parallel/job.py", line 141, in process_event task = obj.task_results() File "/work/programs/MODELLER/modlib/modeller/parallel/slave.py", line 54, in task_results r = self.get_data(allow_heartbeat=True) File "/work/programs/MODELLER/modlib/modeller/parallel/communicator.py", line 81, in get_data (cmdtype, obj) = self._recv() File "/work/programs/MODELLER/modlib/modeller/parallel/communicator.py", line 119, in _recv raise RemoteError(obj.exc, self) modeller.parallel.communicator.RemoteError: AttributeError: 'module' object has no attribute 'mymodel' from <Slave on localhost> ---- (end) in the .slave0 and .slave1 log file I have this error: ---- (log) Slave startup: connect to master at 127.0.1.1:59037:0:EABQEAKC Traceback (most recent call last): File "<string>", line 1, in ? File "/work/programs/MODELLER/modlib/modeller/parallel/slaveloop.py", line 63, in slaveloop handle_slave_io(master, slavedict) File "/work/programs/MODELLER/modlib/modeller/parallel/slaveloop.py", line 38, in handle_slave_io exec(cmdstr, slavedict) File "<string>", line 1, in ? File "/work/programs/MODELLER/modlib/modeller/parallel/communicator.py", line 81, in get_data (cmdtype, obj) = self._recv() File "/work/programs/MODELLER/modlib/modeller/parallel/communicator.py", line 117, in _recv (obj, self.buffer) = cmdtype.recv(self.buffer) File "/work/programs/MODELLER/modlib/modeller/parallel/data_types.py", line 71, in recv return (pickle.loads(obj), buffer[1+p.get_position():]) File "/usr/local/lib/python2.3/pickle.py", line 1394, in loads return Unpickler(file).load() File "/usr/local/lib/python2.3/pickle.py", line 872, in load dispatch[key](self) File "/usr/local/lib/python2.3/pickle.py", line 1104, in load_global klass = self.find_class(module, name) File "/usr/local/lib/python2.3/pickle.py", line 1140, in find_class klass = getattr(mod, name) AttributeError: 'module' object has no attribute 'mymodel' ---- (end) running Modeller in the normal way do not produce any error. Thanks Francesco --- Francesco Musiani francesco.musiani(a)unibo.it ---

2 1

Parallel job
by Francesco Musiani 17 Jun '08

17 Jun '08

Hi, I would like to run a job on a QuadCore PC running linux, but I do not have any experience of parallel programming. Can you tell me how to parallelize a script like this? ---------- (script) from modeller import * from modeller.automodel import * from modeller.scripts import complete_pdb log.verbose() class mymodel(allhmodel): def special_restraints(self, aln): s1 = selection(self.chains['A']) s2 = selection(self.chains['B']) self.restraints.symmetry.append(symmetry(s1, s2, 1.0)) def user_after_single_model(self): self.restraints.symmetry.report(1.0) env = environ() env.io_atom_files_directory = './' a = mymodel(env, alnfile = 'HpUreE.ali', knowns = 'dimerBp', sequence = 'HpUreE', assess_methods=(assess.DOPE, assess.GA341)) a.starting_model = 1 a.ending_model = 25 a.make() # Output data ok_models = filter(lambda x: x['failure'] is None, a.outputs) key = 'DOPE score' ok_models.sort(lambda a,b: cmp(a[key], b[key])) m = ok_models[0] print "Top model: %s (DOPE score %.3f)" % (m['name'], m[key]) env.libs.topology.read(file='$(LIB)/top_heav.lib') env.libs.parameters.read(file='$(LIB)/par.lib') # read model file mdl = complete_pdb(env, m['name']) # Assess with DOPE: s = selection(mdl) s.assess_dope(output='ENERGY_PROFILE NO_REPORT', file='HpUreE.best.profile', normalize_profile=True, smoothing_window=15) ---------- (end script) Thanks Francesco --- Francesco Musiani francesco.musiani(a)unibo.it ---

2 1

Problem with running Flex-em
by Hua Li 13 Jun '08

13 Jun '08

Hi, I am very new to the program Modeller. I got a problem as I tried to run the program Modeller 9v4 on Linux. Is there anybody that can enlighten me on how to solve this problem? Any advice gratefully received. Error message: 'import site' failed; use -v for traceback Traceback (most recent call last): File "flex-em.py", line 10, in ? import shutil ImportError: No module named shutil In fact the module "shutil" is available at python library and I have added "setenv PYTHONHOME /usr/lib64/python2.4" to my .cshrc file. Thank you. Hua

2 1

PIR format clarification
by Thomas Juettemann 01 Jun '08

01 Jun '08

Dear all, a question about the PIR format in the align input file. I could not find the answer in the manual or the archives, apologies if I overead it. I created some PIR alignments with comment lines like these (2 different files): >cdk-cyclin;1W98.core >CDK2HUMANaCGA2HUMAN;1FIN both times MODELLER crashed and I got these error messages: read_al_373E> Protein specified in ALIGN_CODES(i) was not found in the alignment file; ALIGN_CODES( 1) = 1W98.core read_al_373E> Protein specified in ALIGN_CODES(i) was not found in the alignment file; ALIGN_CODES( 1) = 1FIN.core changing the comment lines to: >P1;1W98.core >P1;1FIN solved the problem. Must the comment line always start with ">P1"? If not, what are the limitations length and/or alphabet-wise? Many thanks, Thomas

2 2