- modeller_usage - salilab.org

symmetric hexamer
by o.h.weiergraeber＠fz-juelich.de 16 Jul '08

16 Jul '08

Hello, we are trying to build a symmetric hexamer of a 735 aa protein molecule. Modelling the monomer works without problems. For the hexamer, we have generated the hexameric template and replicated the target sequence in the alignment file accordingly. This works flawlessly, as well. However, if we insert these symmetry retraints (adopted from the example in the manual) ------------------------------------------- # Override the 'special_restraints' and 'user_after_single_model' methods: class MyModel(automodel): def special_restraints(self, aln): # Constrain the A and B chains to be identical (but only restrain # the C-alpha atoms, to reduce the number of interatomic distances # that need to be calculated): s1 = selection(self.chains['A']).only_atom_types('CA') s2 = selection(self.chains['B']).only_atom_types('CA') s3 = selection(self.chains['C']).only_atom_types('CA') s4 = selection(self.chains['D']).only_atom_types('CA') s5 = selection(self.chains['E']).only_atom_types('CA') s6 = selection(self.chains['F']).only_atom_types('CA') self.restraints.symmetry.append(symmetry(s1, s2, s3, s4, s5, s6, 1.0)) def user_after_single_model(self): # Report on symmetry violations greater than 1A after building # each model: self.restraints.symmetry.report(1.0) ------------------------------------------- leaving both alignment and template files untouched, then the program stops with the following error: ------------------------------------------- Traceback (most recent call last): File "get-model2.py", line 42, in ? a.make() # do homology modeling File "/usr/local/modeller_9v4/modlib/modeller/automodel/automodel.py", line 98, in make self.homcsr(exit_stage) File "/usr/local/modeller_9v4/modlib/modeller/automodel/automodel.py", line 436, in homcsr self.mkhomcsr(selection(self), aln) File "/usr/local/modeller_9v4/modlib/modeller/automodel/automodel.py", line 524, in mkhomcsr self.special_restraints(aln) File "get-model2.py", line 23, in special_restraints self.restraints.symmetry.append(symmetry(s1, s2, s3, s4, s5, s6, 1.0)) TypeError: __init__() takes exactly 4 arguments (8 given) ------------------------------------------- We are a bit lost here :( Which init call is the message referring to? Any ideas how to resolve this? Oliver ------------------------------------------------------------------- ------------------------------------------------------------------- Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzende des Aufsichtsrats: MinDir'in Baerbel Brumme-Bothe Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr. Harald Bolt, Dr. Sebastian M. Schmidt ------------------------------------------------------------------- -------------------------------------------------------------------

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GA341 assessment
by Lella Sana 02 Jul '08

02 Jul '08

Dear all, how could I carry out GA341 assessment on a model not produced by MODELLER but by an ab initio method? I'm using MODELLER 9v2. Thanx in advance Hai un indirizzo email difficile da ricordare? Scegli quello che hai sempre desiderato su Yahoo! Mail http://it.docs.yahoo.com/nuovo_indirizzo.html

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restraint check
by Ryan 01 Jul '08

01 Jul '08

I am currently modelling a system with a fair amount of restraints (symmetry, secondary structure, and distance) that takes over an hour to model. I have found that if i make a mistake in naming one of the residues/atoms in one of my restraints, that the program does not catch this right away, but will crash after about an hour when it finally notices that the restraint is invalid. This is a pretty inconvenient way in realizing my input mistakes, and am wondering if there is a way to have Modeller check that all of my restraints are valid before the program begins processing the models. Thanks, ryan

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non-proline cis-peptide bonds
by François Sampieri 01 Jul '08

01 Jul '08

Hi all, I want to force a non-proline peptide bond to the cis configuration in a 64-residue model. I found a routine to force Pro residue to the cis configuration in the FAQ. I assumed that it would not make a difference if the residue it applies to is not an actual proline and I include the routine in my .py script, but I got only models with the trans peptide configuration. This is an example of my .py file : # Homology modelling by the automodel class from modeller import * # Load standard Modeller classes from modeller.automodel import * # Load the automodel class # Redefine the special_patches routine to include the additional disulfides # (this routine is empty by default): class mymodel(automodel): def special_patches(self, aln): # A disulfide between residues 12 and 63: self.patch(residue_type='DISU', residues=(self.residues['12'], self.residues['63'])) # A disulfide between residues 16 and 36: self.patch(residue_type='DISU', residues=(self.residues['16'], self.residues['36'])) # A disulfide between residues 22 and 46: self.patch(residue_type='DISU', residues=(self.residues['22'], self.residues['46'])) # A disulfide between residues 26 and 48: self.patch(residue_type='DISU', residues=(self.residues['26'], self.residues['48'])) # Redefine the special_restraints routine to force Pro to cis conformation: # (this routine is empty by default): class mymodel(automodel): def special_restraints(self, aln): a = self.atoms cispeptide(self.restraints, atom_ids1=(a['O:9'], a['C:9'], a['N:10'], a['CA:10']), atom_ids2=(a['CA:9'], a['C:9'], a['N:10'], a['CA:10'])) log.verbose() # request verbose output env = environ() # create a new MODELLER environment to build this model in # directories for input atom files env.io.atom_files_directory = ['./'] a = automodel(env, alnfile = 'AahII-cis.ali', # alignment filename knowns = '1PTX', # codes of the templates sequence = 'AahII-cis') # code of the target a.starting_model= 1 # index of the first model a.ending_model = 1 # index of the last model # (determines how many models to calculate) a.make() # do the actual homology modelling ---------------------------------------------------------------------------------------------- I noticed only 3 lines in the log file with warnings: ... getf_______W> RTF restraint not found in the atoms list: residue type, indices: 7 64 atom names : C +N atom indices : 503 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 7 64 atom names : C CA +N O atom indices : 503 496 0 504 ... 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. ... ---------------------------------------------------------------------------------------------- Please could somebody tell me what is wrong in this modeling? Thank you! Regards, François Sampieri

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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"

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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 ---

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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 ---

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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

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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

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multiple templates
by Petr Danecek 30 May '08

30 May '08

Hello, I am attempting to build a model from multiple templates, but I am getting very bad results. After doing some tests I have discovered that the problem lies most probably in the unwanted 3D orientation of the blocks which the model is built from. To test this, I took a single PDB file and splitted it into three chunks aligned as: aaaaaaaaa------------------------- ------aaaaaaaaaaa----------------- --------------aaaaaaaaaaaaaaaaaaaa aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa In this test, I would like to reconstruct the original structure. Is it possible? I tried to set the variable a.initial_malign3d=1, but the modeller ends with the error "_modeller.ModellerError: fit2xyz_296E> Number of equivalent positions < 3: 0" Any help would be greatly appreciated. Best regards, Petr Danecek

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