November 2011 - modeller_usage

Error in align codes
by si yang 17 Nov '11

17 Nov '11

Hi, i am Yang here.. I am trying to build my model by using basic tutorial, however during build_profile, i have encountered a problem,Modeller error: read_al_373E> Protein specified in ALIGN_CODES<i> was not found in the alignment files; ALIGN_CODES< 1>= ALL, because i am looking for potential templates to my target. I have saved my alignment file (bleg1_2439.ali) in plain text format with suffix .ali, is that affect the reading? Your feedback is important and appreciated.. Thank you

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Problem in running script file
by Anushree Tripathi 16 Nov '11

16 Nov '11

I have installed Modeller and python2.3 version.After making all three files (i.e.,atom,alignment and script files in a folder placed on desktop) and changing directory, when I run command i.e., mod9v8 model-default.py.<http://model-default.py.it/>It is showing result i.e.,'mod9v8' is not recognised as an internal and external command,operable file or batch file.Please guide me to troubleshoot this problem as soon as possible.

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error with loops in transmembrane receptor model
by Vasillis Myrianthopoulos 16 Nov '11

16 Nov '11

Hi everybody, I am trying to build a model of a transmembrane receptor and I get serious problems and obvious steric errors on the loops which connect the TM helices. The alignment is correct on a biological and phylogenetic basis however there are large insertions on the loops. As a result, there are two main errors that appear in the model. First, the loops are modelled as packed between the TM helices and not as free moving segments that can float in the solvent environment and second, in some cases the loops form kind of knots which are obviously wrong. I guess that there must be some kind of parameter within MODELLER that directs the construction towards the maximum intramolecular contact, this is the only way I can explain this wrong output. Does anybody have an idea on the matter? many thanks, Vassilis

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error with loops in transmembrane receptor model
by Vasillis Myrianthopoulos 16 Nov '11

16 Nov '11

Hi everybody, I am trying to build a model of a transmembrane receptor and I get serious problems and obvious steric errors on the loops which connect the TM helices. The alignment is correct on a biological and phylogenetic basis however there are large insertions on the loops. As a result, there are two main errors that appear in the model. First, the loops are modelled as packed between the TM helices and not as free moving segments that can float in the solvent environment and second, in some cases the loops form kind of knots which are obviously wrong. I guess that there must be some kind of parameter within MODELLER that directs the construction towards the maximum intramolecular contact, this is the only way I can explain this wrong output. Does anybody have an idea on the matter? many thanks, Vassilis

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Lucky16: Ordered search across multiple models?
by R K Belew 10 Nov '11

10 Nov '11

hi Ben, i'm finding an odd pattern across what i think of as random trials, and i wonder why. Suppose i run N independently seeded runs from the same alignment and generate K models each time; ie, i have a distribution of N * K models. Now consider a small fraction EPSILON of these with good GA341 scores. i would expect the fraction of models which happened to be model "target.B ..._k" ( ie, the model that gets generated the k-th time by Modeller) to be uniform over choice of k, wouldn't you? instead, i find that for some values of k, ~50% have very good GA341 scores (across various random seed instances), while some have none. here's a sample distribution with K=20: > ModNum Freq > 1 0.01 > 3 0.03 > 4 0.02 > 5 0.01 > 6 0.09 > 7 0.01 > 8 0.01 > 9 0.05 > 11 0.06 > 12 0.08 > 15 0.01 > 16 0.50 > 19 0.05 > 20 0.01 what makes model#16 so consistently good?1 rik

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[clustering] does MODELLER provide tools to cluster structures ?
by Benjamin SCHWARZ 08 Nov '11

08 Nov '11

I am looking for tools that would allow me to cluster a set of superposed structures such as those obtained for instance through an iterative salign run. Does MODELLER provide anything to perform (structures) clustering ?

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Fwd: Fwd: automodel.max_molpdf recommended values and usage format
by Andrew Voronkov 08 Nov '11

08 Nov '11

Something was wrong with that script, I have taken model-outputs.py modified it and it worked fine. Best regards, Andrew -------- Пересылаемое сообщение -------- 08.11.2011, 16:41, "Andrew Voronkov" <drugdesign(a)yandex.ru>: Does it have name molpdf? I can't find DOPE or GA341 words in the log file. I have also got an error while ranking the solutions. Like this? But I have both DOPE and GA341, which of them is this? >> Summary of successfully produced models: Filename molpdf ---------------------------------------- chimera.B99990001.pdb 1580.34619 chimera.B99990002.pdb 1593.52393 chimera.B99990003.pdb 1693.15637 chimera.B99990004.pdb 1743.10718 chimera.B99990005.pdb 1586.12122 chimera.B99990006.pdb 1652.49170 chimera.B99990007.pdb 1477.14709 chimera.B99990008.pdb 1681.59668 chimera.B99990009.pdb 1625.87500 chimera.B99990010.pdb 1632.77686 chimera.B99990011.pdb 1689.23584 chimera.B99990012.pdb 1557.99890 chimera.B99990013.pdb 1622.84631 chimera.B99990014.pdb 1805.83228 chimera.B99990015.pdb 1525.45911 Also I have got an error while trying to select best solutions based on DOPE score (script is below): ok_models.sort(lambda a,b:cmp(a[key]), b[key])) KeyError: 'DOPE score' Here is the script, which was used: from modeller import * from modeller.automodel import * import sys 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 = ['.'] # Read in HETATM records from template PDBs env.io.hetatm = True a = automodel(env, alnfile = '2rf53mhj.pir', # alignment filename knowns = ('3mhj', '2rf5'), # codes of the templates sequence = 'chimera') # code of the target assess_methods=(assess.DOPE, assess.GA341) # assess each loop with DOPE a.starting_model= 1 # index of the first model a.ending_model = 15 # index of the last model # (determines how many models to calculate) # Thorough MD optimization: a.md_level = refine.slow a.make() # do the actual homology modeling # Get a list of all successfully built models from a.outputs ok_models = [x for x in a.outputs if x['failure'] is None] # Rank the models by DOPE score key = 'DOPE score' if sys.version_info[:2] == (2,3): # Python 2.3's sort doesn't have a 'key' argument ok_models.sort(lambda a,b: cmp(a[key], b[key])) else: ok_models.sort(key=lambda a: a[key]) # Get top model m = ok_models[0] print("Top model: %s (DOPE score %.3f)" % (m['name'], m[key])) Best regards, Andrew 07.11.2011, 19:51, "Modeller Caretaker" <modeller-care(a)salilab.org>: > On 11/7/11 5:21 AM, Andrew Voronkov wrote: >> Dear Ben, very simple question . I have used DOPE assessment, but in >> which file can I find the assessment results for the models? It's not >> in resulted PDB, there is only objective function.Where can I find >> those DOPE and GA341 values? > In the log file. They are not put in the PDB file. > > Ben Webb, Modeller Caretaker > > -- > modeller-care(a)salilab.org http://www.salilab.org/modeller/ > Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage -------- Завершение пересылаемого сообщения --------

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Fwd: automodel.max_molpdf recommended values and usage format
by Andrew Voronkov 07 Nov '11

07 Nov '11

Dear Ben, very simple question . I have used DOPE assessment, but in which file can I find the assessment results for the models? It's not in resulted PDB, there is only objective function.Where can I find those DOPE and GA341 values? I have used the next Python script for the assessment: # Loop refinement of an existing model from modeller import * from modeller.automodel import * log.verbose() env = environ() # directories for input atom files env.io.atom_files_directory = ['.'] # Read in HETATM records from template PDBs env.io.hetatm = True # Create a new class based on 'dopehr_loopmodel' so that we can redefine # select_loop_atoms (necessary) class MyLoop(dopehr_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('92:', '111:')) m = MyLoop(env, inimodel='3mhj.pdb', # initial model of the target sequence='3mhj' # code of the target ) assess_methods=(assess.DOPE, assess.GA341) # assess each loop with DOPE m.loop.starting_model= 1 # index of the first loop model m.loop.ending_model = 20 # index of the last loop model m.loop.md_level = refine.slow_large # loop refinement method m.make() Should those scores be available as molpdf values in .log file? Best regards, Andrew 01.11.2011, 22:55, "Modeller Caretaker" <modeller-care(a)salilab.org>: > On 11/01/2011 10:28 AM, Andrew Voronkov wrote: >> how on your opinion modeller objective function correlates with >> quality of the models. For example I have objective function value >> 1730 for one modelk and -750 which as I understand reflects free >> energy. Does it mean that I shouldn t consider the first one at >> all? > The Modeller objective function is simply a measure of how many > restraints were violated in building your model. While the score could > be thought of roughly as an "energy" (not free energy) this is certainly > not a rigorous measure of model quality. Use an assessment function such > as normalized DOPE for this purpose. >> Let's say I want to make cutoff -100 for the objective function. In >> which format it should be done? >> >> automodel.max_molpdf -100 > Build your models, then assess them and pick the best ones. max_molpdf > is designed as a filter to throw away the very worst models - it doesn't > act on the final PDF, but the score of intermediate (partially > optimized) models - the reasoning being to not waste time on trying to > optimize a model that is very bad. Thus max_molpdf is not really what > you want here. > > Ben Webb, Modeller Caretaker > > -- > modeller-care(a)salilab.org http://www.salilab.org/modeller/ > Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage -------- Завершение пересылаемого сообщения --------

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parallelization with randomize.dihedrals?
by R K Belew 04 Nov '11

04 Nov '11

hi Ben et al, just when i thought i had my parallel version working nicely... i tried doing a run that had only one difference from previous: a.rand_method = randomize.dihedrals vs previous: a.rand_method = randomize.xyz but this throws an error: > File "seed_align_pp.py", line 93, in doAllAlign > for results in j.yield_tasks_unordered(): > File "/usr/lib/python2.6/dist-packages/modeller/parallel/job.py", line 145, in yield_tasks_unordered > for task in self._finish_all_tasks(): > File "/usr/lib/python2.6/dist-packages/modeller/parallel/job.py", line 163, in _finish_all_tasks > task = self._process_event(obj, s) > File "/usr/lib/python2.6/dist-packages/modeller/parallel/job.py", line 179, in _process_event > task = obj.task_results() > File "/usr/lib/python2.6/dist-packages/modeller/parallel/slave.py", line 61, in task_results > r = self.get_data(allow_heartbeat=True) > File "/usr/lib/python2.6/dist-packages/modeller/parallel/communicator.py", line 84, in get_data > (cmdtype, obj) = self._recv() > File "/usr/lib/python2.6/dist-packages/modeller/parallel/communicator.py", line 125, in _recv > raise RemoteError(obj.exc, self) > modeller.parallel.communicator.RemoteError: <type 'NameError'>: global name 'alignment' is not defined from <Slave on localhost> any guesses as to why? thanks again for your help. Rik

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Build a model with multiple models
by junior 02 Nov '11

02 Nov '11

Hi, How do I build a PDB file containing more than 10 models? Thank you. Sam Kauba

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