- modeller_usage - salilab.org

Loop Model ranking
by flavio seixas 23 Nov '11

23 Nov '11

Hi Ben First of all I would like to apologise for a so basic question. However, I am not a pyton expert and do not have another one to ask here. I run the loop.py scritp to generate 200 models. However, my attempt to rank the models by DOPE score fails. I am using the script below: ############################################ from modeller import * from modeller.automodel import * log.verbose() env = environ() env.io.atom_files_directory = ['.', '../atom_files'] # Read in HETATM records from template PDBs env.io.hetatm = True # Create a new class based on 'loopmodel' so that we can redefine # select_loop_atoms class MyLoop(loopmodel): # This routine picks the residues to be refined by loop modeling def select_loop_atoms(self): # Two residue ranges (both will be refined simultaneously) return selection(self.residue_range('23:A', '25:A'), self.residue_range('73:A', '75:A')) m = MyLoop(env, inimodel='Modeloutput23.pdb', sequence='Target1', loop_assess_methods=(assess.DOPE, assess.GA341)) m.loop.starting_model= 1 # index of the first loop model m.loop.ending_model = 200 # index of the last loop model m.loop.md_level = refine.very_fast # loop refinement method m.make() # Get a list of all successfully built models from a.outputs ok_models = filter(lambda x: x['failure'] is None, a.outputs) # Rank the models by DOPE score key = 'DOPE score' ok_models.sort(lambda a,b: cmp(a[key], b[key])) # Get top model m = ok_models[0] print "Top model 1: %s (DOPE score %.3f)" % (m['name'], m[key]) m = ok_models[1] print "Top model 2: %s (DOPE score %.3f)" % (m['name'], m[key]) m = ok_models[2] print "Top model 3: %s (DOPE score %.3f)" % (m['name'], m[key]) m = ok_models[3] print "Top model 4: %s (DOPE score %.3f)" % (m['name'], m[key]) m = ok_models[4] print "Top model 5: %s (DOPE score %.3f)" % (m['name'], m[key]) ############################## I realise that "loop assess methods" could not be the same sintax for "model assess methods", but I do not know how to correct it in the script Could you give me any help? Thanks in advance, Flavio

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error in align codes
by si yang 17 Nov '11

17 Nov '11

Hi, i am Yang here.. I try to build a model by using basic tutorial, that begin with only protein sequence, to look for potential templates. However, i have encountered a problem during build_profile.py loading, it generate problem as below: Protein specified in ALIGN_CODES<i>, was not found in the alignment file;ALIGN_CODES< 1>= ALL The alignment file i saved in plain text format, with suffix .ali (bleg1_2439.ali), is that affected the reading by modeller? I don't specified the templates are used, so just follow the python file from basic example, the only thing i change, is only the align file that attached above.. Your feedback is important and appreciated.. Thank you

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Protein-DNA loop model
by Rubben Torella 17 Nov '11

17 Nov '11

Hi all, I used Modeller in the past to create small loops from scratch. Now I have a protein-DNA complex, and I have to build and model 4 loops of my protein. My first problem is that MODELLER does not support DNA, so I have to strip the DNA from the PDB and use the protein alone. Considering the problem that I have to "paste" the DNA to the modelled structure, I use the options *a.md_level= None* to keep the rest of the protein fixed and the option * a.loop.md_level* to model the loops. Now, these two commands work on three of the 4 loops, but I have another problem now: I have a very long loop to build (35 aa) and using these two commands, MODELLER create a very strange hairpin loop to connect these two positions. I know which will be the correct structure of this loop because I have a similar protein that present this loop, and the modelling is wrong. Finally, if I don't usage a.md_level=None, MODELLER builds a very good loop, but all the protein is in a complete different position with respect of the starting one. Any suggestion? Best regards Rubben -- PhD Student, Prof.Glen Group University of Cambridge, Unilever Center, Lensfield Road CB2 1EW Cambridge, Cambridgeshire, United Kingdom University Phone : +44 (0)1223 336432 Cell Phone: +44 (0)774 3358973

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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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