- modeller_usage - salilab.org

distance restraint
by flavio seixas 13 Aug '14

13 Aug '14

Hi Ben, I try to make a distance restraint between two atoms (protein and cofator) in a homodimer protein. However, I face another error: [flavios@localhost]$ mod9.13 model-mult-simmetry-bond.py Could not find platform independent libraries <prefix> Could not find platform dependent libraries <exec_prefix> Consider setting $PYTHONHOME to <prefix>[:<exec_prefix>] 'import site' failed; use -v for traceback Traceback (most recent call last): File "model-mult-simmetry-bond.py", line 40, in ? a.make() File "/usr/lib/modeller9.13/modlib/modeller/automodel/automodel.py", line 108, in make self.multiple_models(atmsel) File "/usr/lib/modeller9.13/modlib/modeller/automodel/automodel.py", line 212, in multiple_models self.outputs.append(self.single_model(atmsel, num)) File "/usr/lib/modeller9.13/modlib/modeller/automodel/automodel.py", line 308, in single_model self.model_analysis(atmsel, filename, out, num) File "/usr/lib/modeller9.13/modlib/modeller/automodel/automodel.py", line 350, in model_analysis self.user_after_single_model() File "model-mult-simmetry-bond.py", line 34, in user_after_single_model rsr.add(forms.gaussian(group=physical.xy_distance, feature=features.distance(at['NZ:38'], at['C4:382']), mean=1.5, stdev=0.1)) NameError: global name 'rsr' is not defined I am certain that it must be an script error, but I do not know how to fix (I am not familiar with python script). My script is: # Homology modeling with single template from modeller import * # Load standard Modeller classes from modeller.automodel import * # Load the automodel class 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 = ['.', '../atom_files'] # Read in HETATM records from template PDBs env.io.hetatm = True env.io.water = True class MyModel(automodel): def special_restraints(self, aln): rsr = self.restraints at = self.atoms # Constrain the A, B, C and D 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') self.restraints.symmetry.append(symmetry(s1, s2, 1)) def user_after_single_model(self): # Report on symmetry violations greater than 1A after building # each model: self.restraints.symmetry.report(1.0) #Restrain between LYS and PLP (st. dev.=0.1) #Use a harmonic potential and X-Y distance group. rsr.add(forms.gaussian(group=physical.xy_distance, feature=features.distance(at['NZ:38'], at['C4:382']), mean=1.5, stdev=0.1)) rsr.add(forms.gaussian(group=physical.xy_distance, feature=features.distance(at['NZ:424'], at['C4:768']), mean=1.5, stdev=0.1)) a=MyModel(env, alnfile='AlRacem-mult.ali', knowns=('4A3Q', '1BD0'), sequence='AlRacem', assess_methods=(assess.DOPE, assess.GA341)) a.starting_model = 1 a.ending_model = 10 a.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]) ------------------------------------- Flavio Augusto Vicente Seixas Laboratory of Structural Biochemistry Department of Biochemistry Universidade Estadual de Maringá, PR, Brazil http://www.uem.br

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User restriction
by flavio seixas 11 Aug '14

11 Aug '14

Hi, I was trying to make a restriction to generate a covalent bond between NZ atom from Lisine with C4 atom of PLP cofator. I search Manual and modeler-List to find some clues about how to do, but USER restriction appears to be not supported by 9.13 version: [flavios@localhost AlaninaRacemase-Saureus-T9]$ mod9.13 model-mult-simmetry-restr.py & Could not find platform independent libraries <prefix> Could not find platform dependent libraries <exec_prefix> Consider setting $PYTHONHOME to <prefix>[:<exec_prefix>] 'import site' failed; use -v for traceback Traceback (most recent call last): File "model-mult-simmetry-restr.py", line 35, in ? a.make() File "/usr/lib/modeller9.13/modlib/modeller/automodel/automodel.py", line 103, in make self.rd_restraints() File "/usr/lib/modeller9.13/modlib/modeller/automodel/automodel.py", line 191, in rd_restraints self.restraints.append(file=self.csrfile) File "/usr/lib/modeller9.13/modlib/modeller/restraints.py", line 77, in append return _modeller.mod_restraints_read(self.__mdl.modpt, fh.file_pointer) _modeller.ModellerError: rdcsrs__703E> USER restraints format is no longer supported. My script contains model-mult-simmetry-restr.py contains: # Homology modeling from modeller import * # Load standard Modeller classes from modeller.automodel import * # Load the automodel class 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 = ['.', '../atom_files'] # Read in HETATM records from template PDBs env.io.hetatm = True env.io.water = True class MyModel(automodel): def special_restraints(self, aln): rsr = self.restraints at = self.atoms # Constrain the A, 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') self.restraints.symmetry.append(symmetry(s1, s2, 1)) def user_after_single_model(self): # Report on symmetry violations greater than 1A after building # each model: self.restraints.symmetry.report(1.0) a=MyModel(env, alnfile='AlRacem-mult.ali', knowns=('4A3Q', '1BD0'), sequence='AlRacem', csrfile='my.rsr', assess_methods=(assess.DOPE, assess.GA341)) a.starting_model = 1 a.ending_model = 1 a.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]) my.rsr file contains: MODELLER5 VERSION: USER FORMAT R 3 1 1 1 2 2 0 1.5000 0.2000 NZ:38:A C4:382:A R 3 1 1 1 2 2 0 1.5000 0.2000 NZ:424:B C4:768:B I appreciate any help. Best regards, Flavio ------------------------------------- Flavio Augusto Vicente Seixas Laboratory of Structural Biochemistry Department of Biochemistry Universidade Estadual de Maringá, PR, Brazil http://www.uem.br

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Auto Response
by Filipe Natalio 29 Jul '14

29 Jul '14

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Modeller 9.14 release
by Modeller Caretaker 29 Jul '14

29 Jul '14

The new version of Modeller, 9.14, is now available for download! Please see the download page at http://salilab.org/modeller/ for more information. If you have a license key for Modeller 8 or 9, there is no need to reregister for Modeller 9.14 - the same license key will work. (It won't do any harm to reregister if you want to, though!) 9.14 is primarily a bugfix release relative to the last public release (9.13). Major user-visible changes include: # The new PDB format (PDBx/mmCIF) is now handled. Templates can be mmCIF files, and model.read() and model.write() also support mmCIF. See also automodel.set_output_model_format() to write out models in mmCIF format. # Add Python 3.4 support. # Add support for 64-bit Windows. # density.read() now uses the origin in the MRC/CCP4 file if it is not specified. See the Modeller manual for a full change log: http://salilab.org/modeller/9.14/manual/node40.html If you encounter bugs in Modeller 9.14, please see http://salilab.org/modeller/9.14/manual/node10.html for information on how to report them. Note: you are receiving this email either because you subscribed to the modeller_usage mailing list, or you provided this address when you requested a Modeller license and you ticked the "notify me of new releases" box. In the latter case, if you no longer wish to receive announcements of new Modeller releases, simply reply to this email and let us know. Ben Webb, Modeller Caretaker -- modeller-care(a)salilab.org http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage

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Advanced clustering
by James Starlight 23 Jul '14

23 Jul '14

Dear modeller users! I wounder if it would possible to perform advanced clustering of all generated models (e.g using automodel.cluster()) based on the selected criterium from the built models (e.g percent and composition of secondary structure in the selected region, number of salt-bridges in selected region, distance between selected pair of atoms etc). Many thanks for suggestion, James

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Problem regarding 3D structure prediction
by Vishal Nemaysh 22 Jul '14

22 Jul '14

Respected Sir, I have faced a problem during 3D structure prediction of my target protein of interest. The length of the protein sequence is (1106 amino acids). Sir i have tried to find out some templates for covering the whole query sequence during BLAST or psiBLAST. But there is no any single template or multiple templates are found to occupied this whole query sequence. Kindly suggest me how to overcome this problem. Thanks in advance. -- Vishal Research Scholar, Neuropharmaceutical Chemistry lab., Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi-110007 Email: *vishal.bioinfotech(a)gmail.com <vishal.bioinfotech(a)gmail.com>* Phone: 91-11-27662778 Mobile: 91+9650736653

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Join me on LinkedIn to share updates and stay in touch
by Jayashankar Selvadurai 22 Jul '14

22 Jul '14

Hi , I'd like to add you to my professional network on LinkedIn. - Jayashankar Accept: https://www.linkedin.com/e/v2?e=-xaf1me-hxx2izlh-6y&a=preRegInvite&tracking… You are receiving Invitation emails. Unsubscribe here: https://www.linkedin.com/e/v2?e=-xaf1me-hxx2izlh-6y&t=uns&midToken=AQFmrFVh… Learn why we included this at the following link: http://www.linkedin.com/e/v2?e=-xaf1me-hxx2izlh-6y&a=customerServiceUrl&ek=… © 2014, LinkedIn Corporation. 2029 Stierlin Ct. Mountain View, CA 94043, USA

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Protein:Protein complex PIR format
by Parker de Waal 15 Jul '14

15 Jul '14

Hello MODELLER users, After looking through the mailing list I have been able to find numerous discussions about protein:protein complex homology modeling, however I have been unable to find any examples for proper PIR formatting and was wondering if someone would be willing to help. I would like to perform modeling for unknown complex A2:B1 where A1:B1 is known and while holding B1 completely frozen. Would the following PIR snippet below work for such modeling or is more information required on the second line as shown here https://salilab.org/modeller/9v8/manual/node454.html? >P1;Comp1 Known Complex AAABBAAAA/ CCCCCCCCC* >P1;Comp2 Unknown Complex AAADDAAAA/ CCCCCCCCC* Cheers, Parker

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conjugate gradients or molecular dynamics optimizations with automodel.make()
by Li SUN 15 Jul '14

15 Jul '14

Hi everyone, I have a question regarding the usage of automodel.make() for modelling a protein structure from known structures. Does this function include optimization methods e.g. conjugate gradients or molecular dynamics so that it will output a structure close to the native state (lowest-energy state), or do I have to call conjugate_gradients() or molecular_dynamics() explicitly after automodel.make() to do an energy minimization? Thanks in advance. -- Li Sun Department of Physics University of California, San Diego

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Mismatch in the alignment
by Sajeewa Pemasinghe 07 Jul '14

07 Jul '14

Hi everyone, I am trying to fill 11 missing residues in a protein. 5 of them are at the N-terminal and the other 6 are at the C-terminal. Other than that there are 9 non-standard residues and 228 waters in the pdb as well. My alignment file looks as below. >P1;2ABC structureX:2ABC: 6 :A:+402 :A:MOL_ID 1; -----PRFTTGLVYDTLMLKHQCTCGSSSSHPEHAGRIQSIWSRLQETGLRGKCECIRGRKATLEELQTVHSEAHTLLYG TNPLNRQKLDSKKLLGSLASVFVRLPCGGVGVDSDTIWNEVHSAGAARLAVGCVVELVFKVATGELKNGFAVVRP PGHHAEESTPMGFCYFNSVAVAAKLLQQRLSVSKILIVDWDVHHGNGTQQAFYSDPSVLYMSLHRYDDGNFFPGS GAPDEVGTGPGVGFNVNMAFTGGLDPPMGDAEYLAAFRTVVMPIASEFAPDVVLVSSGFDAVEGHPTPLGGYNLS ARCFGYLTKQLMGLAGGRIVLALEGGHDLTAICDASEACVSALLGNELDPLPEKVLQQRPNANAVRSMEKVMEIH SKYWRCLQRTTSTAGRSLIEAQTCENE------.........wwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwww wwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwww wwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwww wwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwww* >P1;2ABC_fill sequence::::::::: GAMTKPRFTTGLVYDTLMLKHQCTCGSSSSHPEHAGRIQSIWSRLQETGLRGKCECIRGRKATLEELQTVHSEAHTLLYG TNPLNRQKLDSKKLLGSLASVFVRLPCGGVGVDSDTIWNEVHSAGAARLAVGCVVELVFKVATGELKNGFAVVRP PGHHAEESTPMGFCYFNSVAVAAKLLQQRLSVSKILIVDWDVHHGNGTQQAFYSDPSVLYMSLHRYDDGNFFPGS GAPDEVGTGPGVGFNVNMAFTGGLDPPMGDAEYLAAFRTVVMPIASEFAPDVVLVSSGFDAVEGHPTPLGGYNLS ARCFGYLTKQLMGLAGGRIVLALEGGHDLTAICDASEACVSALLGNELDPLPEKVLQQRPNANAVRSMEKVMEIH SKYWRCLQRTTSTAGRSLIEAQTCENEEAETVT.........wwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwww wwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwww wwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwww wwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwww* I get the following error when I run the python script. read_te_290E> Number of residues in the alignment and pdb files are different: 639 402 For alignment entry: 1 2ABC x (mismatch at alignment position 403) Alignment QRTTSTAGRSLIEAQTCENE.........wwwwwwwwwwwwwwwwwwwwwwwwwwwwwwww PDB QRTTSTAGRSLIEAQTCENE Match ********************************* I have been trying many modifications for a few hours now but I just cannot figure out what is wrong. I would highly appreciate some advice to get around this problem. Thank you very much Sajeewa Dewage

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