December 2014 - modeller_usage

using Modeller for building models using contacts and secondary structures
by Adhikari, Badri (MU-Student) 06 Jan '15

06 Jan '15

Hello, I used Modeller to reconstruct around a 100 proteins with true residue-residue contacts and secondary structure information. I could reconstruct only a few proteins with high accuracy. Below is a sample script I used for Modelling. I did not use any templates. (I found that Modeller satisfies more contact restraints when I provided a template with just one residue's coordinates instead of an extended structure as a template.) I wonder why Modeller could not satisfy true contact restraints. Is there any specific way to reconstruct proteins using true residue contacts? My PY files and PIR files look like this: from modeller import * from modeller.automodel import * log.verbose() env = environ() env.io.atom_files_directory = ['.'] class MyModel(automodel): def special_restraints(self, aln): rsr = self.restraints at = self.atoms # Helices and Strands rsr.add(secondary_structure.strand(self.residue_range('3:', '11:'))) rsr.add(secondary_structure.strand(self.residue_range('16:', '26:'))) rsr.add(secondary_structure.alpha(self.residue_range('126:', '140:'))) # Contacts: rsr.add(forms.upper_bound(group=physical.xy_distance,feature=features.distance(at['CA:9'], at['CA:18']),mean=8.0, stdev=0.1)) rsr.add(forms.upper_bound(group=physical.xy_distance,feature=features.distance(at['CB:3'], at['CB:24']),mean=8.0, stdev=0.1)) rsr.add(forms.upper_bound(group=physical.xy_distance,feature=features.distance(at['CB:5'], at['CB:22']),mean=8.0, stdev=0.1)) rsr.add(forms.upper_bound(group=physical.xy_distance,feature=features.distance(at['CB:122'], at['CB:132']),mean=8.0, stdev=0.1)) a = MyModel(env, alnfile = '1f21.pir', # alignment filename knowns = 'empty', # codes of the templates sequence = '1f21') # code of the target a.starting_model= 1 a.ending_model = 20 a.make() C; >P1;empty structureX:empty: 1: : 152: : : :1.0: K-------------------------------------------------------------------------------------------------------------------------------------------------------* C; >P1;1f21 : : : : : : : : : KQVEIFTDGSALGNPGPGGYGAILRYRGREKTFSAGYTRTTNNRMELMAAIVALEALKEHAEVILSTDSQYVRQGITQWIHNWKKRGWKTADKKPVKNVDLWQRLDAALGQHQIKWEWVKGHAGHPENERADELARAAAMNPTLEDTGYQVE* Badri Adhikari University of Missouri ?

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Error
by Sakshi Rajput 27 Dec '14

27 Dec '14

Hi, I am using Modeller9.14 and python2.7 version. When I execute the script, it shows error 'import site' failed; use -v for traceback Cannot open logfile align2d.log: Permission denied I hope you will solve my problem as soon as possible. Thanking you Yours Sincerely, Sakshi Singh -- Yours Sincerely, Sakshi Singh Research Scholar, Dept. of Molecular and Human Genetics,BHU, Varanasi, India

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Re: [modeller_usage] Disulfide bridge between residues into different monomers
by bharat lal 12 Dec '14

12 Dec '14

Hi, I am working on a decameric protein and want to create disulfide bridge between cysteines of adjacent monomers. I used the following script (model-disulfide.py): # Homology modeling by the automodel classfrom modeller import * # Load standard Modeller classesfrom 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 8 and 45: self.patch(residue_type='DISU', residues=(self.residues['14:A'], self.residues['44:D'])) log.verbose() # request verbose outputenv = environ() # create a new MODELLER environment to build this model in # directories for input atom filesenv.io.atom_files_directory = ['.', '../atom_files'] a = MyModel(env, alnfile = 'twochain.ali', # alignment filename knowns = 'em', # codes of the templates sequence = 'query') # code of the targeta.starting_model= 1 # index of the first modela.ending_model = 1 # index of the last model # (determines how many models to calculate)a.make() # do the actual homology modeling First I tried making only one hydrogen bond between residue 14 of chain A and 44 of chain D but I am getting the following errors:- H:\Modeller9.13\examples\automodel\Lysine Decarboxylase>mod9.13 model-disulfide. py'import site' failed; use -v for tracebackTraceback (most recent call last): File "model-disulfide.py", line 26, in ? a.make() # do the actual homology modeling File "H:\Modeller9.13\modlib\modeller\automodel\automodel.py", line 97, in make self.homcsr(exit_stage) File "H:\Modeller9.13\modlib\modeller\automodel\automodel.py", line 436, in homcsr self.make_initial_model(aln) File "H:\Modeller9.13\modlib\modeller\automodel\automodel.py", line 450, in make_initial_model self.generate_method(self, aln) File "H:\Modeller9.13\modlib\modeller\automodel\generate.py", line 39, in transfer_xyz mdl.create_topology(aln) File "H:\Modeller9.13\modlib\modeller\automodel\automodel.py", line 677, in create_topology self.special_patches(aln) File "model-disulfide.py", line 10, in special_patches self.patch(residue_type='DISU', residues=(self.residues['14:A'], File "H:\Modeller9.13\modlib\modeller\coordinates.py", line 254, in __getitem__ (self.offset, self.length, self.suffix)) File "H:\Modeller9.13\modlib\modeller\util\modutil.py", line 23, in handle_seq_indx int_indx = lookup_func(*args) File "H:\Modeller9.13\modlib\modeller\coordinates.py", line 318, in _indxres raise KeyError("No such residue: %s" % indx)KeyError: 'No such residue: 44:D' I even tried giving the residue information as: 14:A and 44:D, but still I am getting the same error (as above). Just to inform you further my template does not have cysteines for the formation of disulfide bridges, so I also generated a mutant with cysteines and tried the patch.py script: from modeller import *from modeller.scripts import complete_pdb env = environ()env.io.atom_files_directory = ['../atom_files']env.libs.topology.read(file='$(LIB)/top_heav.lib')env.libs.parameters.read(file='$(LIB)/par.lib') # Create the disulfide bond:def patches(mdl): mdl.patch(residue_type='DISU', residues=(mdl.residues['14:A'], mdl.residues['44:D']))# Read the sequence:code = 'em-2.pdb'mdl = complete_pdb(env, code, special_patches=patches) # Create the stereochemical restraintssel = selection(mdl)mdl.restraints.make(sel, restraint_type='stereo', spline_on_site=False) # Calculate the energy to test the disulfide:sel.energy() This is the error I got: H:\Modeller9.13\examples\automodel\Lysine Decarboxylase>mod9.13 patch.py'import site' failed; use -v for tracebackTraceback (most recent call last): File "patch.py", line 19, in ? mdl = complete_pdb(env, code, special_patches=patches) File "H:\Modeller9.13\modlib\modeller\scripts\complete_pdb.py", line 39, in complete_pdb special_patches(mdl) File "patch.py", line 15, in patches mdl.patch(residue_type='DISU', residues=(mdl.residues['14:A'], File "H:\Modeller9.13\modlib\modeller\coordinates.py", line 254, in __getitem__ (self.offset, self.length, self.suffix)) File "H:\Modeller9.13\modlib\modeller\util\modutil.py", line 23, in handle_seq_indx int_indx = lookup_func(*args) File "H:\Modeller9.13\modlib\modeller\coordinates.py", line 318, in _indxres raise KeyError("No such residue: %s" % indx)KeyError: 'No such residue: 44:D' Can anybody help me in this regard? Monu

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Using unpublished structures for template to create models?
by Geoffrey Lippa 10 Dec '14

10 Dec '14

Hi all, I was hoping to get some help on the modeling of a protein target by sequence alignment using a 41% similar structure template I recently solved, in place of a published structure on the PDB. The resolution has changed and may help create a more accurate model for ligand docking. Thanks. Geoff Dr. Geoffrey Lippa Post-doctoral Research Associate Laboratory of Dr. Andrew Gulick Hauptman Woodward Medical Research Institute 700 Ellicott St., Buffalo, NY 14203 Phone: 585-690-0850 Email: glippa(a)hwi.buffalo.edu

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