- modeller_usage - salilab.org

Modeller API
by Mouses Stamboulian 04 Feb '15

04 Feb '15

?Hi, I'm a student at the Lebanese American University and I was wondering if there is an API for Modeller. I want to use modeller in my java code. am I able to call modeller methods through Java? for instance feed the program with two alignments and give a command in my java code to model the 3D strcutre. Thank you.

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Fwd: Request for you Assistance - Molecular modeling
by Swetha Kumari 12 Jan '15

12 Jan '15

---------- Forwarded message ---------- From: Swetha Kumari <swethakumari.k(a)gmail.com> Date: 12 January 2015 at 14:10 Subject: Request for you Assistance - Molecular modeling To: modeller-care(a)salilab.org Dear Sir, I have requested for Modeller 9.13 software, got License and installed ti successfully. I am following the script files and commands as per the manual exactly. But, unable to run some script files in the process of modelling. I have troubleshooted a lot and finally mailing you for your assistance. I want to do modeling using Modeller software. It gives the best possible models. I request you to kindly help me in sending modeling procedure little more in detail. I need ".py" file creation steps too. I will be highly thankful, if am done with modelling using modeller.. Awaiting your reply Thanking you, Yours faithfully, Swetha kumari K.

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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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alpha-helix
by Juan Munoz-Garcia 24 Nov '14

24 Nov '14

Dear Modeller users, I’ve tried to make an alpha helix from the peptide sequence (21 amino acids) using the script shown in the website (http://www.salilab.org/modeller/wiki/Make%20alpha%20helix) i.e., imposing restraints to force the alpha helical structure. I’ve tried with conjugate_gradients, molecular_dynamics and quasi_newton methods, but the output just showed a helix for a small part of the peptide, showing a coil for the rest of it. Although this is providing some information itself, and it roughly agrees with experimental data, I do want to force an alpha helical structure for the whole peptide. Do you know how this can be done? I was wondering if there is any method to grow an alpha helix just based on the backbone and once formed growing the side chains from it, thus avoiding possible highly destabilising side chain - side chain interactions precluding the helix formation. Regards. Juan C.

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Modelling loop region in homodimer
by aneesh cna 14 Nov '14

14 Nov '14

Drear members, I am a new comer to modeller. I am trying to model a ~15AA long missing loop region in a homo-dimer. Both monomer units in the homo-dimer missing the loop region. Unfortunately, my template is a monomer unit. How can I model the loop region in both monomer together.? I have tried modelling each monomer units separately, since the available template was a monomer. But, when I built the dimer from the modelled monomers (just by putting the modelled monomers together in a pdb file) the loop in one of the monomer got interlocked within a helix of the second monomer. Is there a different way to model the loop here? Many thanks in advance Regards Anu

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Modelling loop region in homodimer
by aneesh cna 11 Nov '14

11 Nov '14

Drear members, I am a new comer to modeller. I am trying to model a ~15AA long missing loop region in a homo-dimer. Both monomer units in the homo-dimer missing the loop region. Unfortunately, my template is a monomer unit. How can I model the loop region in both monomer together.? I have tried modelling each monomer units separately, since the available template was a monomer. But, when I built the dimer from the modelled monomers (just by putting the modelled monomers together in a pdb file) the loop in one of the monomer got interlocked within a helix of the second monomer. Is there a different way to model the loop here? Many thanks in advance Regards Anu

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Physical.values
by chris.wood＠stfc.ac.uk 30 Oct '14

30 Oct '14

In the modeller.physical module, is there a way to select to select the physical types given the index? Something like: >> import modeller >> print modeller.physical.types[1] physical.bond I see that each modeller.physical.<restraint type> has a _num method which returns the index, but I'd like to avoid looping through all the object types if possible! Cheers, Chris ------------------- Dr Chris Wood STFC Rutherford Appleton Laboratory Didcot OX11 0QX chris.wood(a)stfc.ac.uk www.ccpem.ac.uk Tel: +44(0)1235 567864 Tel: +44(0)7909 586624 Fax: +44(0)1235 567801 Skype: chris_c_wood<callto://chris_c_wood/> -- Scanned by iCritical.

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