- modeller_usage - salilab.org

multichain modeling
by MUSTAFA BUGHIO 13 Jul '11

13 Jul '11

Dear Modeller This is python file which i am giving to run multichain modeling : # Homology modeling by the automodel class # # Demonstrates how to build multi-chain models, and symmetry restraints # from modeller import * from modeller.automodel import * # Load the automodel class log.verbose() # Override the 'special_restraints' and 'user_after_single_model' methods: class MyModel(automodel): def special_restraints(self, aln): # Constrain the A and 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, 1.0)) def user_after_single_model(self): # Report on symmetry violations greater than 1A after building # each model: self.restraints.symmetry.report(1.0) env = environ() # directories for input atom files env.io.atom_files_directory = ['.', '../atom_files'] # Be sure to use 'MyModel' rather than 'automodel' here! a = MyModel(env, alnfile = 'twochain.ali' , # alignment filename knowns = '3RHW', # codes of the templates sequence = 'hGLR') # code of the target a.starting_model= 1 # index of the first model a.ending_model = 1 # index of the last model # (determines how many models to calculate) a.make() # do homology modeling model-multichain.py lines 1-37/37 (END) But i get following error: 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-multichain.py", line 37, in ? a.make() # do homology modeling File "/usr/lib/modeller9.9/modlib/modeller/automodel/automodel.py", line 98, in make self.homcsr(exit_stage) File "/usr/lib/modeller9.9/modlib/modeller/automodel/automodel.py", line 424, in homcsr self.check_alignment(aln) File "/usr/lib/modeller9.9/modlib/modeller/automodel/automodel.py", line 406, in check_alignment aln.check() File "/usr/lib/modeller9.9/modlib/modeller/alignment.py", line 200, in check self.check_structure_structure(io=io) File "/usr/lib/modeller9.9/modlib/modeller/alignment.py", line 209, in check_structure_structure return f(self.modpt, io.modpt, self.env.libs.modpt, eqvdst) _modeller.SequenceMismatchError: read_te_291E> Sequence difference between alignment and pdb : May i kindly know how can i solve this problem.... -- MUSTAFA BUGHIO Junior Research Fellow Lab # P-133 Computational Medicinal Chemistry and Drug Design Panjwani Center For Molecular Medicine and Drug Research, International Center for Chemical Sciences, University of Karachi, Karachi 75270 Pakistan, +923313425010

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Disulphide patch
by MUSTAFA BUGHIO 13 Jul '11

13 Jul '11

Dear Modeller This is with reference to the python file *** examples/commands/patch_disulfides.py<http://salilab.org/modeller/examples/commands/patch_disulfides.py>i am building a model with two disulphide bridges position: *138 CYS -> 152 CYS 198 CYS -> 209 CYS where as the python file contains example for one disulphide bridge, how can i edit the file or there is any other procedure to solve this problem. Should i use above mentioned py file or patch.py for assigning developing disulphide bridge. Regards -- MUSTAFA BUGHIO Junior Research Fellow Lab # P-133 Computational Medicinal Chemistry and Drug Design Panjwani Center For Molecular Medicine and Drug Research, International Center for Chemical Sciences, University of Karachi, Karachi 75270 Pakistan, +923313425010

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Multi-chain modeling
by MUSTAFA BUGHIO 13 Jul '11

13 Jul '11

Dear Modeller I am trying to develop multichain model using /model-multichain.py file but as my model is pentamer in nature the example given is for dimer, i dont know how to make mult-chain.ali file and what i should mention in header since my template chains are 5 A-E the given example has only 1 :A:74 :B: option, how should i change the script to run all five chain modelling together. plz help Regards Mustafa -- MUSTAFA BUGHIO Junior Research Fellow Lab # P-133 Computational Medicinal Chemistry and Drug Design Panjwani Center For Molecular Medicine and Drug Research, International Center for Chemical Sciences, University of Karachi, Karachi 75270 Pakistan, +923313425010

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Modelling of multi-domain protein from oligomeric template
by Chugunov Anton 06 Jul '11

06 Jul '11

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optimize.py
by MUSTAFA BUGHIO 06 Jul '11

06 Jul '11

Dear I am trying to do energy minimization step by running optimize.py script file but it does not execute every time i tried to run and got the following error, i will be thankful if you help me get this problem resolved. IOError: pdbnam_____E> Filename for PDB code not found: hGLR Directories: ../atom_files Extensions : :.atm:.pdb:.ent:.crd (Also tried prepending 'pdb', looking for .Z, .gz, .bz2, .7z, .xz, and trying PDB-style subdirectories - e.g. ab for pdb1abc.ent) # Example for: conjugate_gradients(), molecular_dynamics(), model.switch_trace() # This will optimize stereochemistry of a given model, including # non-bonded contacts. # non-bonded contacts. from modeller import * from modeller.scripts import complete_pdb from modeller.optimizers import conjugate_gradients, molecular_dynamics, actions env = environ() env.io.atom_files_directory = ['../atom_files'] env.edat.dynamic_sphere = True env.libs.topology.read(file='$(LIB)/top_heav.lib') env.libs.parameters.read(file='$(LIB)/par.lib') code = '*hGLR*' mdl = complete_pdb(env, code) mdl.write(file=code+'.ini') # Select all atoms: atmsel = selection(mdl) # Generate the restraints: mdl.restraints.make(atmsel, restraint_type='stereo', spline_on_site=False) mdl.restraints.write(file=code+'.rsr') mpdf = atmsel.energy() # Create optimizer objects and set defaults for all further optimizations cg = conjugate_gradients(output='REPORT') md = molecular_dynamics(output='REPORT') # Open a file to get basic stats on each optimization trcfil = file(code+'.D00000001', 'w') # Run CG on the all-atom selection; write stats every 5 steps cg.optimize(atmsel, max_iterations=20, actions=actions.trace(5, trcfil)) # Run MD; write out a PDB structure (called '1fas.D9999xxxx.pdb') every # 10 steps during the run, and write stats every 10 steps md.optimize(atmsel, temperature=300, max_iterations=50, actions=[actions.write_structure(10, code+'.D9999%04d.pdb'), actions.trace(10, trcfil)]) # Finish off with some more CG, and write stats every 5 steps cg.optimize(atmsel, max_iterations=20, actions=[actions.trace(5, trcfil)]) mpdf = atmsel.energy() mdl.write(file=code+'.B') I am trying to give the code which i have got after my pdb files are dveveloped. -- MUSTAFA BUGHIO Junior Research Fellow Lab # P-133 Computational Medicinal Chemistry and Drug Design Panjwani Center For Molecular Medicine and Drug Research, International Center for Chemical Sciences, University of Karachi, Karachi 75270 Pakistan, +923313425010

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reproduction
by Jean-Paul Armache 05 Jul '11

05 Jul '11

hi, i would like to ask for a bit of an input. you see, i have an alignment of two proteins, one is an xray structure, serves as a template. the other one is the target. the template consists of a globular domain which gets reproduced very nicely, and of an extended part, which gets somehow randomized, or differs substantially from the template. the question of mine is, how to inform modeller to reproduce this part, of just the whole protein which as little deviation as possible (ie. to closely resemble the template) ? thank you for any input, best, jean-paul

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Re: [modeller_usage] FATAL ERROR: MODINSTALL9v9 environment variable not set: incomplete MODELLER installation on Ubuntu 10.4
by R K Belew 03 Jul '11

03 Jul '11

(i'm trying to tack on to the thread closest to my experience) i've successfully installed mod9.9 on MacOS, but want to have less-mediated Python access, and so am re-installing on Ubuntu. i grabbed modeller_9.9-1_i386.deb, invoked dpkg as recommended: > sudo env KEY_MODELLER=<myCode> dpkg -i modeller_9.9-1_i386.deb and the install seemed to work fine. but then going to .../examples/ and trying to run_tests: > monk:/usr/share/doc/modeller-9.9/examples> ./run_tests > Entering directory: all-steps > #!/bin/sh -v > mod9.9 search.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 > ... (similar errors for all other scripts) going thru the archives, you (Ben) say things like: "it needs certain environment variables set first, which python or mod9.9 take care of. " "... You don't actually need to set *any* of the environment variables you have above" regarding previous releases, and so i don't want to mess until i have to! i can also go back to the generic Unix version, but thought you must want Ubuntu's .deb option also working? thanks for your great work, rik

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Regarding Modeller model building script
by Ashish Runthala 01 Jul '11

01 Jul '11

Dear Modellers & Respected Sir Benn, If i am correct Modeller uses distance restraints from multiple templates based on alignment, Tell me the way to use one complete template during modeling and chunks from others. I tried doing that but GDT score decreased when i aligned chunks to one complete template alignment. The aligned chunks were covering target region which was unaligned by one selected complete template span. So HOW TO GENERATE FOLD BASED ALIGNMENT WHICH IMPROVES GDT SCORES BY INCREASING CONSIDERATION WEIGHT OF A SINGLE TEMPLATE AS COMPARED TO OTHERS IN MODELLING. Thanks Ashish Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA

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Two domains get oriented randomly although modelled from a single template
by Чугунов Антон 30 Jun '11

30 Jun '11

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loop_refine.py parallel error
by 刘吉元 30 Jun '11

30 Jun '11

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