- modeller_usage - salilab.org

Model Multi chain
by MUSTAFA BUGHIO 15 Jul '11

15 Jul '11

Dear Modeller I am repeating my question again regarding multi chain modeling, i have been successful in developing two chain alignment by giving model-multichain.py command but when i want to create pentamer model it shows error, can you tell me which py file i can use for it or how i can change this py file given below # 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 = 'multchain.ali' , # alignment filename knowns = '3EAM', # 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) The above given python is used for dimer to be produce help me generate pentamer structure directly by given any python file. 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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Re: [modeller_usage] modeller_usage Digest, Vol 10, Issue 98
by Ashish Runthala 15 Jul '11

15 Jul '11

Dear Mustafa, Don't fall in multichain scripts etc. Specify chains in model_mult.py or model_multiple.py from all of your n chains using n different copies of your template, available in the same folder. This will solve purpose for alignment too. Good Luck Ashish Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA ----- Original Message ----- From: "modeller usage-request" <modeller_usage-request(a)salilab.org> To: "modeller usage" <modeller_usage(a)salilab.org> Sent: Wednesday, July 13, 2011 1:46:00 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi Subject: modeller_usage Digest, Vol 10, Issue 98 Send modeller_usage mailing list submissions to modeller_usage(a)salilab.org To subscribe or unsubscribe via the World Wide Web, visit https://salilab.org/mailman/listinfo/modeller_usage or, via email, send a message with subject or body 'help' to modeller_usage-request(a)salilab.org You can reach the person managing the list at modeller_usage-owner(a)salilab.org When replying, please edit your Subject line so it is more specific than "Re: Contents of modeller_usage digest..." Today's Topics: 1. Re: optimize.py (Modeller Caretaker) 2. Re: Modelling of multi-domain protein from oligomeric template (Modeller Caretaker) 3. Multi-chain modeling (MUSTAFA BUGHIO) 4. Disulphide patch (MUSTAFA BUGHIO) ---------------------------------------------------------------------- Message: 1 Date: Wed, 06 Jul 2011 12:18:04 -0700 From: Modeller Caretaker <modeller-care(a)salilab.org> Subject: Re: [modeller_usage] optimize.py To: MUSTAFA BUGHIO <mustafab4(a)gmail.com> Cc: modeller_usage(a)salilab.org Message-ID: <4E14B4EC.5060207(a)salilab.org> Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 07/06/2011 06:58 AM, MUSTAFA BUGHIO wrote: > 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) Just like it says, you asked it to open a PDB file called "hGLR" and told it to look for it in the ../atom_files directory, and it can't find it in there. Set env.io.atom_files_directory to the directory containing your PDB file (or remove that line entirely if it's in the same directory as the script). Ben Webb, Modeller Caretaker -- modeller-care(a)salilab.org http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage ------------------------------ Message: 2 Date: Wed, 06 Jul 2011 12:21:23 -0700 From: Modeller Caretaker <modeller-care(a)salilab.org> Subject: Re: [modeller_usage] Modelling of multi-domain protein from oligomeric template To: Chugunov Anton <batch2k(a)yandex.ru> Cc: modeller_usage(a)salilab.org Message-ID: <4E14B5B3.9050709(a)salilab.org> Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 07/06/2011 07:40 AM, Chugunov Anton wrote: > What I expect, is a single-chain model that consists of four domains, > each built from respective template's chain according to the alignment. > What I get (as far as I see from the *.ini file, since no models output > due to high energy-function) is the first domain followed by a huge > non-structured loop If the alignment you posted is the one you're actually using, then you have aligned DOM 2 through 4 with gaps in your template, so obviously Modeller has no structure to work with in that region. Remove all of those gaps from your template so that DOM-2 is aligned with BBBB, DOM-3 with CCCC and DOM-4 with DDDD. Ben Webb, Modeller Caretaker -- modeller-care(a)salilab.org http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage ------------------------------ Message: 3 Date: Wed, 13 Jul 2011 13:09:47 +0500 From: MUSTAFA BUGHIO <mustafab4(a)gmail.com> Subject: [modeller_usage] Multi-chain modeling To: modeller_usage(a)salilab.org Message-ID: <CALHZR27Esm9NCFGUutQku919GY4k01vAMKTv_3-+ObC=u_s+QQ(a)mail.gmail.com> Content-Type: text/plain; charset="iso-8859-1" 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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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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