July 2011 - modeller_usage

Help with modeller 9.9 in windows
by Greene, Brandon Lee 18 Jul '11

18 Jul '11

Hey, having an issue modelling inorganic ligands in a large dimer protein. My pdb file is a vmd cut-up of a larger pdb that looks as follows.. ATOM 1 N ALA A 3 -60.617 -12.474 -31.114 1.00 43.43 N ATOM 2 CA ALA A 3 -59.796 -11.349 -30.513 1.00 46.97 C ATOM 3 C ALA A 3 -59.651 -11.332 -28.938 1.00 48.20 C ATOM 4 O ALA A 3 -60.595 -11.655 -28.205 1.00 47.64 O ATOM 5 CB ALA A 3 -60.235 -9.947 -31.052 1.00 48.47 C ATOM 6 N ARG A 4 -58.445 -10.979 -28.485 1.00 44.79 N ... TER 2039 ATOM 2040 N GLU B1003 -60.710 -26.975 -64.326 1.00 44.60 N ... ATOM 6402 OXT HIS B1561 -32.057 -14.269 -58.556 1.00 23.80 O ANISOU 6402 OXT HIS B1561 3054 3146 2843 -160 47 -56 O TER 6403 HIS B1561 HETATM25650 FE1 SF4 A2001 -31.581 -9.338 -45.929 1.00 15.82 FE HETATM25651 FE2 SF4 A2001 -34.045 -9.711 -44.672 0.50 17.11 FE ... HETATM25689 O4 NFV B2005 -32.416 -23.476 -49.460 1.00 19.96 O END There are three inorganic residues in the first chain and one in the second placed as "." in my ali file. >P1;TrHyd sequence:TrHyd:::::::0.00: 0.00 AKRPSVIWLSFQECTGCTESLTRSHAPTLEDLILDVISLDYHHTLQAAAGDAAEHAREQAMAANPGEYLVIVDGSIPGPDSNPGYSTVAGHSNYAMLMETVENAAAVIAVGTCATFGGLPGANPNPTGAMSVMDLVKDKPVINVSGCPPIPMVITGVIAHYLTFGRLPELDAYNRPMAFFGQSIHDRCYRRPFYDKGLFAKTFDDEGARLGWCLYELGCKGPTTYNACATMRWNDGTSWPVEAGHPCLGCSEPRFWDAGGFYNTVSVP.../ERIVVDPVTRIEGHLRIEAQMDGENIAQAYSSGTSVRGLETILKGRDPRDAWAFAQRICGVCTLVHGIASVRSVEDALKIELPPNAQLIRNLMISSQFVHDHVMHFYHLHALDWVDVVSALSADPKATSDLAQSISSWPKSSPGYFADTQKRIKTFVESGQLGIFANGYWGHPAYKLPPEANLMAVAHYLEALAWQRDVARLHAIFGGKNPHPNFVVGGVPSPIDIDSDSAINAKRLAEVQQILQSMQTFVDQVYVPDTLAIASFYKDWGERGEGLGNFMSYGDLPATGTMDPAQFLFPRGVILNRDLSTIHEIDLHDAGQIQEYVAHSWYEYSGGNDQGLHPYDGETNLEYDARGGVKPPYTQLDVNDGYSWMKAPRWKGHAMEVGPLARVLLLYASGHEQTKELVEMTLTTLDLPVRALYSTLGRTAARTLETKILTDTAQDWYNQLIANIKAGDSRTFNETLWEPSSWPAEARGAGYMEAPRGALGHWIVIKDRKIANYQAVVPSTWNAGPRDPSDQPGAYEAALQDNHQLVDVKQPIEILRTIHSFDPCIACAVH.* Using this structure and the template ali file to do the alignment (w/ salign) I get poor alignment in the PAP file, but not in the PIR file??? (P/---XXXX instead of P---/XXX in PAP). I figured this wasn't a huge issue since modeller doesn't use the PAP file but it is odd. Anyway my alignment looks like this... >P1;Avfull structureX:Avfull.pdb: 3 :A:+827 :B:::-1.00:-1.00 ARRPSVIWLSFQECTGCTESLTRAHAPTLEDLILDFISLDYHHTLQAASGEAAEAARLQAMDENRGQYLVIVDGS IPGPDANPGFSTVAGHSNYSILMETVEHAAAVIAVGTCAAFGGLPQARPNPTGAMSVMDLVRDKPVINVPGCPPI PMVITGVIAHYLVFGRLPELDGYGRPLAFYGQSIHDRCYRRPFYDKGLFAESFDDEGAKQGWCLYRLGCKGPTTY NACATMKWNDGTSWPVEAGHPCLGCSEPQFWDAGGFYEPVSVP---/ERIVVDPITRIEGHLRIEAQMDGATIAQ AYSSGTMVRGIETILKGRDPRDAWAFVQRICGVCTLVHGIASVRAVEDALRIELPLNAQLIRNLMIGAQYIHDHV MHFYHLHALDWVDVVSALSADPRATSELAQSISAWPKSSPGYFADTQKRIKTFVESGQLGIFANGYWGHPAYRLP PEANLMAVAHYLEALAWQRDTAKFHAIFGGKNPHPNFVVGGVPSPIDLDSDSALNAKRLAEVRNLIQSMRTFVDQ VYVPDTLAIAGFYKDWGERGEGLGNFLCYGDLPTGASLDPATFLFPRGAILDRDLSTIHEVDLEATGEIQEFVNH SWYEYSVGNDRGLHPYEGQTNLEYDRRGGVAPPYKQLDVSDGYSWLKAPRWKGRSVEVGPLARVLMLYATGHDQA RELVDSTLSRLDLPVDALYSTLGRTAARALESKILVDAMQGWYDGLIANVKSGDTKTFNETLWEPSSWPSRAQGV GIMEAPRGALGHWIVIEDGRIANYQAVVPSTWNAGPRDGRGQAGAYEAALQDNHQLVDVKQPIEILRTIHSFDPC IACAVH-* >P1;TrHyd sequence:TrHyd: : : : ::: 0.00: 0.00 AKRPSVIWLSFQECTGCTESLTRSHAPTLEDLILDVISLDYHHTLQAAAGDAAEHAREQAMAANPGEYLVIVDGS IPGPDSNPGYSTVAGHSNYAMLMETVENAAAVIAVGTCATFGGLPGANPNPTGAMSVMDLVKDKPVINVSGCPPI PMVITGVIAHYLTFGRLPELDAYNRPMAFFGQSIHDRCYRRPFYDKGLFAKTFDDEGARLGWCLYELGCKGPTTY NACATMRWNDGTSWPVEAGHPCLGCSEPRFWDAGGFYNTVSVP.../ERIVVDPVTRIEGHLRIEAQMDGENIAQ AYSSGTSVRGLETILKGRDPRDAWAFAQRICGVCTLVHGIASVRSVEDALKIELPPNAQLIRNLMISSQFVHDHV MHFYHLHALDWVDVVSALSADPKATSDLAQSISSWPKSSPGYFADTQKRIKTFVESGQLGIFANGYWGHPAYKLP PEANLMAVAHYLEALAWQRDVARLHAIFGGKNPHPNFVVGGVPSPIDIDSDSAINAKRLAEVQQILQSMQTFVDQ VYVPDTLAIASFYKDWGERGEGLGNFMSYGDLPATGTMDPAQFLFPRGVILNRDLSTIHEIDLHDAGQIQEYVAH SWYEYSGGNDQGLHPYDGETNLEYDARGGVKPPYTQLDVNDGYSWMKAPRWKGHAMEVGPLARVLLLYASGHEQT KELVEMTLTTLDLPVRALYSTLGRTAARTLETKILTDTAQDWYNQLIANIKAGDSRTFNETLWEPSSWPAEARGA GYMEAPRGALGHWIVIKDRKIANYQAVVPSTWNAGPRDPSDQPGAYEAALQDNHQLVDVKQPIEILRTIHSFDPC IACAVH.* Using the template code in advanced modeling with similar for loops for all constraints of the inorganic ligand connections to the protein backbone through side chains modeller begins to compute the model and quickly returns this error... "No aligned template residues for BLK residue; number of templates: 1 Make sure that each BLK residue in your target sequence is aligned with your templates..." So my question is, is there a problem with my alignment that I am not seeing or is it some formating issue in the pdb that needs to be resolved? Any ideas would be much appreciated! ________________________________ This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments).

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ModWeb details -> Modeller?
by richard k belew 18 Jul '11

18 Jul '11

i've done a couple of runs using the ModWeb server, and i'm wondering how to recapitulate its results using Modeller directly? ModWeb gives a .pdb file as a result, with a header that tells the template it selected, and regions in it that were used for modeling. but: - what method is used for selecting this template? - is it possible to get the alignment that was used? thanks for any leads, Rik

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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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