January 2014 - modeller_usage

Select and remove atoms from automodel
by Ignacio Ibarra 04 Mar '14

04 Mar '14

Hello, Currently I am generating nucleic acid models using the MODELLER suite. I would like to remove the initial phosphate group declared in the first residue of each nucleic acid chain. Those atoms should not be present in real structures. I would like to do it without writing new text in the .lib files that are into the modlib folder I read about a pick_atoms() method in an older version of MODELLER, but it is not commented in the 9v11 manual ( http://binf.gmu.edu/software/MODELLER/node131.html) Is there something similar currently available for removing atoms from the model in the automodel or another class? Regards, Ignacio

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model.patch
by Roland Rivera 31 Jan '14

31 Jan '14

Hi there, I'm having some trouble using the model_patch() command to create a disulfide bond. If I use the following alignment file: >P1;1PRX_edited structure:1PRX_edited.pdb:2 :B:224 :B: : : : -PGGLLLGDVAPNFEANTTVGRIRFHDFLGDSWGILFSHPRDFT--.-----------PE FAKRNVKLIALSIDS---------------SEEPTEKLPFPIIDDRNRELAILLGMLDPA E-----MPVTARVVFVFGPDKKLKLSILYPATTGRNFDEILRVVISLQLTAEKRVATPVD WKDGDSVMVLPTIPEEEAKKLFPKGVFTKELPSGKKYLRYTPQP* >P1;1PRX_WT sequence:1PRX_WT:2 :A:224 :A: : : : MPGGLLLGDVAPNFEANTTVGRIRFHDFLGDSWGILFSHPRDFTPVCTTELGRAAKLAPE FAKRNVKLIALSIDSVEDHLAWSKDINAYNCEEPTEKLPFPIIDDRNRELAILLGMLDPA EKDEKGMPVTARVVFVFGPDKKLKLSILYPATTGRNFDEILRVVISLQLTAEKRVATPVD WKDGDSVMVLPTIPEEEAKKLFPKGVFTKELPSGKKYLRYTPQP* in conjunction with the following script: # Modeling a cysteine bond in a new model from modeller import * from modeller.automodel import * # Load the automodel class from modeller.scripts import complete_pdb log.verbose() # Verbose error description - helps with troubleshooting! env = environ() # Defines the environment # directories for input atom files env.io.atom_files_directory = ['.','../atom-files'] #Enables MODELLER to read HETATM entries from a PDB file env.io.hetatm = True env.libs.topology.read(file='$(LIB)/top_heav.lib') env.libs.parameters.read(file='$(LIB)/par.lib') # Make the disulfide bond: def patches (mdl): mdl.patch(residue_type='DISU', residues=(mdl.residues['47:A'], mdl.residues['91:A'])) # Read the sequence: code = '1PRX' mdl = complete_pdb(env, code, special_patches=patches) # Create the stereochemical restraints: sel = selection(mdl) mdl.restraints.make(sel, restraint_type='stereo', spline_on_site=False) # Calculate the energy to test the disulfide: sel.energy() a = automodel(env, alnfile = '1PRX_edited-1PRX_WT.ali', # alignment filename knowns = '1PRX_edited', # codes of the templates sequence = '1PRX_WT', # code of the target assess_methods=(assess.DOPE, assess.GA341)) a.starting_model= 1 # index of the first model a.ending_model = 1 # index of the last model # (together, they determine how many models to calculate) a.make() # do homology modeling It generates a PDB file that has the desired sequence, but no disulfide bond. If I use the following alignment: >P1;1PRX structure:1PRX.pdb:2 :B:224 :B: : : : -PGGLLLGDVAPNFEANTTVGRIRFHDFLGDSWGILFSHPRDFTPV.TTELGRAAKLAPE FAKRNVKLIALSIDSVEDHLAWSKDINAYNSEEPTEKLPFPIIDDRNRELAILLGMLDPA E-----MPVTARVVFVFGPDKKLKLSILYPATTGRNFDEILRVVISLQLTAEKRVATPVD WKDGDSVMVLPTIPEEEAKKLFPKGVFTKELPSGKKYLRYTPQP* >P1;1PRX_WT sequence:1PRX_WT:2 : :224 : : : : : MPGGLLLGDVAPNFEANTTVGRIRFHDFLGDSWGILFSHPRDFTPVCTTELGRAAKLAPE FAKRNVKLIALSIDSVEDHLAWSKDINAYNCEEPTEKLPFPIIDDRNRELAILLGMLDPA EKDEKGMPVTARVVFVFGPDKKLKLSILYPATTGRNFDEILRVVISLQLTAEKRVATPVD WKDGDSVMVLPTIPEEEAKKLFPKGVFTKELPSGKKYLRYTPQP* Combined with the following script: # Modeling a cysteine bond in a new model from modeller import * from modeller.automodel import * # Load the automodel class from modeller.scripts import complete_pdb log.verbose() # Verbose error description - helps with troubleshooting! env = environ() # Defines the environment # directories for input atom files env.io.atom_files_directory = ['.','../atom-files'] #Enables MODELLER to read HETATM entries from a PDB file env.io.hetatm = True env.libs.topology.read(file='$(LIB)/top_heav.lib') env.libs.parameters.read(file='$(LIB)/par.lib') # Special distance restraints class MyModel (automodel): # Make the disulfide bond: def patches (mdl): mdl.patch(residue_type='DISU', residues=(mdl.residues['47:'], mdl.residues['91:'])) # Read the sequence: code = '1PRX' mdl = complete_pdb(env, code, special_patches=patches) # Create the stereochemical restraints: sel = selection(mdl) mdl.restraints.make(sel, restraint_type='stereo', spline_on_site=False) # Calculate the energy to test the disulfide: sel.energy() a = MyModel(env, alnfile = '1PRX-1PRX_WT.ali', # alignment filename knowns = '1PRX', # codes of the templates sequence = '1PRX_WT', # code of the target assess_methods=(assess.DOPE, assess.GA341)) a.starting_model= 1 # index of the first model a.ending_model = 1 # index of the last model # (together, they determine how many models to calculate) a.make() # do homology modeling It returns a KeyError: 'No such residue'. I researched this in the answer archives and found the suggestion to create a .ini file to determine the model residue numbers, which are exactly correspondent to those found in the script. I would appreciate any help deciphering what exactly I'm doing wrong. Thanks, -- Roland F. Rivera-Santiago Ph.D. Candidate Biochemistry & Molecular Biophysics Graduate Group Speicher Lab, Wistar Institute E-mail: roland.f.rivera.santiago(a)gmail.com

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Re: [modeller_usage] problem in generating models
by Nupur Bansal 29 Jan '14

29 Jan '14

Hi, Thanks for replying. Now, after making that change, I am getting the following error: Alignment sequence not found in PDB file: 1 atom_files/2hzv.pdb (You didn't specify the starting and ending residue numbers and chain IDs in the alignment, so Modeller tried to guess these from the PDB file.) But, I don’t know how to specify the starting and ending residue numbers. On Jan 29, 2014, at 12:11 PM, Nupur Bansal <nupur.b298(a)gmail.com> wrote: > Hi, > > I am new to Modeller and has been trying to use it for generating models for my system. > > I have done sequence alignment using Clustalw in .pir format. But, the error I am getting is : > check_a_282E> Unable to read structural information for alignment > sequence: 1 2hzv > This command requires structures. > > > My alignment file is : 2ca9_2hzv.ali > > >P1;2hzv > NMR:2hzv.pdb:FIRST:@ END:::::: > --MQRVTITLDDDLLETLDSLSQRRGYNNRSEAIRDILRSALAQEATQQHGTQG---FAV > LSYVYEHEKRDLASRIVSTQHHHHDLSVATLHVHINHDDCLEIAVLKGDMGDVQHFADDV > IAQRGVRHGHLQCLP--KEDMQRVTITLDDDLLETLDSLSQRRGYNNRSEAIRDILRSAL > AQEATQQHGTQG---FAVLSYVYEHEKRDLASRIVSTQHHHHDLSVATLHVHINHDDCLE > IAVLKGDMGDVQHFADDVIAQRGVRHGHLQCLP----KEDMQRVTITLDDDLLETLDSLS > QRRGYNNRSEAIRDILRSALAQEATQQHGTQG---FAVLSYVYEHEKRDLASRIVSTQHH > HHDLSVATLHVHINHDDCLEIAVLKGDMGDVQHFADDVIAQRGVRHGHLQCLP--KEDMQ > RVTITLDDDLLETLDSLSQRRGYNNRSEAIRDILRSALAQEATQQHGTQG---FAVLSYV > YEHEKRDLASRIVSTQHHHHDLSVATLHVHINHDDCLEIAVLKGDMGDVQHFADDVIAQR > GVRHGHLQCLPKED--* > > >P1;2CA9_apo > sequence:2CA9_apo:FIRST:@ END:::::: > DSIIRFSVSLQQNLLDELDNRIIKNGYSSRSELVRDMIREKLVEDNWAEDNPNDESKIAV > LVVIYDHHQRELNQRMIDIQHASGTHVLCTTHIHMDEHNCLETIILQGNSFEIQRLQLEI > GGLRGVKFAKLTKASSFEYSIIRFSVSLQQNLLDELDNRIIKNGYSSRSELVRDMIREKL > VEDNWAEDNPNDESKIAVLVVIYDHHQRELNQRMIDIQHASGTHVLCTTHIHMDEHNCLE > TIILQGNSFEIQRLQLEIGGLRGVKFAKLTKASSFEYNDSIIRFSVSLQQNLLDELDNRI > IKNGYSSRSELVRDMIREKLVEDNWAEDNPNDESKIAVLVVIYDHHQRELNQRMIDIQHA > SGTHVLCTTHIHMDEHNCLETIILQGNSFEIQRLQLEIGGLRGVKFAKLTKASSFEYSII > RFSVSLQQNLLDELDNRIIKNGYSSRSELVRDMIREKLVEDNWAEDNPNDESKIAVLVVI > YDHHQRELNQRMIDIQHASGTHVLCTTHIHMDEHNCLETIILQGNSFEIQRLQLEIGGLR > GVKFAKLTKASSFEYN* > > > I am also attaching my pdb file for reference. > > Any help would be appreciated. > > Thanks, > Nupur > <2hzv.pdb>

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Refinement step questions
by gbanoczi＠mail.bme.hu 21 Jan '14

21 Jan '14

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Loop optimization starting from a structure with ligand
by ms 21 Jan '14

21 Jan '14

Hello, I am trying to perform loop optimization on a protein structure which contains a non-standard ligand. The optimization I am attempting requires constrains between the ligand and the loops. Protein is chain A, ligand is a single residue defined as chain B, described as heteroatoms. I had no trouble performing homology modeling from a structure containing the ligand, and it was correctly carried upon once I define env.io.hetatm = True .However this seems not to work anymore when doing loop optimization only on the same structure. When I try to run the job, I always get: Traceback (most recent call last): File "tas2r463pbl_mod.py", line 42, in ? a.make() File "/usr/lib/modeller9.10/modlib/modeller/automodel/loopmodel.py", line 36, in make self.build_seq(self.inimodel, 1) File "/usr/lib/modeller9.10/modlib/modeller/automodel/loopmodel.py", line 167, in build_seq self.loop_restraints(atmsel, aln) File "/usr/lib/modeller9.10/modlib/modeller/automodel/loopmodel.py", line 361, in loop_restraints self.special_restraints(aln) File "tas2r463pbl_mod.py", line 24, in special_restraints rsr.add(forms.gaussian(group=physical.bond,feature=features.distance(at['CA:70:A'],at['C16:309:B']), mean=1.00, stdev=0.10)) File "/usr/lib/modeller9.10/modlib/modeller/coordinates.py", line 376, in __getitem__ (self.offset, self.length, self.suffix)) File "/usr/lib/modeller9.10/modlib/modeller/util/modutil.py", line 23, in handle_seq_indx int_indx = lookup_func(*args) File "/usr/lib/modeller9.10/modlib/modeller/coordinates.py", line 289, in _indxatm raise KeyError("No such atom: %s" % indx) KeyError: 'No such atom: C16:309:B' Looking in the log, I think this is the relevant warning: transfe_404W> At least one template is aligned with model residue 309:B but no coordinates could be transferred. This usually occurs when your input files do not use the official PDBv3 atom names. Please check your templates. The script follows: ---- #!/usr/bin/env python from modeller import * from modeller.automodel import * from modeller.scripts import complete_pdb log.verbose() env = environ() env.io.atom_files_directory = ['.'] env.io.hetatm = True class MyModel(loopmodel): def select_loop_atoms(self): #return selection(self.residue_range('68:A','83:A'),self.residue_range('149:A','176:A'),self.residue_range('249:A','258:A'),self.residue_range('309:B','309:B')) return selection(self.residue_range('68:A','83:A'),self.residue_range('149:A','176:A'),self.residue_range('249:A','258:A')) def special_restraints(self,aln): rsr = self.restraints at = self.atoms rsr.add(forms.gaussian(group=physical.bond,feature=features.distance(at['CA:70:A'],at['C16:309:B']), mean=1.00, stdev=0.10)) rsr.add(forms.gaussian(group=physical.bond,feature=features.distance(at['CA:71:A'],at['C16:309:B']), mean=1.00, stdev=0.10)) rsr.add(forms.gaussian(group=physical.bond,feature=features.distance(at['CA:253:A'],at['C16:309:B']), mean=1.00, stdev=0.10)) a = MyModel(env, inimodel="cluster_A.pdb", sequence='tas2r46', loop_assess_methods=(assess.DOPE, assess.GA341, assess.normalized_dope)) #a = MyModel(env, inimodel="cluster_A.pdb", loop_assess_methods=(assess.DOPE, assess.GA341, assess.normalized_dope)) a.loop.starting_model = 1 a.loop.ending_model = 1 a.loop.md_level = refine.very_fast a.make() env = environ() env.libs.topology.read(file='$(LIB)/top_heav.lib') env.libs.parameters.read(file='$(LIB)/par.lib') #for some reason, this has to be done env = environ() env.libs.topology.read(file='$(LIB)/top_heav.lib') env.libs.parameters.read(file='$(LIB)/par.lib') #in case we output bad models... ok_models = filter(lambda x: x['failure'] is None, a.outputs) for model in ok_models: mdl = complete_pdb(env, model['name']) s = selection(mdl) s.assess_dope(output='ENERGY_PROFILE NO_REPORT', file= model['name']+'.profile', normalize_profile=True, smoothing_window=15) Any help on what information should I look for to troubleshoot this is very welcome. thanks, Massimo

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Missed residues
by James Starlight 16 Jan '14

16 Jan '14

Dear Modeller users, I used Modeller for creation of the Chimeric proteins (linked from C to N termi) consisted of merged two tempates. Below you can see my aligment file for such task. >P1;1gfl structureX:1gfl:1 ::238 : :::-1.00:-1.00 ASKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTFSYGVQCFSRYPDHMKRHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLLEFVTAAGITHGMDELYK----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------* >P1;3u10 structureN:3u10:470 ::671 : :A::-1.00:-1.00 ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DSSRRQYQEKYKQVEQYMSFHKLPADFRQKIHDYYEHRYQGKMFDEDSILGELNGPLREEIVNFNCRKLVASMPLFANADPNFVTAMLTKLKFEVFQPGDYIIREGTIGKKMYFIQHGVVSVLTKGNKEMKLSDGSYFGEICLLTRGRRTASVRADTYCRLYSLSVDNFNEVLEEYPMMRRAFETVAIDRLDRIGKKNSILL* >P1;seq sequence:seq: : : : ::: 0.00: 0.00 ASKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTFSYGVQCFSRYPDHMKRHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLLEFVTAAGITHGMDELYKDSSRRQYQEKYKQVEQYMSFHKLPADFRQKIHDYYEHRYQGKMFDEDSILGELNGPLREEIVNFNCRKLVASMPLFANADPNFVTAMLTKLKFEVFQPGDYIIREGTIGKKMYFIQHGVVSVLTKGNKEMKLSDGSYFGEICLLTRGRRTASVRADTYCRLYSLSVDNFNEVLEEYPMMRRAFETVAIDRLDRIGKKNSILL* I wounder to know if it possible to add to my resulted chimeric protein some missed residues (commonly in N, C termi and loops regions) which are absent in both templates .In the above example in first PDB template 1-5 residues from N- term are absent (this residues are not listed in aligment file too). Does it posible to add to the final model ? Please provide me with some examples where modeller is used for the addition of missed loops and termi. Thanks for help, James

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Reg modeller
by Manjula Mummadisetti 08 Jan '14

08 Jan '14

I have a protein which has its N-terminal region missing from its cyrstal structure. On generating a model using modeller, it formed a loop at the N-terminus. I would like to try making an alpha helix and a beta sheet at the N-terminus in place of loop. In the addrsr file, I mentioned the residues which have to be used to form the alpha helix, but the modeller is giving an error message: syntax error. I am not sure what is going wrong. I just changed the residue numbers to the desired residues, and didn't change anything else in the script file. I am a new user, and I am a little stuck at this point. Any advice will be highly appreciated. Thanks

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(no subject)
by Dermot Mallon 02 Jan '14

02 Jan '14

<<apologies for duplicate - I hit 'send' by mistake''>> Dear all, I have a large number of homology models to produce which have ~90 - 95% homology with 10 high quality crystal structure templates. Once I create my models I will be using GROMACS to relax the structure before comparing various properties of the models. I wonder, is it a reasonable approach to energy minimize the templates and use these as templates for producing models thereby reducing the need for energy minimization on (a much larger number of) models? Your opinion would be appreciated. Best wishes, Dermot

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Exclude residues from modeling
by Jurgens de Bruin 02 Jan '14

02 Jan '14

Hi, I would like to know what would be the best option to exclude residues from the N and C terminal of the target. The sequence can be truncated in the fasta file before modelling I believe would be the easy answer but does MODDELLER have a option/function that would have this? Thanks -- Regards/Groete/Mit freundlichen Grüßen/recuerdos/meilleures salutations/ distinti saluti/siong/duì yú/привет Jurgens de Bruin

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