- modeller_usage - salilab.org

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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DOPE for multiple template-based homology modeling
by HERBERT MAX VENTHUR PE¥A 19 Dec '13

19 Dec '13

Hi... Recently, I performed homology modeling using multiple templates with success (following the advanced tutorial). However, I could not pick a specific structure because I didn't find a dope score into the log file. Is there any posibility to obtain this dope score for multiple templates-based models?. thanks a lot for your answers Best wishes Herbert -- *Herbert Venthur PeñaProfesor de Estado en Ciencias con Mención en Química* *Estudiante de Doctorado en Ciencias de Recursos Naturales* *Laboratorio de Química Ecológica* *Departamento de Ciencias Químicas y Recursos Naturales* *Universidad de La FronteraTemuco, Chile* *08-3104992*

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Energy minimization
by Dermot Mallon 19 Dec '13

19 Dec '13

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 this

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Replacing cysteine with homocysteine
by Arjun Ray 16 Dec '13

16 Dec '13

Hi, I wanted to replace a specific cysteine residue with homocysteine. Has someone done a similar operation with Modeller? Could someone suggest a methodology or script to do so? Thanks in advance. Regards Arjun -- **************************************************** The dream is not that you see in sleep , dream is which does not let you sleep. ~Dr. Abdul Kalam (Former President of Republic of India) ***************************************************** Arjun Ray Mobile : +919910497608 Email : arjun(a)ebi.ac.uk / arjun(a)cbr.su.se <arjun.ray(a)cbr.su.se> ***********************************************

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