- modeller_usage - salilab.org

refine a loop in a multi-chain complex
by Li Xue 11 Jul '22

11 Jul '22

Hello, I am trying to refine a loop in a multi-chain complex. During the refinement/remodelling phase of the loop, does modeller molPDF include non-bonded energies between chains? Or it will only include the energies within the loop? Many thanks. Best, Li

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Error in multichain modeller
by Zara Saeed 23 Jun '22

23 Jun '22

I am using the following python file for multichain modelling. I am sending you my script, structure file and alignment file in the attachment. When I run this script it gives the following error. *raise KeyError("No such chain: %s" % indx)* *KeyError: 'No such chain: F'* I read about it in the modeller 's problem and came to know that it can be due to unavailability of chain breaker. But as you can see in my ali. file chain breaker is present in sequence. Can you identify the problem please? Best regards, zeenat

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(no subject)
by LEE Seayoung 15 Jun '22

15 Jun '22

Dear Whom it may concern, I am writing this email to request you a suggestion about settings in Modeller. Currently, I have trouble in running Modeller program. It seems like the program doesn't have the right Pythonpath. In the error message, it says that referring to modv10, the pythonpath is system/library/framework........ and it turns out that corresponding file doesn't exist. I am using iMac (version12.4) and I need to use Modeller10.2. Would you please suggest me to resolve this problem? Thank you Sincerely Seayoung LEE

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Fwd: ImportError
by Airy Sanjeev 12 May '22

12 May '22

---------- Forwarded message --------- From: Airy Sanjeev <airy.sanjeev01(a)gmail.com> Date: Thu, May 12, 2022 at 12:27 PM Subject: ImportError To: <modeller_usage(a)salilab.org> Hello I have installed python 2.7.11 and modeller 10.2, after running the command *python mutate_selection.py > mutate_selection.log* Following error is showed up: *Traceback (most recent call last): File "mutate_selection.py", line 12, in <module> from modeller import * File "C:\Users\Asus\Desktop\Modeller10.2\modlib\modeller\__init__.py", line 96, in <module> import _modellerImportError: No module named _modeller* Please do the needful -- with best regards, Airy Sanjeev, PhD Research Associate Center for Computational Biology and Bioinformatics TATA MEMORIAL CENTRE ACTREC Navi Mumbai, India -- with best regards, Airy Sanjeev, PhD Research Associate Center for Computational Biology and Bioinformatics TATA MEMORIAL CENTRE ACTREC Navi Mumbai, India

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Per-residue RMSD
by Karolina Mitusińska (Markowska) 21 Apr '22

21 Apr '22

Dear Modeller Users, I would like to compare my predicted model with a crystal structure. I know how to calculate RMSD between these two models, but I would also like to have more detailed information on the RMSD between corresponding atoms, for example C-alphas. Is there a way I can have that in Modeller? Can you help me with some code? Best regards, Karolina Mitusińska

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Fill_pdb
by Hocine EL KHAOUDI ENYOURY 18 Feb '22

18 Feb '22

Hello, I am trying to use the following script to fill small regions of a pdf: from modeller import * from modeller.scripts import complete_pdb log.verbose() env = Environ() env.libs.topology.read(file='$(LIB)/top_heav.lib') # read topology env.libs.parameters.read(file='$(LIB)/par.lib') # read parameters env.io.atom_files_directory =['.'] m=complete_pdb(env, ‘innput.pdb') m.write(file="output.pdb") My problem is that at the end, the input and output are the same. I missed a step? Would you have any advice to solve my problem? Thanks in advance, Hocine El Khaoudi Enyoury

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Loop modelling
by Hocine EL KHAOUDI ENYOURY 09 Feb '22

09 Feb '22

Hello, Im trying to refine some loops of my structure. I was wondering if it was possible, with modeller, to force the loop to adapt an alpha helix or beta stand motif while refining. Thanks in advance, Hocine El Khaoudi Enyoury

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Number of equivalent positions <3
by Hocine EL KHAOUDI ENYOURY 27 Jan '22

27 Jan '22

Dear users, I am getting this error, when I am running modeller (sailing.py): _modeller.ModellerError: fit2xyz_296E> Number of equivalent positions < 3: 0 I am trying to make a multi-template model to reconstruct a loop region for a protein. I am using a experimental structure of the loop (it has only 7 aminoacids), and several whole structures from the PDB and derived from modeller. There is any way to force the alignement or to solve this problem? Thanks for your attention, Hocine El Khaoudi Enyoury

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Reg: Ligand HETATM atoms missing in model
by Samdani A 04 Jan '22

04 Jan '22

Hi all, I am trying to model an ion, water and ligand from a template and below is my alignment file. >P1;SAM_docked structureX:SAM_docked.pdb:3:A:+1048:B:::-1.00:-1.00 -S-QVEHPAGGYKKLFETVEELSSPLTAHVTGRIPLWLTGSLLRCGPGLFEVGSEPFYHLFDGQALLHKFDFKEG HVTYHRRFIRTDAYVRAMTEKRIVITEFGTCAFPDPCKNIFSRFFSYFRGVEVTDNALVNIYPVGEDYYACTETN FITKVNPETLETIKQVDLCNYVSVNGATAHPHIENDGTVYNIGNCF-----IAYNIVKIPPLQADKEDPISKSEI VVQFPCSDRFKPSYVHSFGLTPNYIVFVETPVKINLFKFLSS----GANYMDCFESNETMGVWLHIADKKRKKYI NNKYRTSPFNLFHHINTYEDHEFLIVDLCCWKGFEFVYNYLYLANLRENWEEVKKNARKAPQPEVRRYVLPLNID KADTGKNLVTLPNTTATAILCSDETIWLEPEVLFSGPRQAFEFPQINYQKYGGKPYTYAYGLGLNHFVPDRLCKL NVKTKETWVWQEPDSYPSEPIFVSHPDALEEDDGVVLSVVVSPGAGQKPAYLLILNAKDLSEVARAEVEINIPVT FHGLFKKS.w./S--QVEHPAGGYKKLFETVEELSSPLTAHVTGRIPLWLTGSLLRCGPGLFEVGSEPFYHLFDG QALLHKFDFKEGHVTYHRRFIRTDAYVRAMTEKRIVITEFGTCAFPDPCKNIFSRFFSYFRGVEVTDNALVNIYP VGEDYYACTETNFITKVNPETLETIKQVDLCNYVSVNGATAHPHIENDGTVYNIGNCF-----IAYNIVKIPPLQ ADKEDPISKSEIVVQFPCSDRFKPSYVHSFGLTPNYIVFVETPVKINLFKFLG------ANYMDCFESNETMGVW LHIADKKRKKYINNKYRTSPFNLFHHINTYEDHEFLIVDLCCWKGFEFVYNYLYLANLRENWEEVKKNARKAPQP EVRRYVLPLNIDKADTGKNLVTLPNTTATAILCSDETIWLEPEVLFSGPRQAFEFPQINYQKYGGKPYTYAYGLG LNHFVPDRLCKLNVKTKETWVWQEPDSYPSEPIFVSHPDALEEDDGVVLSVVVSPGAGQKPAYLLILNAKDLSEV ARAEVEINIPVTFHGLFKKS.w.* >P1;EGR sequence:EGR:: :: ::: 0.00: 0.00 MSIQVEHPAGGYKKLFETVEELSSPLTAHVTGRIPLWLTGSLLRCGPGLFEVGSEPFYHLFDGQALLHKFDFKEG HVTYHRRFIRTDAYVRAMTEKRIVITEFGTCAFPDPCKNIFSRFFSYFRGVEVTDNALVNVYPVGEDYYACTETN FITKINPETLETIKQVDLCNYVSVNGATAHPHIENDGTVYNIGNCFGKNFSIAYNIVKIPPLQADKEDPISKSEI VVQFPCSDRFKPSYVHSFGLTPNYIVFVETPVKINLFKFLSSWSLWGANYMDCFESNETMGVWLHIADKKRKKYL NNKYRTSPFNLFHHINTYEDNGFLIVDLCCWKGFEFVYNYLYLANLRENWEEVKKNARKAPQPEVRRYVLPLNID KADTGKNLVTLPNTTATAILCSDETIWLEPEVLFSGPRQAFEFPQINYQKYCGKPYTYAYGLGLNHFVPDRLCKL NVKTKETWVWQEPDSYPSEPIFVSHPDALEEDDGVVLSVVVSPGAGQKPAYLLILNAKDLSEVARAEVEINIPVT FHGLFKKS.w./MSIQVEHPAGGYKKLFETVEELSSPLTAHVTGRIPLWLTGSLLRCGPGLFEVGSEPFYHLFDG QALLHKFDFKEGHVTYHRRFIRTDAYVRAMTEKRIVITEFGTCAFPDPCKNIFSRFFSYFRGVEVTDNALVNVYP VGEDYYACTETNFITKINPETLETIKQVDLCNYVSVNGATAHPHIENDGTVYNIGNCFGKNFSIAYNIVKIPPLQ ADKEDPISKSEIVVQFPCSDRFKPSYVHSFGLTPNYIVFVETPVKINLFKFLSSWSLWGANYMDCFESNETMGVW LHIADKKRKKYLNNKYRTSPFNLFHHINTYEDNGFLIVDLCCWKGFEFVYNYLYLANLRENWEEVKKNARKAPQP EVRRYVLPLNIDKADTGKNLVTLPNTTATAILCSDETIWLEPEVLFSGPRQAFEFPQINYQKYCGKPYTYAYGLG LNHFVPDRLCKLNVKTKETWVWQEPDSYPSEPIFVSHPDALEEDDGVVLSVVVSPGAGQKPAYLLILNAKDLSEV ARAEVEINIPVTFHGLFKKS.w.* and I tried a model using the below specified script. from modeller import * from modeller.automodel import * #from modeller import soap_protein_od env = Environ() env.io.hetatm = True env.io.water = True class MyModel(AutoModel): def special_restraints(self, aln): rsr = self.restraints at = self.atoms # Add some restraints from a file: rsr.add(secondary_structure.Alpha(self.residue_range('111:A', '123:A'))) rsr.add(secondary_structure.Alpha(self.residue_range('646:B', '658:B'))) a = MyModel(env, alnfile='alignment.ali', knowns='SAM_docked', sequence='EGR', assess_methods=(assess.DOPE, #soap_protein_od.Scorer(), assess.GA341)) a.starting_model = 1 a.ending_model = 1 a.make() The modelled structure generated without any error containing ion and water. But only two atoms were observed in the modelled structure but the ligand in the template contains 38 atoms. The atoms in ligand were not retained in the model from the template. Please provide me with suggestions to solve this error? Samdani

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Modelling missing residues
by Karki, Sudeep 15 Dec '21

15 Dec '21

Hi, I have a structure with a small molecule bound in the active site. There are missing residues in the structure, how can I model it? I tried without the small molecule but it forces the neighbor loop to go in the active site and definitely I don´t want that. Sudeep

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