modeller_usage

modeller_usage@salilab.org

2 participants
3148 discussions

(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

3 3

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

2 1

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

2 1

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

2 1

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

3 4

Mutate Model -reg.
by Swapnil Bhujbal 07 Dec '21

07 Dec '21

Hello, I want to use this script (*https://salilab.org/modeller/wiki/Mutate%20model <https://salilab.org/modeller/wiki/Mutate%20model>*) for mutating a single amino acid residue from aspartic acid to tyrosine. How and where do I need to modify the script? Thank you in advance. Sincerely, Dr. Swapnil.

2 2

Modeller 10.2 release
by Modeller Caretaker 30 Nov '21

30 Nov '21

A new version of Modeller, 10.2, is now available for download! Please see the download page at https://salilab.org/modeller/ for more information. If you have a license key for Modeller 8 or 9, there is no need to reregister for Modeller 10.2 - the same license key will work. (It won't do any harm to reregister if you want to, though!) 10.2 is a minor update that adds support for Python 3.10. The Mac .dmg installer should now also work with Apple's Python 3 (although we generally recommend Homebrew or Anaconda for Python 3 users on Mac). If you encounter bugs in Modeller 10.2, please see https://salilab.org/modeller/10.2/manual/node10.html for information on how to report them. Note: you are receiving this email either because you subscribed to the modeller_usage mailing list, or you provided this address when you requested a Modeller license and you ticked the "notify me of new releases" box. In the latter case, if you no longer wish to receive announcements of new Modeller releases, simply unsubscribe from the modeller_announce mailing list, or reply to this email and let us know. Ben Webb, Modeller Caretaker -- modeller-care(a)salilab.org https://salilab.org/modeller/ Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage

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