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