Thank you. As you`ve said, the problem was with the alignment (I should have put "." instead of "-" in my seq) and with chain labeling.

Modeller Caretaker wrote: > Dimitry.A.Suplatov wrote: >> I am having a great problem with modeller 9v1. >> My aim is to model 2 chain protein from a 2 chain template with a >> ligands. I want two ligands: Ca metal ion and SOX (Penicillin G >> sulphoxide). My template pdb file briefly looks like this: >> ---------------------------------------------------------------------------------------------------- >> >> ATOM 1 N SER A 3 27.496 31.222 28.262 1.00 >> 48.33 N ATOM 2 CA SER A 3 27.785 31.042 >> 26.803 1.00 43.97 C ... etc to the end of chain a >> TER 1679 ALA A 209 >> ATOM 1684 N SER B 1 14.845 1.596 -1.736 1.00 >> 6.93 N >> ATOM 1685 CA SER B 1 15.548 2.917 -1.659 1.00 >> 6.75 C ATOM 1686 C SER B 1 16.489 3.059 >> -2.844 1.00 8.04 C >> ..... >> ATOM 6113 NE ARG B 557 26.460 16.023 30.916 1.00 >> 23.74 N ATOM 6114 CZ ARG B 557 27.175 15.276 >> 30.094 1.00 19.20 C ATOM 6115 NH1 ARG B 557 >> 28.016 15.921 29.310 1.00 21.83 N ATOM 6116 NH2 ARG B >> 557 27.069 13.952 30.055 1.00 20.49 N ATOM 6117 >> OXT ARG B 557 23.973 18.664 34.656 1.00 29.98 O >> TER 6118 ARG B 557 >> .... Cutting useless HETATM >> HETATM 6159 CA CA B1568 23.187 -16.230 6.242 1.00 >> 10.86 CA << Ca ion >> HETATM 6160 O8 SOX B1569 13.279 0.047 0.037 1.00 >> 37.00 O << SOX ... >> HETATM 6161 C7 SOX B1569 13.688 -1.062 0.060 1.00 >> 38.52 C >> .. >> HETATM 6166 O12 SOX B1569 13.790 -4.072 -2.049 1.00 >> 54.27 O ...etc to the end of SOX (I guess resid for SOX = >> 569, chain B1, ?) > > No - see the definition of the PDB file format at > http://www.wwpdb.org/documentation/format23/sect9.html > > Your SOX residue is number 1569 in chain B. The PDB file format has > only one character for the chain ID, so chain "B1" is impossible. > >> My alignment looks like this: >> ----------------------------------------------------------------------------------------------------- >> >> >P1;1gm9 >> structureX:1gm9.pdb:3:A:569:B1:::: #Starting from A resid =3(because >> first two are missing) and finishing with SOX > > Consequently, this should also be 3:A:1569:B. > >> --SSSEIKIVRDEYG-PHIYANDTWHLFYGYGYVVAQDRLFQMEMARRSTQGTVAEVLGK >> DFVKFDKDIRRNYWPDAIRAQIAALSPEDMSILQGYADGMNAWIDKVNTNPETLLPKQFN >> TFGFTPKRWEPFDVAMIFVGTMANRFSDSTSEIDNLALLTALKDKYGVSQGMAVFNQLKW >> LVNPSAPTTIAVQESNYPLKFNQQNSQTA/ #Chain break = ending chain A >> SNMWVIGKSKAQDAKAIMVNGPQFGWYAPAY >> TYGIGLHGAGYDVTGNTPFAYPGLVFGHNGVISWGSTAGFGDDVDIFAERLSAEKPGYYL >> HNGKWVKMLSREETITVKNGQAETFTVWRTVHGNILQTDQTTQTAYAKSRAWDGKEVASL >> LAWTHQMKAKNWQEWTQQAAKQALTINWYYADVNGNIGYVHTGAYPDRQSGHDPRLPVPG >> TGKWDWKGLLPFEMNPKVYNPQSGYIANWNNSPQKDYPASDLFAFLWGGADRVTEIDRLL >> EQKPRLTADQAWDVIRQTSRQDLNLRLFLPTLQAATSGLTQSDPRRQLVETLTRWDGINL >> LNDDGKTWQQPGSAILNVWLTSMLKRTVVAAVPMPFDKWYSASGYETTQDGPTGSLNISV >> GAKILYEAVQGDKSPIPQAVDLFAGKPQQEVVLAALEDTWETLSKRYGNNVSNWKTPAMA >> LTFRANNFFGVPQAAAEETRHQAEYQNRGTENDMIVFSPTTSDRPVLAWDVVAPGQSGFI >> APDGTVDKHYEDQLKMYENFGRKSLWLTKQDVEAHKESQEVLHVQR/..* >> #Chain break = ending chain B and ".." for two HETATM > > That's fine except that there is no chain break between chain B and > your two HETATMs in your PDB. The HETATMs are also in chain B, so you > should leave out that last chain break. > >> >P1;1klc >> sequence:1klc: : : : ::: 0.00: 0.00 >> ASPPTEVKIVRDEYGMPHIYADDTYRLFYGYGYVVAQDRLFQMEMARRSTQGTVSEVLGK >> AFVSFDKDIRQNYWPDSIRAQIASLSAEDKSILQGYADGMNAWIDKVNASPDKLLPQQFS >> TFGFKPKHWEPFDVAMIFVGTMANRFSDSTSEIDNLALLTAVKDKYGNDEGMAVFNQLKW >> LVNPSAPTTIAARESSYPLKFDLQNTQTA/ >> SNMWVIGKNKAQDAKAIMVNGPQFGWYAPAY >> TYGIGLHGAGYDVTGNTPFAYPGLVFGHNGTISWGSTAGFGDDVDIFAEKLSAEKPGYYQ >> HNGEWVKMLSRKETIAVKDGQPETFTVWRTLDGNVIKTDTRTQTAYAKARAWAGKEVASL >> LAWTHQMKAKNWPEWTQQAAKQALTINWYYADVNGNIGYVHTGAYPDRQPGHDPRLPVP- >> DGKWDWKGLLSFDLNPKVYNPQSGYIANWNNSPQKDYPASDLFAFLWGGADRVTEIDTIL >> DKQPRFTADQAWDVIRQTSLRDL-LRLFLPALKDATANLAENDPRRQLVDKLASWDGENL >> VNDDGKTYQQPGSAILNAWLTSMLKRTVVAAVPAPFGKWYSASGYETTQDGPTGSLNISV >> GAKILYEALQGDKSPIPQAVDLFGGKPEQEVILAALDDAWQTLSKRYGNDVTGWKTPAMA >> LTFRANNFFGVPQAAAKEARHQAEYQNRGTENDMIVFSPTSGNRPVLAWDVVAPGQSGFI >> APDGKADKHYDDQLKMYESFGRKSLWLTPQDVDEHKESQEVLQVQR/--* > > The last chain break is thus also not necessary here. Plus, Modeller > won't build any ligands in your model because you aligned your ligands > with gaps in the model. Replace that final '--' with '..' to get the > ligands. > >> Modeller starts with this error: "import site' failed; use -v for >> traceback" > > That's a Python warning, which you can ignore: see > http://salilab.org/modeller/release.html#issues > >> KeyError: 'No such atom: O12:766:C' >> ---------------------------------------------------------------------------------------------------------- >> >> That means, that it can not see atom O12:766:C. > > It can't find the SOX residue because your alignment does not say to > build any ligands. To be sure of the residue numbers, look at the > initial model (.ini) file that Modeller generated. > >> If I remove user restraints and just use automodel, it output good >> model, but without ligands at all! >> And the latter is what I absolutely do no understand. > > Fix your alignment and everything should work correctly. > >> My log has this note about SOX: >> ----------------------------------------------------------------------------------------------------------- >> >> read_pd_459W> Residue type SOX not recognized. 'automodel' model >> building >> will treat this residue as a rigid body. >> To use real parameters, add the residue type to >> ${LIB}/restyp.lib, >> its topology to ${LIB}/top_*.lib, and suitable forcefield >> parameters to ${LIB}/par.lib. > > Indeed. > >> And nothing about CA (may be the program takes CA as Calpha?). > > No, of course not - Calpha is an atom type, not a residue. Modeller > already knows what the "CA" residue type is - it's defined in restyp.lib. > >> 2. Why modeller outputs model with no ligands if I use default >> automodel with no restraints (env.io.hetatm =True)?. > > Turning on env.io.hetatm instructs Modeller to read HETATM residues > from your template PDBs. It does not force those HETATMs to appear in > your model - the alignment controls that. > >> P.S. I am using windows compilation. May it be some platform specific >> modeller bug? > > No. Ligand modeling works fine in Windows. > > Ben Webb, Modeller Caretaker