hi all, i got success to build a 2chain model with two ligand.I am sincerely thankful to Ben Webb,modeller care taker for all this thing .but now I have another question :P...last portion of my final PDB look like this ATOM  6730  C  ASN B 852      5.358  41.203  4.902  1.00 44.07      2SG6732 ATOM  6731  O  ASN B 852      5.201  40.108  4.300  1.00 44.07      2SG6733 ATOM  6732  OXT ASN B 852      4.554  41.656  5.760  1.00 44.07      2SG6734 TER    6732      ASN  852                                              2SG6735 HETATM 6733  S  SO4 C 853      2.345  45.702  73.000  0.40 17.18      3SG6736 HETATM 6734  O1  SO4 C 853      1.549  46.638  73.796  1.00 17.18      3SG6737 HETATM 6735  O2  SO4 C 853      3.775  45.879  73.250  1.00 17.18      3SG6738 HETATM 6736  O3  SO4 C 853      2.020  44.340  73.405  1.00 17.18      3SG6739 HETATM 6737  O4  SO4 C 853      2.051  45.892  71.587  1.00 17.18      3SG6740 HETATM 6738  S  SO4 C 854      1.214  44.486  35.947  0.40 11.34      3SG6741 here you can see that modeller take HEATATMs as chain C.then my question is whether ir hamper the model or not.will it acceptable??? regards sanjay On Fri, 15 Aug 2008 modeller_usage-request@salilab.org wrote : >Send modeller_usage mailing list submissions to >      modeller_usage@salilab.org > >To subscribe or unsubscribe via the World Wide Web, visit >      https://salilab.org/mailman/listinfo/modeller_usage >or, via email, send a message with subject or body 'help' to >      modeller_usage-request@salilab.org > >You can reach the person managing the list at >      modeller_usage-owner@salilab.org > >When replying, please edit your Subject line so it is more specific >than "Re: Contents of modeller_usage digest..." > > >Today's Topics: > >    1. Re: using modeller to refine a docking conformation >      (Modeller Caretaker) >    2. problem with model-multiple-hetero.py (sanjay singh) > > >---------------------------------------------------------------------- > >Message: 1 >Date: Thu, 14 Aug 2008 11:27:49 -0700 > From: Modeller Caretaker <modeller-care@salilab.org> >Subject: Re: [modeller_usage] using modeller to refine a docking >      conformation >To: Jake Gunn-Glanville <dr.jake@gmail.com> >Cc: modeller_usage@salilab.org >Message-ID: <48A47925.2030504@salilab.org> >Content-Type: text/plain; charset=ISO-8859-1; format=flowed > >Jake Gunn-Glanville wrote: > > Does modeller provide a means of generating models that differ only > > slightly from an input template? > >Sure - you could build some models using a simple 1:1 alignment to the >template. The final models will look very similar to the input (by >construction) but you should expect to see some variability, >particularly in the regions that are not strongly restrained (e.g. >sidechains). You could add in some extra restraints around the docked >region, if you have some extra data or intuition about the interactions. >But Modeller is designed to generate good solutions to your scoring >function, not to sample from an ensemble - if you want to do that you >might have more luck with an MD package. > >      Ben Webb, Modeller Caretaker >-- >modeller-care@salilab.org            http://www.salilab.org/modeller/ >Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage > > >------------------------------ > >Message: 2 >Date: 15 Aug 2008 08:03:14 -0000 > From: "sanjay singh" <sanjay_singh765@rediffmail.com> >Subject: [modeller_usage] problem with model-multiple-hetero.py >To: modeller_usage@salilab.org >Message-ID: <20080815080314.10238.qmail@f5mail-237-208.rediffmail.com> >Content-Type: text/plain; charset="iso-8859-1" > >My aim is to model single chain protein from a 2 chain template with 2 ligands ( PLP).following the advance tutorial I have edited template PDB ( i.e.1IAX) as per my requirement.I have deleted chain B in the ligand which  will interact with it.now template is look like this- > >ATOM  2020  N  SER A 277      6.836  50.703  64.530  1.00 50.02          N >ATOM  2021  CA  SER A 277      5.736  50.683  65.488  1.00 52.57          C >ATOM  2022  C  SER A 277      6.158  50.953  66.920  1.00 53.76          C >ATOM  2023  O  SER A 277      5.656  51.877  67.558  1.00 53.78          O >ATOM  2024  CB  SER A 277      5.023  49.340  65.432  1.00 53.52          C >ATOM  2025  OG  SER A 277      4.399  49.181  64.168  1.00 60.54          O >ATOM  2026  N  LYS A 278      7.083  50.145  67.425  1.00 55.18          N >ATOM  2027  CA  LYS A 278      7.540  50.304  68.795  1.00 56.49          C >ATOM  2028  C  LYS A 278      8.430  51.529  69.009  1.00 56.08          C >ATOM  2029  O  LYS A 278      8.170  52.321  69.915  1.00 56.54          O >ATOM  2030  CB  LYS A 278      8.218  49.013  69.274  1.00 59.46          C >ATOM  2031  CG  LYS A 278      7.268  47.807  69.271  1.00 63.38          C >ATOM  2032  CD  LYS A 278      6.048  48.015  70.191  1.00 69.44          C >ATOM  2033  CE  LYS A 278      4.984  46.952  69.962  1.00 73.69          C >ATOM  2034  NZ  LYS A 278      5.598  45.765  69.377  1.00 82.22          N >TER    2035         LYS A 278 >HETATM 6623  S  SO4  600      2.001  43.793  71.949  0.40 47.42          S >HETATM 6624  O1  SO4  600      1.250  44.661  72.856  1.00 49.68          O >HETATM 6625  O2  SO4  600      3.441  43.960  72.132  1.00 48.63          O >HETATM 6626  O3  SO4  600      1.702  42.399  72.263  1.00 51.95          O >HETATM 6627  O4  SO4  600      1.623  44.087  70.571  1.00 47.72          O >HETATM 6633  N1  PLP A 500      6.942  41.456  67.024  1.00 91.96          N >HETATM 6634  C2  PLP A 500      7.237  41.844  68.301  1.00 92.40          C >HETATM 6635  C2A PLP A 500      8.277  41.064  69.104  1.00 91.84          C >HETATM 6636  C3  PLP A 500      6.579  42.967  68.880  1.00 91.52          C >HETATM 6637  O3  PLP A 500      6.876  43.351  70.176  1.00 90.45          O >HETATM 6638  C4  PLP A 500      5.613  43.677  68.118  1.00 90.22          C >HETATM 6639  C4A PLP A 500      4.901  44.884  68.713  1.00 86.77          C >HETATM 6640  C5  PLP A 500      5.327  43.248  66.794  1.00 91.55          C >HETATM 6641  C6  PLP A 500      6.014  42.124  66.269  1.00 92.40          C >HETATM 6642  C5A PLP A 500      4.287  43.977  65.936  1.00 92.05          C >HETATM 6643  O4P PLP A 500      4.919  44.983  65.137  1.00 91.48          O >HETATM 6644  P  PLP A 500      3.850  45.746  64.212  0.40 89.98          P >HETATM 6645  O1P PLP A 500      2.942  46.559  65.059  1.00 90.28          O >HETATM 6646  O2P PLP A 500      3.052  44.763  63.428  1.00 89.69          O >HETATM 6647  O3P PLP A 500      4.581  46.636  63.284  1.00 90.10          O >HETATM 6663  O  HOH    1      -2.199  65.598  27.605  1.00 37.63          O >HETATM 6664  O  HOH    2      13.146  43.997  69.980  1.00 28.90          O >HETATM 6665  O  HOH    3      3.514  34.147  84.461  1.00 40.65          O >HETATM 6666  O  HOH    4      14.245  36.668  40.667  1.00 33.18          O >HETATM 6667  O  HOH    5      6.748  58.168  71.500  1.00 37.09          O >HETATM 6668  O  HOH    6      -3.541  20.765  51.638  1.00 34.79          O >HETATM 6669  O  HOH    7      -4.102  61.235  21.691  1.00 38.94          O >HETATM 6670  O  HOH    8      10.326  70.845  65.572  1.00 35.43          O >HETATM 6671  O  HOH    9      -4.995  51.193  45.379  1.00 38.86          O >HETATM 6672  O  HOH    10      -6.557  33.928  65.811  1.00 39.72          O >HETATM 6673  O  HOH    11      -1.108  49.863  77.220  1.00 41.22          O >HETATM 6674  O  HOH    12    -26.403  30.845  53.499  1.00 43.93          O >HETATM 6675  O  HOH    13      -6.662  49.811  60.632  1.00 20.93          O >HETATM 6676  O  HOH    14      0.524  46.344  51.157  1.00 30.77          O >HETATM 6677  O  HOH    15      4.444  27.533  53.723  1.00 45.47          O >HETATM 6678  O  HOH    16      -9.377  50.142  40.921  1.00 38.67          O >HETATM 6679  O  HOH    17      16.732  42.270  53.224  1.00 43.17          O >HETATM 6680  O  HOH    18      36.203  41.041  67.666  1.00 41.06          O >HETATM 6681  O  HOH    19    -23.753  42.588  51.308  1.00 39.07          O >CONECT 2034 6639 >CONECT 5345 6654 >CONECT 6623 6624 6625 6626 6627 >CONECT 6624 6623 >CONECT 6625 6623 >CONECT 6626 6623 >CONECT 6627 6623 >CONECT 6628 6629 6630 6631 6632 >CONECT 6629 6628 >CONECT 6630 6628 >CONECT 6631 6628 >CONECT 6632 6628 >CONECT 6633 6634 6641 >CONECT 6634 6633 6635 6636 >CONECT 6635 6634 >CONECT 6636 6634 6637 6638 >CONECT 6637 6636 >CONECT 6638 6636 6639 6640 >CONECT 6639 2034 6638 >CONECT 6640 6638 6641 6642 >CONECT 6641 6633 6640 >CONECT 6642 6640 6643 >CONECT 6643 6642 6644 >CONECT 6644 6643 6645 6646 6647 >CONECT 6645 6644 >CONECT 6646 6644 >CONECT 6647 6644 >CONECT 6648 6649 6656 >CONECT 6649 6648 6650 6651 >CONECT 6650 6649 >CONECT 6651 6649 6652 6653 >CONECT 6652 6651 >CONECT 6653 6651 6654 6655 >CONECT 6654 5345 6653 >CONECT 6655 6653 6656 6657 >CONECT 6656 6648 6655 >CONECT 6657 6655 6658 >CONECT 6658 6657 6659 >CONECT 6659 6658 6660 6661 6662 >CONECT 6660 6659 >CONECT 6661 6659 >CONECT 6662 6659 >MASTER      342    0    4  47  25    0    0    6 6679    2  42  66 >END >II have made alignment in PIR using chain breaks "/" and block residues "." for SO4,PLP AND HOH.My alignment looks like this: > > > >P1;TvLDH >sequence:TvLDH:    : :    : ::: 0.00: 0.00 >MRIYGEEHPNQQILSRIATNDGHGENSSYFDGWKAYEKDPFHLTDNPTGVIQMGLAENQL >SLDLIRDWMKKNPQASICTEEGVSEFKAIANFQDYHGLPTFRKAIAQFMEKVRGGRTRFD >PDRIVMSGGATGAQETIAFCLADPGEAFLIPTPYYPGFDR-FRWRTGVQLLPIHCHSSNK >FKITQAALETAYRKARNSHIRVKGILVTNPSNPLGTTMDRETLRTLVSFVNEKRMHLVCD >EIFSGTAFDKPSYVSVSEVIEDE--PYCDRDLIHIAYSLSKDLGVPGFRVGVIYSYNDAV >VSCARKMSSFGLVSSQTQHLLASMLGDEELTTSFLATSRTGLCGRRRVFTDGLKRVGIHC >LDGNAGLFCWMDLRPLLKEATVEAELRLWRVIINDVKLNISPGSSFHCSEPGWFRVCFAN >MDDTAMKIALRRIESFVYRENDAAVQAKNKRRWDEALRLSLPRRRFEDPTIMTPHLMSPH >SPLVQAAT/..* > >P1;TvLDH_model >structureX:TvLDH-loop:1    : :485  : ::: 0.00: 0.00 >MRIYGEEHPNQQILSRIATNDGHGENSSYFDGWKAYEKDPFHLTDNPTGVIQMGLAENQL >SLDLIRDWMKKNPQASICTEEGVSEFKAIANFQDYHGLPTFRKAIAQFMEKVRGGRTRFD >PDRIVMSGGATGAQETIAFCLADPGEAFLIPTPYYPGFDR-FRWRTGVQLLPIHCHSSNK >FKITQAALETAYRKARNSHIRVKGILVTNPSNPLGTTMDRETLRTLVSFVNEKRMHLVCD >EIFSGTAFDKPSYVSVSEVIEDE--PYCDRDLIHIAYSLSKDLGVPGFRVGVIYSYNDAV >VSCARKMSSFGLVSSQTQHLLASMLGDEELTTSFLATSRTGLCGRRRVFTDGLKRVGIHC >LDGNAGLFCWMDLRPLLKEATVEAELRLWRVIINDVKLNISPGSSFHCSEPGWFRVCFAN >MDDTAMKIALRRIESFVYRENDAAVQAKNKRRWDEALRLSLPRRRFEDPTIMTPHLMSPH >SPLVQAAT/--* > >P1;1IAX >structureX:1IAX: 126  :A : 500  : :undefined:undefined:-1.00:-1.00 >------------------------------------------------------------ >------------------------------------------------------------ >--------GATGANETIIFCLADPGDAFLVPSPYYPAFNRDLRWRTGVQLIPIHCESSNN >FKITSKAVKEAYENAQKSNIKVKGLILTNPSNPLGTTLDKDTLKSVLSFTNQHNIHLVCD >EIYAATVFDTPQFVSIAEILDEQEMTYCNKDLVHIVYSLSK------------------- >------------------------------------------------------------ >------------------------------------------------------------ >------------------------------------------------------------ >--------/..* > > >Then I used advanced example as a template to write my input script: > > from modeller import * > from modeller.automodel import * > >class mymodel(automodel): >    def special_restraints(self, aln): >        rsr = self.restraints >        for ids in (('NZ:278:A','C4A:500:A')): > > >            atoms = [self.atoms[i] for i in ids] >            rsr.add(forms.upper_bound(group=physical.upper_distance, >                                      feature=features.distance(*atoms), >                                      mean=3.5, stdev=0.1)) > >env = environ() >env.io.hetatm = True >a = mymodel(env, alnfile='align-ligand.ali', >              knowns=('TvLDH_model','1IAX'), sequence='TvLDH') >a.starting_model = 1 >a.ending_model = 5 >a.make() > > >then program starts calculating, and then I always get : > > > > >check_ali___> Checking pairwise structural superpositions. > >Equivalent CA pairs with distance difference larger than  6.0 angstroms: > >ALN_POS TMPL1 TMPL2  RID1  RID2  NAM1  NAM2    DIST >---------------------------------------------------- >END OF TABLE > >check_ali___> Checking the sequence-structure alignment. > >Implied target CA(i)-CA(i+1) distances longer than  8.0 angstroms: > >ALN_POS  TMPL  RID1  RID2  NAM1  NAM2    DIST >---------------------------------------------- >END OF TABLE >read_to_681_> topology.submodel read from topology file:        3 > >getf_______W> RTF restraint not found in the atoms list: >              residue type, indices:    17  485 >              atom names          : C    +N >              atom indices        :  3847    0 > >getf_______W> RTF restraint not found in the atoms list: >              residue type, indices:    17  485 >              atom names          : C    CA    +N    O >              atom indices        :  3847  3843    0  3848 > > >fndatmi_285W> Only      153 residues out of      155 contain atoms of type  CA >              (This is usually caused by non-standard residues, such >              as ligands, or by PDB files with missing atoms.) >mdtrsr__446W> A potential that relies on one protein is used, yet you have at >              least one known structure available. MDT, not library, potential is used. >iup2crm_280W> No topology library in memory or assigning a BLK residue. >              Default CHARMM atom type assigned:  S -->  S >              This message is written only for the first such atom. >20 atoms in HETATM residues constrained >to protein CA atoms within 10.00 angstroms >20 atoms in residues without defined topology >constrained to be rigid bodies >indxatm_278E> No ":" in ATOM:RESID[:CHAINID] atom identifier:  N > > > >but when I used model-ligand.py command it generate model including ligands successfully. >So my questions are: >1. What am I doing wrong with model-multiple-hetero.py command? >2.how 2 solve this problem?? > >What do you think? Thank you for your suggestions.Sorry for my bad english. >sanjay > > > > > >sanjay Kumar singh kolkata >Bose Institute >Department of Botany >Main Campus >93\1 A.P.C.Road >Kolkata 700 009 >India >-------------- next part -------------- >An HTML attachment was scrubbed... >URL: http://salilab.org/archives/modeller_usage/attachments/20080815/07a82fbb/attachment.html > >------------------------------ > >_______________________________________________ >modeller_usage mailing list >modeller_usage@salilab.org >https://salilab.org/mailman/listinfo/modeller_usage > > >End of modeller_usage Digest, Vol 7, Issue 54 >********************************************* sanjay Kumar singh kolkata Bose Institute Department of Botany Main Campus 93\1 A.P.C.Road Kolkata 700 009 India