modeller_usage

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Re: [modeller_usage] modeller_usage Digest, Vol 7, Issue 54
by sanjay singh 19 Aug '08

19 Aug '08

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(a)salilab.org wrote : >Send modeller_usage mailing list submissions to > modeller_usage(a)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(a)salilab.org > >You can reach the person managing the list at > modeller_usage-owner(a)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(a)salilab.org> >Subject: Re: [modeller_usage] using modeller to refine a docking > conformation >To: Jake Gunn-Glanville <dr.jake(a)gmail.com> >Cc: modeller_usage(a)salilab.org >Message-ID: <48A47925.2030504(a)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(a)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(a)rediffmail.com> >Subject: [modeller_usage] problem with model-multiple-hetero.py >To: modeller_usage(a)salilab.org >Message-ID: <20080815080314.10238.qmail(a)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 >

2 1

problem with ligand modelling
by sanjay singh 18 Aug '08

18 Aug '08

hi, I am facing a great problem with modeller 9v3. My aim is to model 2 chain protein from a 2 chain template with a ligands. I want two ligands: so4 and PLP . Last part of my template pdb file briefly looks like this: ATOM 6617 CG LYS B 438 1.294 41.930 2.754 1.00 92.99 C ATOM 6618 CD LYS B 438 -0.149 41.634 3.105 1.00 93.43 C ATOM 6619 CE LYS B 438 -0.497 40.199 2.765 1.00 93.98 C ATOM 6620 NZ LYS B 438 -1.930 39.900 3.035 1.00 94.74 N ATOM 6621 OXT LYS B 438 4.571 44.878 1.525 1.00 92.93 O TER 6622 LYS B 438 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 6628 S SO4 601 -1.057 44.770 34.953 0.40 54.22 S HETATM 6629 O1 SO4 601 -0.255 45.682 34.134 1.00 54.47 O HETATM 6630 O2 SO4 601 -2.472 45.080 34.803 1.00 53.56 O HETATM 6631 O3 SO4 601 -0.879 43.378 34.512 1.00 56.11 O HETATM 6632 O4 SO4 601 -0.655 44.930 36.347 1.00 55.09 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 6648 N1 PLP B 501 -5.783 42.808 39.108 1.00 86.12 N HETATM 6649 C2 PLP B 501 -5.828 43.152 37.781 1.00 84.21 C HETATM 6650 C2A PLP B 501 -6.726 42.368 36.828 1.00 82.77 C HETATM 6651 C3 PLP B 501 -5.053 44.236 37.298 1.00 83.34 C HETATM 6652 O3 PLP B 501 -5.098 44.562 35.960 1.00 81.37 O HETATM 6653 C4 PLP B 501 -4.219 44.961 38.203 1.00 83.20 C HETATM 6654 C4A PLP B 501 -3.382 46.155 37.713 1.00 78.97 C HETATM 6655 C5 PLP B 501 -4.188 44.570 39.573 1.00 85.23 C HETATM 6656 C6 PLP B 501 -4.989 43.485 40.001 1.00 85.99 C HETATM 6657 C5A PLP B 501 -3.301 45.301 40.567 1.00 87.11 C HETATM 6658 O4P PLP B 501 -4.052 45.705 41.701 1.00 89.48 O HETATM 6659 P PLP B 501 -3.055 46.187 42.850 0.40 90.61 P HETATM 6660 O1P PLP B 501 -2.152 47.241 42.323 1.00 89.77 O HETATM 6661 O2P PLP B 501 -2.247 45.036 43.343 1.00 89.52 O HETATM 6662 O3P PLP B 501 -3.851 46.742 43.973 1.00 90.54 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 my alignment looks like this >P1;1iax structureX:1iax:11 :A :438 :B :ferredoxin:Azotobacter vinelandii: 1.90: 0.19 ILSKLATNE-----SPYFDGWKAYDSDPFHPLKNPNGVIQMGLAENQLCLDLIEDWIKRN PKGSIS-------FKAIANFQDYHGLPEFRKAIAKFMEKTRGGRVRFDPERVVMAGGATG ANETIIFCLADPGDAFLVPSPYYPAFNRDLRWRTGVQLIPIHCESSNNFKITSKAVKEAY ENAQKSNIKVKGLILTNPSNPLGTTLDKDTLKSVLSFTNQHNIHLVCDEIYAATVFDTPQ FVSIAEILDEQEMTYCNKDLVHIVYSLSKDMGLPGFRVGIIYSFNDDVVNCARKMSSFGL VSTQTQYFLAAMLSDEKFVDNFLRESAMRLGKRHKHFTNGLEVVGIKCLKNNAGLFCWMD LRPLLRESTFDSEMSLWRVIINDVKLNVSPGSSFECQEPGWFRVCFANMDDGTVDIALAR IRRFVGVEK/ILSKLATNE-----SPYFDGWKAYDSDPFHPLKNPNGVIQMGLAENQLCLD LIEDWIKRNPKGSIS-------FKAIANFQDYHGLPEFRKAIAKFMEKTRGGRVRFDPER VVMAGGATGANETIIFCLADPGDAFLVPSPYYPAFNRDLRWRTGVQLIPIHCESSNNFKI TSKAVKEAYENAQKSNIKVKGLILTNPSNPLGTTLDKDTLKSVLSFTNQHNIHLVCDEIY AATVFDTPQFVSIAEILDEQEMTYCNKDLVHIVYSLSKDMGLPGFRVGIIYSFNDDVVNC ARKMSSFGLVSTQTQYFLAAMLSDEKFVDNFLRESAMRLGKRHKHFTNGLEVVGIKCLKN NAGLFCWMDLRPLLRESTFDSEMSLWRVIINDVKLNVSPGSSFECQEPGWFRVCFANMDD GTVDIALARIRRFVGVEK/..* >P1;1fdx sequence:1fdx: : : : :ferredoxin:Peptococcus aerogenes: 2.00:-1.00 ILSRIATNDGHGENSSYFDGWKAYEKDPFHLTDNPTGVIQMGLAENQLSLDLIRDWMKKN PQASICTEEGVSEFKAIANFQDYHGLPTFRKAIAQFMEKVRGGRTRFDPDRIVMSGGATG AQETIAFCLADPGEAFLIPTPYYPGFDR-FRWRTGVQLLPIHCHSSNKFKITQAALETAY RKARNSHIRVKGILVTNPSNPLGTTMDRETLRTLVSFVNEKRMHLVCDEIFSGTAFDKPS YVSVSEVIEDE--PYCDRDLIHIAYSLSKDLGVPGFRVGVIYSYNDAVVSCARKMSSFGL VSSQTQHLLASMLGDEELTTSFLATSRTGLCGRRRVFTDGLKRVGIHCLDGNAGLFCWMD LRPLLKEATVEAELRLWRVIINDVKLNISPGSSFHCSEPGWFRVCFANMDDTAMKIALRR IESFVYREN/ILSRIATNDGHGENSSYFDGWKAYEKDPFHLTDNPTGVIQMGLAENQLSLD LIRDWMKKNPQASICTEEGVSEFKAIANFQDYHGLPTFRKAIAQFMEKVRGGRTRFDPDR IVMSGGATGAQETIAFCLADPGEAFLIPTPYYPGFDR-FRWRTGVQLLPIHCHSSNKFKI TQAALETAYRKARNSHIRVKGILVTNPSNPLGTTMDRETLRTLVSFVNEKRMHLVCDEIF SGTAFDKPSYVSVSEVIEDE--PYCDRDLIHIAYSLSKDLGVPGFRVGVIYSYNDAVVSC ARKMSSFGLVSSQTQHLLASMLGDEELTTSFLATSRTGLCGRRRVFTDGLKRVGIHCLDG NAGLFCWMDLRPLLKEATVEAELRLWRVIINDVKLNISPGSSFHCSEPGWFRVCFANMDD TAMKIALRRIESFVYREN/..* and mt python script is # Homology modeling with ligand transfer from the template from modeller import * # Load standard Modeller classes from modeller.automodel import * # Load the automodel class log.verbose() # request verbose output env = environ() # create a new MODELLER environment to build this model in # directories for input atom files env.io.atom_files_directory = './:../atom_files' # Read in HETATM records from template PDBs env.io.hetatm = True a = automodel(env, alnfile = 'align-ligand.ali', # alignment filename knowns = '1iax', # codes of the templates sequence = '1fdx') # code of the target a.starting_model= 4 # index of the first model a.ending_model = 4 # index of the last model # (determines how many models to calculate) a.make() # do the actual homology modeling but it ends with following error # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 1iax 836 3 1iax ferredoxin 2 1fdx 854 3 1fdx ferredoxin check_a_343_> >> BEGINNING OF COMMAND openf___224_> Open ./\1iax.pdb Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 4277067 4176.823 4.079 openf___224_> Open ./\1iax.pdb read_te_290E> Number of residues in the alignment and pdb files are different: 836 834 For alignment entry: 1 1iax x (mismatch at alignment position 835) Alignment VDIALARIRRFVGVEK.. PDB VDIALARIRRFVGVEK Match **************** Please check your alignment file header to be sure you correctly specified the starting and ending residue numbers and chains. The alignment sequence must match that from the atom file exactly. Another possibility is that some residues in the atom file are missing, perhaps because they could not be resolved experimentally. (Note that Modeller reads only the ATOM and HETATM records in PDB, NOT the SEQRES records.) In this case, simply replace the section of your alignment corresponding to these missing residues with gaps. read_te_288W> Protein not accepted: 1 1iax Please solve this puzzle as i am fade-up with this :( regards sanjay sanjay Kumar singh kolkata Bose Institute Department of Botany Main Campus 93\1 A.P.C.Road Kolkata 700 009 India

2 1

Rino Ragno è fuori ufficio/ is out of office
by Rino.Ragno＠uniroma1.it 18 Aug '08

18 Aug '08

Risposta automatica dal 17/08/2008 fino al 10/09/2008 This is an automatic reply. I will not available till Sep 10th 2008. During this period I will try to read your message and to send a reply. Best Regards Rino

1 0

Rino Ragno è fuori ufficio/ is out of office
by Rino.Ragno＠uniroma1.it 18 Aug '08

18 Aug '08

1 0

problem with model-multiple-hetero.py
by sanjay singh 15 Aug '08

15 Aug '08

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

2 1

using modeller to refine a docking conformation
by Jake Gunn-Glanville 14 Aug '08

14 Aug '08

Hi, Does modeller provide a means of generating models that differ only slightly from an input template? I have been using modeller to generate models of an antibody, and then docking those models to the solved structure of the target antigen protein for that antibody. Multiple models are required, as the docking is very sensitive to the correct conformation of loops at the docking interface. I have some resulting docked conformations that are receiving pretty high ZRANK scores, but upon inspection, it seems that they could all be just a little bit better fit. I was hoping I could feed these docked conformations as templates into modeller, and generate a large number of very similar models, with slightly differing energies. I'm already comfortable generating input PIR alignments with multiple chains; I'm just interested in hearing what the recommended approach would be for such a refinement process. Cordially, Jake

2 1

side chains turned inside out
by Josmar R. da Rocha 08 Aug '08

08 Aug '08

Hi modellers, I'm trying to build a homology model of a multi-chain heteromeric protein (with model-default.py script) using as template a homomeric protein as showed in the following example: #begin of "ali" file >P1;pdb structureX:pdb:1:A:10::::: AAAAAAAAAA/ AAAAAAAAAA/ AAAAAAAAAA/ AAAAAAAAAA/ AAAAAAAAAA* >P1;ABBAB sequence::::::::: AAAAAAAAAA/ BBBBBBBBBB/ BBBBBBBBBB/ AAAAAAAAAA/ BBBBBBBBBB* #End of "ali" file The model is built normally. However, I noticed that many residues in the active site (which is localized in the interface between each pair of monomers) that are supposed to exposed are turned inside out. I tried to model just as homomeric and so all important side chains in the active site kept the template position. Is there anything I can do to make the modeled residues to adopt the same position as in the template? Would it be reasonable? I'd appreciate any help! Best regards, Josmar Rocha Novos endereços, o Yahoo! que você conhece. Crie um email novo com a sua cara @ymail.com ou @rocketmail.com. http://br.new.mail.yahoo.com/addresses

2 1

question about a mix model
by Jesica MLM 08 Aug '08

08 Aug '08

Hi All, this is the first time i write, i am from Argentina, and I would like to create an model of a short protein ( 96 amino acids) mixing or emsamblin two models, because the protein has two domains very well modeled but with diferet proteins and with diferent cordinates, so i have two models, hte first from 2 to 90 aa, and the second from 91-96 aa. how can i make a one model from these two? thank you very much Jesica Levingston Mac leod Animal Virology Center Milstein Center Buenos Aires Argentina ____________________________________________________________________________________ ¡Buscá desde tu celular! Yahoo! oneSEARCH ahora está en Claro http://ar.mobile.yahoo.com/onesearch

2 1

modeling an oligomer
by Douglas Kojetin 07 Aug '08

07 Aug '08

Hi All, I would like to create an oligomeric (hexamer) model. I have a Ca- only hexameric model (chains A-F) to use for the template and an experimentally determined monomer structure I would like to use for the target. Essentially, I would like to map six of the monomer target structures to chains A-F of the template. I've attempted to do this using the "model-myini.py" script as described here: http://www.salilab.org/modeller/manual/node26.html and here: http://www.salilab.org/modeller/examples/automodel/model-myini.py but my output hexamer structure ends up looking like spaghetti. Am I using the proper modeling script for this task? If so, what should the alignment and target PDB files look like to map the monomer structure to the hexamer structure? Thanks, Doug

2 2

GPCR modeling
by Sharangdhar S. Phatak 07 Aug '08

07 Aug '08

Hello, I was wondering if anyone could help me address the issue of flipped residues. I am modeling a 7-TM GPCR and in one of the TM the residues are flipped. Is there a way to fix this? Thank you Sharang

1 0

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