August 2018 - modeller_usage

Creating a threaded protein template?
by Ahmad Khalifa 27 Aug '18

27 Aug '18

Hello, I want to create a threaded template without building the nonaligned region? is it possible using modeller? How can I modify the code here to do so? https://salilab.org/modeller/tutorial/basic.html Regards.

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Alignment format in fasta
by Ahmad Khalifa 27 Aug '18

27 Aug '18

Can I get an alignment in fasta format between two proteins using modeller? Can I convert the pir or par format to fasta? Regards.

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Modelling with ligands while maintaining correct chain ID
by Ahmad Khalifa 17 Aug '18

17 Aug '18

Hello, I have a template that has the following structure: Chain A Chain B ligand 1 A ligand 2 A ligand 3 B ligand 4 B I edit my ali file to place 4 dots at the end of the second chain before the *. This results however, in having all four ligands as part of of the B chain in my model. How can I fix that? Regards.

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ModellerError: read_te_290E> Number of residues in the alignment and pdb files are different
by Ahmad Khalifa 07 Aug '18

07 Aug '18

Hello, I'm trying to model a sequence of alpha beta tubulin based on template (3jar), with ligand included. After aligning the template and sequence according to this tutorial: https://salilab.org/modeller/tutorial/basic.html I'm doing the model building according to this: https://salilab.org/modeller/9.20/manual/node18.html After alignment, I edited my .ali file to look like this (adding the dots corresponding to the hetero atoms): >P1;3jar_template structureX:3jar_template.pdb: 1 :B:+861 :K:::-1.00:-1.00 MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEAAGNKYVPRAILVDLEPGTMDS VRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVVRKESESCDCLQGFQLTHSLGGGTGSGMGTL LISKIREEYPDRIMNTFSVVPSPKVSDTVVEPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDL NHLVSATMSGVTTCLRFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDAKNMM AACDPRHGRYLTVAAVFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPR---G--L-K-MSAT-F IGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVSEYQQ--YQDAT./MRECISIHVG QAGVQIGNACWELYCLEHGIQPDGQM-PDS------FNTFFSETGAGKHVPRAVFVDLEPTVIDEVRTGTYRQLF HPEQLITGKEDAANNYARGHYTIGKEIIDLVLDRIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYG KKSKLEFSIYPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLISQIVSS ITASLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNACFEPANQMVKCDPRHGKY MACCLLYRGDVVPKDVNAAIATIKTKRSIQFVDWCPTGFKVGINYQPPTVVPGGDLAKVQRAVCMLSNTTAIAEA WARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSEAREDMAALEKDYEEVGVDSVE..* >P1;tetrahymena sequence:tetrahymena: : : : ::: 0.00: 0.00 MREVISIHVGQGGIQVGNACWELFCLEHGI------QPDG--QMDAFNTFFSETGAGKHVPRAVFLDLEPTVIDE VRTGTYRQLFHPEQLISGKEDAANNFARGHYTIGKEIVDLCLDRIRKLADNCTGLQGFLVFNSVGGGTGSGLGSL LLERLSVDYGKKSKLGFTIYPSPQVSTAVVEPYNSILSTHSLLEHTDVAVMLDNEAIYDICRRNLDIERPTYTNL NRLIAQVISSLTASLRFDGALNVDITEFQTNLVPYPRIHFMLSSYAPIISAEKAYHEQLSVAEITNSAFEPANMM AKCDPRHGKYMACSMMYRGDVVPKDVNASIATIKTKRTIQFVDWCPTGFKVGINYQPPTVVPGGDLAKVMRAVCM ISNSTAIAEVFSRLDHKFDLMYAKRAFVHWYVGEGMEEGEFSEAREDLAALEKDYEEVGIETAE./MREIVHIQGG QCGNQIGAKFWEVISDEHGIDPTGTYHGDSDLQLERINVYYNEATGGRYVPRAILMDLEPGTMDSVRAGPFGQLF RPDNFVFGQTGAGNNWAKGHYTEGAELIDSVLDVVRKEAEGCDCLQGFQITHSLGGGTGSGMGTLLISKVREEYP DRIMETFSVVPSPKVSDTVVEPYNATLSVHQLVENADECMVIDNEALYDICFRTLKLTTPTYGDLNHLVSAAMSG VTCCLRFPGQLNSDLRKLAVNLIPFPRLHFFMIGFAPLTSRGSQQYRALTVPELTQQMFDAKNMMCAADPRHGRY LTASALFRGRMSTKEVDEQMLNVQNKNSSYFVEWIPNNIKSSICDIPPK--------GLKMAVTFVGNSTAIQEM FKRVAEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVSEYQQYQ-DAT-..* I'm getting this error "ModellerError: read_te_290E> Number of residues in the alignment and pdb files are different: 864 861 For alignment entry: 1 3jar_template". Thanks a lot.

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