October 2019 - modeller_usage

Modeller 9.23 release
by Modeller Caretaker 29 Oct '19

29 Oct '19

A new version of Modeller, 9.23, is now available for download! Please see the download page at https://salilab.org/modeller/ for more information. If you have a license key for Modeller 8 or 9, there is no need to reregister for Modeller 9.23 - the same license key will work. (It won't do any harm to reregister if you want to, though!) 9.23 adds support for Python 3.8 and improves handling of chain IDs, in particular allowing for multi-character chain IDs to be read from mmCIF files. See the Modeller manual for a full change log: https://salilab.org/modeller/9.23/manual/node40.html If you encounter bugs in Modeller 9.23, please see https://salilab.org/modeller/9.23/manual/node10.html for information on how to report them. Note: you are receiving this email either because you subscribed to the modeller_usage mailing list, or you provided this address when you requested a Modeller license and you ticked the "notify me of new releases" box. In the latter case, if you no longer wish to receive announcements of new Modeller releases, simply reply to this email and let us know. Ben Webb, Modeller Caretaker -- modeller-care(a)salilab.org https://salilab.org/modeller/ Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage

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rwquest for licence key
by shah Faisal 11 Oct '19

11 Oct '19

plz give me key for use of modeller software

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Missing hetatms in model file
by Nirali Desai 10 Oct '19

10 Oct '19

Dear all, I have to model missing residues of the protein. PDB ID: 2hxh I also want to include het atoms (Ligands) in the resultant model. I did the required changes: 1. *env.io.hetatm = True * (Changed this in the model generation script) 2. .ali file >P1;kinesin structure:2hxh:1:A:1290:C:::: MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGKHVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLDRIRKLADQCTGLQGFSVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLIGQIVSSITASLRFDGALNVDLTEFQTNLVPYPRAHFPLATYAPVISAEKAYHEQLSVAEITNACFEPANQMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRTIQFVDWCPTGFKVGINYEPPTVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSEAREDMAALEKDYEEVGVDSVEGEGEEEGEEY/MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEAAGNKYVPRAILVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVVRKESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVVPSPKVSDTVVEPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCLRFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDAKNMMAACDPRHGRYLTVAAVFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRGLKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVSEYQQYQDATADEQGEFEEEGEEDEA/MASMTGGQQMGRDPINMPGASVKVAVRVRPFNSREMSRDSKCIIQMSGSTTTIVNPKQPKETPKSFSFDYSYWSHTSPEDINYASQKQVYRDIGEEMLQHAFEGYNVCIFAYGQTGAGKSYTMMGKQEKDQQGIIPQLCEDLFSRINDTTNDNMSYSVEVSYMEIYCERVRDLLNPKNKGNLRVREHPLLGPYVEDLSKLAVTSYNDIQDLMDSGNKARTVAATNMNETSSRSHAVFNIIFTQKRHDAETNITTEKVSKISLVDLAGSERADSTGAKGTRLKEGANINKSLTTLGKVISALAEMDSGPNKNKKKKKTDFIPYRDSVLTWLLRENLGGNSRTAMVAALSPADINYDETLSTLRYADRAKQIRNTVSVNLELTAEEWKKKHHHHHH/* Bcz, total residue count is 1290 and chains are A, B, C (chains are specified using the chain breaks). Is it correct please guide me on this. Will that read the hetatms too? Because when I run this and generate model. It didn't include the het atoms. Please help me on this. Sorry for the inconvenience. Thanking you, Nirali

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