January 2016 - modeller_usage

3-10 alpha-helix restraints
by Alexey Orlov 27 Jan '16

27 Jan '16

Hi, Is there anyway to make 3-10 alpha-helix restraints? I've searched the archives but haven't found anything connected with it. Best regards, Alexey.

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homo-dimer problem
by Anouk 21 Jan '16

21 Jan '16

Dear modeller users, I have the following problem: I have to model a homo-dimer. There is no template of dimer (there are several templates that cover just some parts of the monomer and thus I do use multiple templates to get a descent model of the monomer). I have an alignment file that looks something like this: >P1;proteintomodel A—AABB-BC—CC / A—AABB-BC—CC* >P1;template1_1 ———BB-BC-CC / ————————* >P1;template1_2 ———————— / ———BB-BC-CC* >P1;template2_1 A-AABB———— / ————————* >P1;template2_2 ———————— / A-AABB————* On the positive side I have a list of constraints, so I want to rely on the constraints when I model the dimer interface. The problems is that since the templates for each of the monomers have the same coordinates (modelling each of the monomers of my dimer) i do obtain a model of my dimer with the 2 monomer chains basically inter-twisted (so there is no any kind of interface in between the chains because the chains are nested one in another). Also i can’t understand why, but one of the chains has secondary structure while the other doesn’t. I hoped the constraints file will push and orient the chains in the right possible way but it doesn’t seem the case. Please suggest me any ideas to overcome this problem. Thanks in advance. Expecting reply from you guys.

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my mail address
by vidya george 21 Jan '16

21 Jan '16

vidyapgb06(a)gmail.com

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Modeller 9.16 release
by Modeller Caretaker 12 Jan '16

12 Jan '16

The new version of Modeller, 9.16, is now available for download! Please see the download page at http://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 9.16 - the same license key will work. (It won't do any harm to reregister if you want to, though!) 9.16 is primarily a bugfix release relative to the last public release (9.15). Major user-visible changes include: # alignment.check_sequence_structure() no longer erroneously warns about the potentially large CA-CA distances between residues in different chains. # Add Python 3.5 support. # Bundled version of HDF5 updated to 1.8.14. See the Modeller manual for a full change log: http://salilab.org/modeller/9.16/manual/node40.html If you encounter bugs in Modeller 9.16, please see http://salilab.org/modeller/9.16/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 http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage

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Assistance in practical problem
by alzhare 1985 11 Jan '16

11 Jan '16

Dears, I modeled two protein domains structure based on comparative modelling byusing MODELLER. I want to link or combine them into one dimer protein based onavailable template. I need you experiences in in this case since Istuck here. I am awaiting your proposed procedure and MODELLERscript. Further informations, I have:1. two different protein domains(NBD and TMD). I got them based on comparative modelling with two differentprotein templates. 2. Two chain template for symmetryinterface with of NBD and TMD as it mentioned in literature it used forthis purpose, but they mentioned they used MODELLER in this task withoutprocedure details. My question is to link these twomodeled domain into one model and make it homodimer based on that templateusing modeller ? Thank you Maytham

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