- modeller_usage - salilab.org

ions and non-standard amino acids problem
by 程中一 04 Mar '16

04 Mar '16

Dear modeller users, I have the following problem: I have to model a metalloenzyme named nitrile hydratase with a cobalt ion as well as two oxidised Cysteines in the active site. The problems is that once the model is established, the structure of the active site is very different from that of the template. I want to figure out how to get an accurate protein model with ions or non-standard amino acids in its active site. Please suggest me any ideas to overcome this problem. Thanks in advance. Expecting reply from you guys.

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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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MOULDER
by Markus Heller 08 Dec '15

08 Dec '15

Hello, Are there any updates on MOULDER? More specifically, will it be available in MODELLER soon? Thanks and Cheers Markus Heller

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Fixed amino acids?
by Kalantzi Alexandra Styliani 16 Nov '15

16 Nov '15

Dear all, I would like to build a protein structure based on multiple homologous proteins. But is it possible to keep few amino acids (main and side chain) of a homologous structure fixed and build the rest of the structure around these? Thank you in advance. Best regards, Alexandra

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Re: [modeller_usage] modeller_usage Digest, Vol 14, Issue 52
by Vijina C 12 Nov '15

12 Nov '15

Sir What is difference between modweb and modeller.can i use modweb instead of modeller.if i use modweb can i publish that result thanking you On Sat, Nov 7, 2015 at 12:49 AM, <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. hiii (Vijina C) > 2. Re: hiii (Modeller Caretaker) > 3. Error using local_alignment=True in salign (David Abia) > 4. Re: Error using local_alignment=True in salign > (Modeller Caretaker) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 2 Nov 2015 10:36:15 +0530 > From: Vijina C <vbioinfo2009(a)gmail.com> > To: modeller_usage(a)salilab.org > Subject: [modeller_usage] hiii > Message-ID: > <CAAMS7Z== > DM_cxp-7rDiyOJXEc-Jh6KaUkw_KbA6EToZHV12aQg(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > hi sir > > i did the programing part but it is not running.i just copied > modeller 9.10 coding...but i installed 9.15..is there any difference in the > coding part please reply >

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Error using local_alignment=True in salign
by David Abia 06 Nov '15

06 Nov '15

Dear Modeller users, I'm trying to force a local alignment while using salign function in mod9.15, and it fails with error: "modeller.ModellerError: align_l_251E> MATRIX_OFFSET probably has an invalid value: 0.0000" My script ( mod-3nnt-prim.cons-aln.py ): from modeller import * env = environ() aln = alignment(env) m = model(env, file='./tmp-NmArZQ.pdb', model_segment=('FIRST:A', 'LAST:B')) aln.append_model(m, atom_files='./tmp-NmArZQ.pdb', align_codes='3nnt_x') aln.append( file='./tmp-q4VfPF.fasta', alignment_format='FASTA', align_codes='prim.cons') aln.salign(local_alignment=True) aln.write(file='mod-3nnt-prim.cons.pir') The output: Traceback (most recent call last): File "mod-3nnt-prim.cons-aln.py", line 8, in ? aln.salign(local_alignment=True) File "/usr/lib/modeller9.15/modlib/modeller/alignment.py", line 395, in salign nsegm, matrix_offset_3d, break_break_bonus) _modeller.ModellerError: align_l_251E> MATRIX_OFFSET probably has an invalid value: 0.0000 The error comes from a call to a function: retval = func(self.modpt, ... , local_alignment, .... , nsegm, matrix_offset_3d, break_break_bonus) that is defined as: func = _modeller.mod_salign If I remove the option "local_alignment=True", it runs flawlessly. Any idea about what can be happening? Thanks in advance, David.

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