- modeller_usage - salilab.org

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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hiii
by Vijina C 02 Nov '15

02 Nov '15

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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loop model and fix other part!
by Qiang Zhong 30 Oct '15

30 Oct '15

I want to model missing loop in a protein, when I use loopmodel method do it, I got the perturbation of whole protein structure , my code is below, could you help me solve this problem? a = loopmodel(env, alnfile = 'alignment.ali', # alignment filename knowns = '5fd1', # codes of the templates sequence = 'xxx') # code of the target a.starting_model= 1 # index of the first model a.ending_model = 1 # index of the last model # (determines how many models to calculate) a.md_level = None # No refinement of model a.loop.starting_model = 1 # First loop model a.loop.ending_model = 1 # Last loop model a.loop.md_level = refine.fast # Loop model refinement level a.make() # do homology modeling Qiang Zhong 010-64889893 Institute of Biophysics, Chinese Academy of Sciences E-mail:zhongqiang(AT)moon.ibp.ac.cn

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Re: [modeller_usage] Modelling with SAXS data
by Edelmiro Moman 30 Oct '15

30 Oct '15

Yet another option would be converting your SAXS envelope to an (pseudo) electron density map, (rigid) docking your model into the map with something like SITUS and then refining your model to fit the (pseudo) electron density with something like NMFF. I have done it in the past with good results (it is very straightforward and you obtain a very nice trajectory/movie of the NM fitting). On 30/10/15 09:59, modeller_usage-request(a)salilab.org wrote: > [modeller_usage] Modelling with SAXS data -- Edelmiro Moman, PhD ProSciens, computer-aided drug design Caminho Bastida, 162 E-15405 Ferrol Galicia, Spain Phone : +352 621-511-423 E-mail : moman(a)prosciens.com http://prosciens.com

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Modelling with SAXS data
by Ajasja Ljubetič 29 Oct '15

29 Oct '15

Hi all! First of all I would just like to say that I'm a very happy modeller user and that things have been running pretty smoothly:) We have obtained recently some SAXS data for a specific protein (that we hope is a monomer in solution). I have already built several models of this protein, but now I would like to refine it using SAXS data. As far as I know I have three options: - Use the SAXS modeller class <https://salilab.org/modeller/manual/node426.html> and hope for the best (I found an old thread <https://salilab.org/archives/modeller_usage/2011/msg00330.html> stating that it's no longer supported). - Use FoXS to screen models after I have generated them using modeller - Switch to IMP (I could only find one example <http://integrativemodeling.org/keystone2015/IMP_SAXS.pdf> of the IMP python interface) and add the restraints in IMP. Any comments and suggestions are welcome. in particular I'd like to know: how/if restraints be added in modeller based on SAXS data? And if it really is a very bad idea to use this unsupported functionality? Thank you & best regards, Ajasja Ljubetič, National Institute of Chemistry, Slovenia

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Bug in documentation: automodel.get_model_filename() takes five arguments
by Ajasja Ljubetič 23 Oct '15

23 Oct '15

Hi! In the documentation <https://salilab.org/modeller/9.15/manual/node75.html> the signature for automodel.get_model_filename() is declared as get_model_filename(sequence, id1, id2, file_ext) But I got the following error: Traceback (most recent call last): File "d:/data/modeller/poly_modeller/ppmod/make_homology_model.py", line 97, in <module> a.make() File "c:\bin\Modeller\modlib\modeller\automodel\automodel.py", line 121, in make self.multiple_models(atmsel) File "c:\bin\Modeller\modlib\modeller\automodel\automodel.py", line 225, in multiple_models self.outputs.append(self.single_model(atmsel, num)) File "c:\bin\Modeller\modlib\modeller\automodel\automodel.py", line 308, in single_model self.pdb_ext) TypeError: get_model_filename() takes exactly 4 arguments (5 given) Of course one must include self as well, so the following works: def get_model_filename(self, sequence, id1, id2, file_ext): Perhaps in the documentation the self could be included as well? It's obvious in hindsight, but still took me 15 minutes to figure out. Or maybe a quick example could be added: How to move the pdb files into subfolder outdir class MyModel(automodel): def get_model_filename(self, sequence, id1, id2, file_ext): print self, sequence, id1, id2, file_ext return "outdir/test-prefix-{id1:02}-{id2:02}{file_ext}".format( id1=id1, id2=id2, file_ext=file_ext) PS: Is there some way to move all the generated files (including traces and sch and rsr files) into a subfolder? Scanning the sourcecode I see that redefining modfile.default could work. Thanks & All the best, Ajasja

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