November 2015 - modeller_usage

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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