March 2013 - modeller_usage

Open spline error
by Ignacio Ibarra 23 Mar '13

23 Mar '13

Hello, When I am defining a distance restraint between heavy atoms through an open spline restraint (open=True) and using restraints.add(), MODELLER writes to console the following message: "_modeller.ModellerError: mod_res_688E> Incorrect range for open cubic spline 2085, dimension 1: xlow ( 0.0500) should be less than xhigh ( 5.0500), and the range should be equal to the delta ( 0.1200) times the modality ( 50) minus 1" the code line that generates this error is the following: rsr.add(forms.spline(physical.lennard_jones, features.distance(*atoms), open=True, low=first_step, high=last_step, delta=0.12, lowderiv=0, highderiv=0, values=values, use_array=True)) low = 0.5 high = 5.05 len(values) = 50 I guess that range was calculated internally as xhigh - xmin (5). Given that delta*modality - 1 = 5, I can't guess if the message is an error or not. Thanks for any advice Regards, Ignacio Ibarra

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automatic alignment pdb file with gap to the similar complete sequence
by THUREAU Aurelien 22 Mar '13

22 Mar '13

Hi all, I want to fill a PDB files with missing residues. I use the help from : http://salilab.org/modeller/wiki/Missing%20residues I just want to optimize by doing automatically the alignment. I try using salign_align2d.py, I change matrix, playing wih gap_penalties, ...: Alignment file: --------------------------------------------------------------------------------------------------------- >P1;3DPL structureX:3DPL.pdb: 401 :C:+465 :R:::-1.00:-1.00 ESKCPEELANYCDMLLRKTPLSKKLTSEEIEAKLKEVLKKLKYVQNKDVFMRYHKAHLTRRLILDISADSEIEEN MVEWLREVGMPADYVNKLARMFQDIKVSEDLNQAFKEMHKNNALPADSVNIKILNAGAWSRSSEKVFVSLPTELE DLIPEVEEFYKKNHSGRKLHWHHLMSNGIITFKNEVGQYDLEVTTFQLAVLFAWNQRPREKISFENLKLATELPD AELRRTLWSLVAFPKLKRQVLLYEPQVNSPKDFTEGTLFSVNQEFSLIKNAKVQKRGKINLIGRLQLTTERMREE ENEGIVQLRILRTQEAIIQIMKMRKKISNAQLQTELVEILKNMFLPQKKMIKEQIEWLIEHKYIRRDESDINTFI YMA/KKRFEVKKWNAVALWAWDIVVDNCAICRNHIMDLCIECQANQASAECTVAWGVCNHAFHFHCISRWLKTRQ VCPLDNREWEFQKYGH* >P1;3DPL-full sequence:3DPL-full:::::::2.60: 0.24 GSESKCPEELANYCDMLLRKTPLSKKLTSEEIEAKLKEVLKKLKYVQNKDVFMRYHKAHLTRRLILDISADSEIEEN MVEWLREVGMPADYVNKLARMFQDIKVSEDLNQAFKEMHKNNKLALPADSVNIKILNAGAWSRSSEKVFVSLPTELE DLIPEVEEFYKKNHSGRKLHWHHLMSNGIITFKNEVGQYDLEVTTFQLAVLFAWNQRPREKISFENLKLATELPD AELRRTLWSLVAFPKLKRQVLLYEPQVNSPKDFTEGTLFSVNQEFSLIKNAKVQKRGKINLIGRLQLTTERMREE ENEGIVQLRILRTQEAIIQIMKMRKKISNAQLQTELVEILKNMFLPQKKMIKEQIEWLIEHKYIRRDESDINTFI YMA/GSMDVDTPSGTNSGAGKKRFEVKKWNAVALWAWDIVVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQ VCPLDNREWEFQKYGH* ------------------------------------------------------------------------------------------------ Missing residues: ('1:A', '2:A'), ('120:A', '121:A'), ('383:B', '398:B'), ('444:B', '446:B')) Script file: ---------------------------------------------------------------------------------------------------- # align2d/align using salign # parameters to be input by the user # 1. gap_penalties_1d # 2. gap_penalties_2d # 3. input alignment file from modeller import * log.verbose() env = environ() env.io.atom_files_directory = ['../atom_files'] aln = alignment(env, file='align2d_in.ali', align_codes='all') aln.salign(rr_file='$(LIB)/id.sim.mat', # Substitution matrix used output='', max_gap_length=20, gap_function=True, # If False then align2d not done feature_weights=(1., 0., 0., 0., 0., 0.), gap_penalties_1d=(-200, 0), gap_penalties_2d=(3.5, 3.5, 3.5, 0.2, 4.0, 6.5, 2.0, 0.0, 0.0), # d.p. score matrix #output_weights_file='salign.mtx' similarity_flag=True) # Ensuring that the dynamic programming # matrix is not scaled to a difference matrix aln.write(file='align2d.ali', alignment_format='PIR') aln.write(file='align2d.pap', alignment_format='PAP') ------------------------------------------------------------------------------------------------ But the alignment in output is not perfect. Is there some parameters I can use to obtain the good alignment ? Any suggestions or pointers would be most appreciate. Aurélien

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Suggested answer to Question 3
by jssnk 18 Mar '13

18 Mar '13

Dear Kevin, It's good you tried genthreader to id the most suitable template. from here, try running a BLAST at NCBI database to locate pdb template sequence that have ideal percentage similarity. Hope this helps. Sam.

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Advice on best template for Modelling
by KEVIN KARIUKI WAMAE 18 Mar '13

18 Mar '13

Hi..I am trying to model two proteins (Plasmodium reticulocyte-binding protein homologue 4 and 5). From Literature review, I have found out that the protein "Py235 of P.yoelii" ( http://www.rcsb.org/pdb/explore/explore.do?structureId=3HGF) is the closest there is to finding a template theoretically. Attached are the alignments that have been generated by MODELLER, and visually I could detect so many gaps. >From the tutorials in the MODELLER website, i saw tutorial number 4 *"Difficult Modeling. <http://salilab.org/modeller/tutorial/difficult.html> Model a sequence based on a low identity to a template" *that employs the use of mGenThreader. <http://bioinf.cs.ucl.ac.uk/psipred/> Is this the best option? Please assist. Regards....kevinkariuki

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Re: [modeller_usage] no_subject...
by DANIEL TAYLOR 10 Mar '13

10 Mar '13

http://www.optimal-consult-hh.com/el/qlf/pyhyh/sfsf/oq.eaotw .

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