- modeller_usage - salilab.org

building missing residues
by Mary Varughese 09 Apr '13

09 Apr '13

Hi, a protein i am dealing with has some missing residues. I am trying to build it with modeller. How could i verify the structure generated? Also the remarks says, CA 5% of the side chains are poorly defined and are currently modelled as alanines. Do any one know the meaning of this remark. Should i do any thing as part of correcting the structure for md simulation?

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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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Reading in a model with multiple chains?
by Patrice Peterson 19 Feb '13

19 Feb '13

Hello, I have created a number of dimeric decoys and wish to create a consensus structure. However, I'd like to omit a few residues fom the respective N- and C-termini of both chains, because they are disordered and would only get in the way of evaluating the clusters. Basically, I'd like something like this: OOMMMMMMOO/OOMMMMMMOO in which 'O' means the residue should be omitted, and 'M' means it should be included. I know I can use the model_segment argument to complete_pdb() or model.read() to select a range of residues when loading a model, but is there a way to read in a *non-contiguous* range of amino acids, as in my example? Or should I just create a new set of decoys without the residues in question (the ones labeled 'O' in the crude sketch above)? Thanks in advance! Patrice Peterson

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How NOT to add missing residues
by Anirban 08 Feb '13

08 Feb '13

Dear Sir, I am trying to model a protein for which there is a gap (resi 65 - resi 75; a loop)between two helices. I do not wish to add the missing 10 residues and want to leave the helices unjoined . But MODELLER always automatically joins the two helices (resi 64 with resi 76). How can I tell MODELLER not to join the helices? Please suggest. Regards, Anirban

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Minimize structure energy
by danashah＠post.tau.ac.il 28 Jan '13

28 Jan '13

Hi all, I've only joined this mailing list lately, so pardon me if this question was asked and answered before. We wish to perform energy minimization to a model we created. We were wondering whether we can use your automodel for that, via "use your own initial model": http://www.salilab.org/modeller/manual/node26.html#SECTION:initialmodel If it's possible, what should be the alignment file, since the sequence we want to use is the same as the model? Thank you, Dana. __ Dana Sachyani Joel Hirsch's Lab Faculty of Life Sciences Tel Aviv University Ramat Aviv, Israel e-mail: danashah(a)post.tau.ac.il

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leave out termini of a structure
by Ahmet yıldırım 25 Jan '13

25 Jan '13

Dear users, I have four similar structures. They are aaa.pdb, bbb.pdb, ccc.pdb and ddd.pdb. Unfotunately, the first 15 residues of of all the structures are missing. I modelled the aaa.pdb using aaa.pdb, bbb.pdb, ccc.pdb and ddd.pdb. When I modelled aaa.pdb, a loop of aaa.pdb goes through the rest of the protein. i.e. occurs knot. My friend said "you should leave out the termini". How will I leave out termini of a structure with Modeller? What do you suggest? Thanks in advance -- Ahmet Yıldırım

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