- modeller_usage - salilab.org

How to get specified residue modelling
by Anogna 29 Apr '13

29 Apr '13

Dear friends, I have been struggling from past one week with the following kind of modelling.... I have a target sequence which is 97% identity with two PDB's (named A and B) I just want to make A as main template, but A has some residues missing, so i thought of making B as template for those missing residues in the "PDB A". But to go with this I am not able to get a python script file in which i can specify build residues. Can anyone can help me with this please. Thanking, Anogna

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Fwd: Run Modeller processes on multiple cpus
by Lalith Kumar 20 Apr '13

20 Apr '13

Hi, Greetings.... I am running mod9v11 on Intel Xeon with 12 cores processor. I have found that modeller is utilizing only single processor. Even though there are few older posts regarding the execution of modeller processors on multiple processors, I am unable to implement them. Sorry, I am newbie to python. It will be a great help if you could help me with a script or procedure to set up the running of modeller processes on multiple processors. This will save my lifetime. Please do the needful. Thank you Regards, Lalith -- Lalith Kumar K Research Associate, CADD Division, Dr. Reddy's Institute of Life Sciences (Formerly known as Institute of Life Sciences) University of Hyderabad Campus Gachibowli, Hyderabad 500046, India

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Modelling ofsymetric dimer
by James Starlight 15 Apr '13

15 Apr '13

Dear Modeller users! I want to model simple symmetric model of the TRP-repressor consist of 2 identical chains based on known PDB structure of that protein where some residues from N and C terms are absent in both monomers. Could you provide mewith some tutorial for such simple task ( as the input I'd like to define pdb consisting of the A and B chains as well as sequence of one monomer. As the output I'd like to obtain the same pdb with two chains included with the refined conformations of the N and C unstructured segments). Thanks for help James

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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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