- modeller_usage - salilab.org

how to build the loop of protein model using modeller
by aixintiankong 03 May '13

03 May '13

Dear, The last email have some errors please see this one. In my system ,the loop is part of the active pocket of the protein. when the ligand is absent, the loop is disordered. if the ligand is present , the loop can transform into helix. In order to simulate the disordered loop transform into helix , i should build a model that the ligand and cofactor are in the disoreded loop site. In my system, there is a NAD+ cofactor in the active site and interact with the ligand.when the ligand and cofactor NAD+ coexist, the disordered loop can transform into helix. In the PDB(protein date base) i find the complex with the liand,NAD+ and the state of the loop is helix. i also find a structure of the protein without the liand, NAD+ and the state of the loop is disordered. The sequences similarity of the two structure is 100% and the RMSD between the two structures of the protein is 0.275 . i don't know how to build a model that the protein, NAD+ and ligand coexsit and the loop of protein is disordered. could give me some advice and tell me how to do it detailed? thank you very much.

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how to build the loop of protein model using modeller
by aixintiankong 29 Apr '13

29 Apr '13

Dear, In my system ,the loop is part of the active pocket of the protein. when the ligand is absent, the loop is disordered and if the ligand is present , the loop can transform into helix. In order to simulate the disordered loop transform into helix , i should build a model that the ligand is in the disoreded loop site. In my system, there is a NAD+ cofactor in the active site and interact with the ligand.when the ligand and cofactor NAD+ coexist, the disordered loop can transform into helix. In the PDB(protein date base) i find the complex with the liand,NAD+ and the state of the loop is helix. i also find a protein structure without the liand, NAD+ and the state of the loop is disordered. The sequences similarity of the two structure is 100% and sturctue the the RMSD bettwen the two protein is 0.275 . i don't know how to build a model that the protein, NAD+ and ligand coexsit,but the loop of protein is disordered. could give me some advice and tell me how to do it detailed? thank you very much.

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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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