- modeller_usage - salilab.org

Error with the Mutate script
by Arjun Ray 08 May '13

08 May '13

Dear Sir, I am trying to mutate a residue THR61. Using the script provided on the website, I am getting following error: rayarjun$ python /usr/bin/mutate.py 1AV1.pdb 61 THR A > 1AV1.log File "/usr/bin/mutate.py", line 36 def refine(atmsel): ^ IndentationError: unindent does not match any outer indentation level Could you kindly help identifying the cause of it? Regards Arjun

2 3

change restraints relative weights
by Pietro Sormanni 03 May '13

03 May '13

dear Users, I am sorry for the naif question, but is there a way to change the relative importance of restraints? I am trying to add a secondary structure (both strand and sheet for H bonds) restraints to a model, in a region that do not align on the template structure (hence it shouldn't contain homology derived restraints). However only a few (up to 2) hydrogen bonds are formed rather than the whole beta sheet. In case you wish to delve further into this I attach at the end the piece of code that I use to add the restraints: Thank you very much for your help. Regards, Pietro from modeller import * from modeller.automodel import * # Load the automodel class # i tried also with automodel but there was no significant difference mdl = loopmodel(env, alnfile=already_done_alignment_filename, \ knowns = pdb_id, sequence = seq_id, \ loop_assess_methods=(assess.DOPE, assess.normalized_dope), \ assess_methods=(assess.DOPE, assess.normalized_dope) ) mdl.make_initial_model(aln) # Construct typical comparative modeling restraints mdl.mkhomcsr(selection(mdl), aln) mdl.restraints.add(secondary_structure.strand(mdl.residue_range('102:A', '108:A'))) # i know both of these regions are do align on anything (chain B is actually a 7 residues peptide I am adding, should be free to move anywhere). The residue numbering is read from initial model generated above mdl.restraints.add(secondary_structure.strand(mdl.residue_range('125:B:', '131:B'))) mdl.restraints.add(secondary_structure.sheet(mdl.atoms['N:102:A'], mdl.atoms['O:131:B'],sheet_h_bonds=-6)) mdl.restraints.make(selection(mdl), restraint_type='stereo', spline_on_site=False) mdl.restraints.condense() mdl.restraints.write(mdl.csrfile) # make the model env.edat.nonbonded_sel_atoms=1 # so that the selection interacts energetically with the unselected region. Actually I don't select anything manually, I added it just to be sure.. mdl.outputs = [] atmsel = mdl._check_select_atoms() mdl.multiple_models(atmsel) mdl.write_summary(mdl.outputs, 'models')

2 1

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.

2 1

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.

1 0

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

2 1

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

3 5

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

2 1

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?

2 1

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

1 2

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

2 1