September 2017 - modeller_usage

Modeller Hardware specifications
by arturossi 26 Sep '17

26 Sep '17

Greetings, I'm Artur, and I'm responsible for the administration of the MHOLline 2 web site (www.mholline2.lncc.br) which has been designed for protein modelling and automation to the scientific community. We are changing our servers to suit better our needs and I'm collecting hardware specifications for all softwares that we use so we can provide a better service to scientific community. From what I've searched about the Modeller, I've not been able to find a recent hardware specifications. Since Modeller is quite used in our servers, it's important to choose the hardware according to the its needs. Which is the recommended hardware specification to run Modeller within a server? Thank you, Artur Duque Rossi Colaborador Grupo de Modelagem Molecular de Sistemas Biológicos Laboratório Nacional de Computação Científica (LNCC) Av. Getúlio Vargas, 333, Bloco A, Sala 1A42 Quitandinha, CEP: 25651-075 Petrópolis - RJ, Brasil Telefone: +55 (24) 2233-6179

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Multimeric Protein Modelling
by Ryan Ehrlich 15 Sep '17

15 Sep '17

Hello Modellers, I'm running into issues when modelling a multimeric (2 chains) protein. When using the multi-chain modelling example seen in the online manual (see below) it throws an error because the monomers aren't the same length, per the special_restraints(). How can I resolve this issue? Regards, Ryan # Comparative modeling by the automodel class## Demonstrates how to build multi-chain models, and symmetry restraints#from modeller import *from modeller.automodel import * # Load the automodel class log.verbose() # Override the 'special_restraints' and 'user_after_single_model' methods:class MyModel(automodel): def special_restraints(self, aln): # Constrain the A and B chains to be identical (but only restrain # the C-alpha atoms, to reduce the number of interatomic distances # that need to be calculated): s1 = selection(self.chains['A']).only_atom_types('CA') s2 = selection(self.chains['B']).only_atom_types('CA') self.restraints.symmetry.append(symmetry(s1, s2, 1.0)) def user_after_single_model(self): # Report on symmetry violations greater than 1A after building # each model: self.restraints.symmetry.report(1.0) env = environ()# directories for input atom filesenv.io.atom_files_directory = ['.', '../atom_files'] # Be sure to use 'MyModel' rather than 'automodel' here!a = MyModel(env, alnfile = 'twochain.ali' , # alignment filename knowns = '2abx', # codes of the templates sequence = '1hc9') # code of the target a.starting_model= 1 # index of the first modela.ending_model = 1 # index of the last model # (determines how many models to calculate)a.make() # do comparative modeling

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Multi-chain/multi-template Modeling
by Ryan Ehrlich 08 Sep '17

08 Sep '17

Hey there Modellers, I appreciate the input I received from my previous questions, but have run into something I need more clarification on. I'm attempting to product models using multiple templates and multiple chains. I'll detail my steps below: Step 1: Build individual chain profiles using build_profile.py, as seen in the basic tutorial (select PDBs based on e-val and identity thresholds). Step 2: Use the multiple template salign.py program as seen in the advanced tutorial (the first script in the tutorial), on PDBs selected in step 1. Step 3: Here I attempted to combine alignment profiles. I wrote a quick python script to do so. I'll show a snippet of the output below, please note that some structures only offer one chain that could be used as a template, if this was the case I use a hyphen a placeholder... which I think is the source of at least one of my problems. >P1;2bnu structure:2bnu: 1 :A:252 :B:::-1.00:-1.00 --QEVTQIPAALSVPEGENLVLNCSFTDSAIYNLQWFRQDPGKGLTSLLLIQSSQREQTSGRLNASLDKSSGRST LYIAASQPGDSATYLCAVRPTSGGSYIPTFGRGTSLIVHPYIQNPDPAVYQLRRSKSSDKSVCLFTDFDSQTNVS QSKD--SDVYITDKCVLDMRSMDFKSNSAVAWSNKSDFACANAFNNSIIPEDTFFPS-----/ --GVTQTPKFQVLKTGQSMTLQCAQDMNHEYMSWYRQDPGMGLRLIHYSVGAGITDQGEVPNGYNVSRSTTEDFP LRLLSAAPSQTSVYFCASSYVG-N-TGELFFGEGSRLTVLEDLKNVFPPEVAVFEPSEAEISHTQKATLVCLATG FYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPALNDSRYALSSRLRVSATFWQDPRNHFRCQVQFYGLSENDEWT QDRAKPVTQIVSAEAWGRAD-------* >P1;5bs0 structure:5bs0: 1 :D:252 :E:::-1.00:-1.00 -AQEVTQIPAALSVPEGENLVLNCSFTDSAIYNLQWFRQDPGKGLTSLLYVRPYQREQTSGRLNASLDKSSGRST LYIAASQPGDSATYLCAVRPGGAGPFFVVFGKGTKLSVIPNIQNPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVS QSKD--SDVYITDKCVLDMRSMDFKSNSAVAWSNKSDFACANAFNNSIIP------------/ --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- ---------------------------* >P1;4grm structure:4grm: 1 :A:252 :B:::-1.00:-1.00 -------------------------------------------------------------------------- -------------------------------------------------------------------------- --------------------------------------------------------------/ --GVTQTPKFQVLKTGQSMTLQCAQDMNHEYMSWYRQDPGMGLRLIHYSVGAGITDQGEVPNGYNVSRSTTEDFP LRLLSAAPSQTSVYFCASRPGL---QPEQYFGPGTRLTVTEDLKNVFPPEVAVFEPSEAEISHTQKATLVCLATG FYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPALNDSRYALSSRLRVSATFWQDPRNHFRCQVQFYGLSENDEWT QDRAKPVTQIVSAEAWGRAD-------* >P1;2pye sequence:2pye: 1 :A:252 :B:::-1.00:-1.00 MKQEVTQIPAALSVPEGENLVLNCSFTDSAIYNLQWFRQDPGKGLTSLLLIQSSQREQTSGRLNASLDKSSGSST LYIAASQPGDSATYLCAVRPLLDGTYIPTFGRGTSLIVHPYIQNPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVS QSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSDFACANAFNNS/ MGVTQTPKFQVLKTGQSMTLQCAQDMNHEYMSWYRQDPGMGLRLIHYSVGAGTTDQGEVPNGYNVSRSTIEDFPL RLLSAAPSQTSVYFCASSYLGNTGELFFGEGSRLTVLEDLKNVFPPEVAVFEPSEAEISHTQKATLVCLATGFYP DHVELSWWVNGKEVHSGVCTDPQPLKEQPALNDSRYALSSRLRVSATFWQDPRNHFRCQVQFYGLSENDEWTQDR AKPVTQIVSAEAWGRAD* Step 4: Next, I attempted to use the second salign.py script in the advanced tutorial, hoping for PDB-multi.ali and PDB-multi.prf files which I did not receive. The error code was as seen below: _modeller.ModellerError: rdpdb___303E> No atoms were read from the specified input PDB file, since the starting residue number and/or chain id in MODEL_SEGMENT (or the alignment file header) was not found; requested starting position: residue number " 1", chain " A"; atom file name: 2bnu.pdb I'm assuming this has to do with the pdbID_fit.pdb files outputted by the program in step 2. So am I merging my alignment file too late? I'm also assuming the pdbID_fit.pdb file must contain both chains. Regardless any guidance for producing models from this would be very useful. Best, Ryan

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Fwd: Modelling protein of interest with RNA
by Saravanan Parameswaran 07 Sep '17

07 Sep '17

Modellers, I am trying to model my protein of interest along with RNA in A-form from template. I am encountering problem in modelling . First, the RNA structure is disordered in the model. I think the residue topology of RNA is not assigned I want to model RNA in A-form, since the protein of interest acts mainly on A-form of RNA Please help me out to rectify and model RNA in A-form with my protein of interest Second , a nucleotide is modified (ARA) in the bound RNA with my protein of interest. I want to model it as such, not ligand. I want it to be a modified nucleotide since, modelling it as ligand may bread the RNA strand. Thanks in advance in log file, i found warnings like below. ------------------------------------------------------ read_pd_459W> Residue type 8AZ not recognized. 'automodel' model building will treat this residue as a rigid body. To use real parameters, add the residue type to ${LIB}/restyp.lib, its topology to ${LIB}/top_*.lib, and suitable forcefield parameters to ${LIB}/par.lib. generat_607W> Cannot find params in params file: CHARMM atoms : CN6 ON2 UNDF IUPAC atoms : C3' O3' P Atom indices : 14507 14508 Residues : URA URA 58 atoms in residues without defined topology constrained to be rigid bodies iatmcls_286W> MODEL atom not classified: URA:OP1 URA iatmcls_286W> MODEL atom not classified: URA:OP2 URA iatmcls_286W> MODEL atom not classified: URA:O5' URA iatmcls_286W> MODEL atom not classified: URA:C5' URA iatmcls_286W> MODEL atom not classified: URA:C4' URA iatmcls_286W> MODEL atom not classified: URA:O4' URA iatmcls_286W> MODEL atom not classified: URA:C1' URA iatmcls_286W> MODEL atom not classified: URA:N1 URA iatmcls_286W> MODEL atom not classified: URA:C6 URA iatmcls_286W> MODEL atom not classified: URA:C2 URA iatmcls_286W> MODEL atom not classified: URA:O2 URA iatmcls_286W> MODEL atom not classified: URA:N3 URA iatmcls_286W> MODEL atom not classified: URA:C4 URA iatmcls_286W> MODEL atom not classified: URA:O4 URA iatmcls_286W> MODEL atom not classified: URA:C5 URA iatmcls_286W> MODEL atom not classified: URA:C2' URA iatmcls_286W> MODEL atom not classified: URA:O2' URA iatmcls_286W> MODEL atom not classified: URA:C3' URA iatmcls_286W> MODEL atom not classified: URA:O3' URA iatmcls_286W> MODEL atom not classified: GUA:P GUA iatmcls_286W> MODEL atom not classified: GUA:OP1 GUA iatmcls_286W> MODEL atom not classified: GUA:OP2 GUA iatmcls_286W> MODEL atom not classified: GUA:O5' GUA iatmcls_286W> MODEL atom not classified: GUA:C5' GUA iatmcls_286W> MODEL atom not classified: GUA:C4' GUA iatmcls_286W> MODEL atom not classified: GUA:O4' GUA iatmcls_286W> MODEL atom not classified: GUA:C1' GUA iatmcls_286W> MODEL atom not classified: GUA:N9 GUA iatmcls_286W> MODEL atom not classified: GUA:C4 GUA iatmcls_286W> MODEL atom not classified: GUA:N3 GUA iatmcls_286W> MODEL atom not classified: GUA:C2 GUA iatmcls_286W> MODEL atom not classified: GUA:N1 GUA iatmcls_286W> MODEL atom not classified: GUA:N2 GUA iatmcls_286W> MODEL atom not classified: GUA:C6 GUA iatmcls_286W> MODEL atom not classified: GUA:O6 GUA iatmcls_286W> MODEL atom not classified: GUA:C5 GUA iatmcls_286W> MODEL atom not classified: GUA:N7 GUA iatmcls_286W> MODEL atom not classified: GUA:C8 GUA iatmcls_286W> MODEL atom not classified: GUA:C2' GUA iatmcls_286W> MODEL atom not classified: GUA:O2' GUA iatmcls_286W> MODEL atom not classified: GUA:C3' GUA iatmcls_286W> MODEL atom not classified: GUA:O3' GUA ------------------------------------------------------ Regards, P. Saravanan

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Modelling T-cell Receptors
by Ryan Ehrlich 06 Sep '17

06 Sep '17

Hello, I'm rather new to using MODELLER and would like to seek out the opinions of other users on how to model a two chain protein complex, the T-cell receptor (TCR). I understand most of the basic formatting for multi-chain.ali files, but a few things are eluding me: 1.) How do I build a profile for multi-chain sequences? When I do this using the script found in the tutorial the build_profile.ali does not include the chain break character ('/') in the alignment output, causing the subsequent multi-template program to produce *_fit.pdb files to read as a single chain. This of course is causing me problems. So I'll repeat my interest again - how do I produce a build_profile.ali that contains the chain break character and the appropriate chain information in the header? 2.) I mentioned this in the first part, but I'd like to use multiple templates for this analysis. Do I used the PDB ID and each chain associated with the TCR, when doing so? Also how should I modify the restraints argument between TCR chains? 3.) Accurate modeling of the CDR loops of the TCR (essentially the active site) is important to my research, should I use loopmodel() or other means for loop refinement? I realize this is rather ambiguous, but any help will be greatly appreciated, in regard to methods that should be used and/or issues discussed (primarily in Q1). Best, Ryan

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