How to use Modeller?

Installation (Linux – debian based)

Go to this page : https://salilab.org/modeller/download_installation.html and download modeller for your system (32 or 64 bits).
Then execute this command :

 sudo env KEY_MODELLER=XXXX dpkg -i modeller_9.14-1_i386.deb 

with XXXX the modeller keys. You can ask the key through the registration form (https://salilab.org/modeller/registration.html). You will need a academic mail to get the key for free.

Usage

To use Modeller, you need 3 files : a alignement file, the reference PDB file, and a python model script (usualy called model-default.py).

  • Alignement file : example (Color code : name of pdb file first amino acid number (on pdb file)ChainEnd of the sequence |   a name )>P1;3U5I
    structureX:3U5I_D: 4:D:297: :RPL5 :: :
    —QKDAKSSAYSSRFQTPFRRRREGKTDYYQRKRLVTQHKAKYNTPKYRLVVRFTNKDIICQIISSTITGDVVLAAAYSHELPRYGITHGLTNWAAAYA/ TGLLIARRTLQKLGLDETYKGVEEVEGEYELTEAVEDGPRPFKVFLDIGLQRTTTGARVFGALKGASDGGLYVPHSENRFPGWDFETEEIDPELLRSYIF/ GGHVSQYMEELADDDEERFSELFKGYLADDIDADSLEDIYTSAHEAIRADPAFKPTEKKFTKEQYAAESKKYRQTKLSKEERAARVAAKIAALAGQQ— —*
    >P1;RPL5_H
    sequence:test: 1 : : 297 : :Unknown :: : MGFVKVVKNKAYFKRYQVKFRRRREGKTDYYARKRLVIQDKNKYNTPKYRMIVRVTNRDIICQIAYARIEGDMIVCAAYAHELPKYGVKVGLTNYAAAYC/
    TGLLLARRLLNRFGMDKIYEGQVEVTGDEYNVESIDGQPSAFTCYLDASLARTTTGNKVFGALKGAVDGGLSIPHSTKRFPGYDSESKEFNAEVHRKHIM/
    GQNVADYMRYLMEEDEDAYKKQFSQYIKNSVTPDMMEEMYKKAHAAIRENPVYEKKPKKEVKK——KRWNRPKMSLAQKKDRVAQKKASFLRAQERA AES*
  • model-default.py (example)
    #!/usr/bin/env python
    # Homology modeling by the automodel class
    from modeller import *                  # Load standard Modeller classes
    from modeller.automodel import *        # Load the automodel class
    log.verbose()                # request verbose output
    env = environ()              # create a new MODELLER environment to build this model in
    # directories for input atom files
    #env.io.atom_files_directory = ’./:../atom_files’
    #env.io.atom_files_directory = '/home/../../../modeller'
    
    a = automodel(env,
    alnfile = 'aligment.ali',      # alignment filename
    knowns   = '3U51',             # codes of the templates
    sequence = 'RPL5_H')           # code of the target
    a.starting_model= 1                     # index of the first model
    a.ending_model = 100                      # index of the last model
    # (determines how many models to calculate)
    a.make()                                # do the actual homology modeling
    

    Be careful, « knowns » is the name of the template (first line « >P1;3U5I« ) and « sequence » is the name of the target (« >P1;RPL5_H« )

Execution :

mod9.14 model-default.py

If you have this error : « ‘import site’ failed; use -v for traceback », it’s not a big deal. Modeller will work without issues.

Get the Best model :

You need to analyse the objective function value. Use this command :

 grep 'OBJECTIVE' file.B9999000*.pdb > FunctionObj.data 

then in FunctionObj.data locate the lower value. Example :


NB2.B99990001.pdb:REMARK 6 MODELLER OBJECTIVE FUNCTION: 4752.2593
NB2.B99990002.pdb:REMARK 6 MODELLER OBJECTIVE FUNCTION: 4577.8940
NB2.B99990003.pdb:REMARK 6 MODELLER OBJECTIVE FUNCTION: 4632.4722
NB2.B99990004.pdb:REMARK 6 MODELLER OBJECTIVE FUNCTION: 4785.2485
NB2.B99990005.pdb:REMARK 6 MODELLER OBJECTIVE FUNCTION: 4628.4385
NB2.B99990006.pdb:REMARK 6 MODELLER OBJECTIVE FUNCTION: 4680.4165
NB2.B99990007.pdb:REMARK 6 MODELLER OBJECTIVE FUNCTION: 4538.2246 <---
NB2.B99990008.pdb:REMARK 6 MODELLER OBJECTIVE FUNCTION: 4616.3188
NB2.B99990009.pdb:REMARK 6 MODELLER OBJECTIVE FUNCTION: 4720.9233
NB2.B99990010.pdb:REMARK 6 MODELLER OBJECTIVE FUNCTION: 4669.3135

Here you best PDB is NB2.B99990007.pdb

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