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 :

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) |  Chain |  End 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)

  1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18

  #!/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 :

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 :

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

Here you best PDB is NB2.B99990007.pdb