Simple usage

The simple example below constructs a single comparative model for the 1fdx sequence from the known 5fd1 structure, using alignment.ali, a PIR format alignment of 5fd1 and 1fdx. The final model is written into the PDB file 1fdx.B99990001.pdb.

Example: examples/automodel/model-default.py

# Homology modelling by the automodel class

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'

a = automodel(env,
              alnfile  = 'alignment.ali',     # alignment filename
              knowns   = '5fd1',              # codes of the templates
              sequence = '1fdx')              # code of the target
a.starting_model= 1                 # index of the first model 
a.ending_model  = 1                 # index of the last model
                                    # (determines how many models to calculate)
a.make()                            # do the actual homology modelling

Example: examples/automodel/alignment.ali

C; A sample alignment in the PIR format; used in tutorial

>P1;5fd1
structureX:5fd1:1    : :106  : :ferredoxin:Azotobacter vinelandii: 1.90: 0.19
AFVVTDNCIKCKYTDCVEVCPVDCFYEGPNFLVIHPDECIDCALCEPECPAQAIFSEDEVPEDMQEFIQLNAELA
EVWPNITEKKDPLPDAEDWDGVKGKLQHLER*

>P1;1fdx
sequence:1fdx:1    : :54   : :ferredoxin:Peptococcus aerogenes: 2.00:-1.00
AYVINDSC--IACGACKPECPVNIIQGS--IYAIDADSCIDCGSCASVCPVGAPNPED-----------------
-------------------------------*