Using automodel model-full python script,

1. Do we get any changes in side chain conformations or coordinates if the query sequence is perfectly aligned with template sequence at sequence level. Because upon point mutations, there is no change in sequence alignment. Whole query sequence is perfectly aligned with template.

I calculated no. of contacts of wild type residues and mutant residues, there is no change at all. I used only distance between C-alpha atoms(CA) while calculating .

Is there any change in side chain conformations in the modeled structures by using this script.

2. Can I get to know the details of a.make() and a.auto_align() commands used in this script. I WANT TO KNOW STEP WISE THE INSIDE DETAILS AND WORKING OF THIS SCRIPT. PLEASE HELP. URGENT !!!

Please bear up with me as I don't know Python..

Example: examples/automodel/model-full.py


# A sample script for fully automated comparative modeling
from modeller import *
from modeller.automodel import *    # Load the automodel class

log.verbose()
env = environ()

# directories for input atom files
env.io.atom_files_directory = ['.', '../atom_files']

a = automodel(env,
              # file with template codes and target sequence
              alnfile  = 'alignment.seg',
              # PDB codes of the templates
              knowns   = ('5fd1', '1fdn', '1fxd', '1iqz'),
              # code of the target
              sequence = '1fdx')
a.auto_align()                      # get an automatic alignment
a.make()                            # do homology modeling