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