Hello
Sorry for the vast number of posts recently, I think I have finally figured
out most of problems.
My main question, which I am desperate for suggestions to, is how to read in
an existing pdb (x-ray crystal structure) and add the missing residue atoms
and the loop region, with minimal disruption to the existing sidechains and
backbone. I appreciate that when adding sidechains there will need to be
some movement of surrrounding sidechains but I am seeing quite a lot of
movement all over my model. I guess however this is possibly because some of
the sidechains are actually within quite closely packed regions.
I have tried to just refine the loop region and the missing sidechains. and
then loop model the missing loop. this works fine for the loop region but
the missing sidechain atoms are added with no refinement at all and clash
with other added atoms and exiisting sidechains.
I have also tried the following script:
# Homology modelling by the automodel class
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 = loopmodel(env,
alnfile = 'phe-1phe.ali', # alignment filename
knowns = '1phe', # codes of the templates
sequence = 'Phe') # 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.md_level = None # No refinement of model
a.loop.starting_model = 1 # First loop model
a.loop.ending_model = 50 # Last loop model
a.loop.md_level = refine.fast # Loop model refinement level
a.make() # do homology modelling
which adds the sidechains, optimises them, adds the loop and then optimises
that via the loop modelling routine.
However this moves all the other atoms also.
Could someone please give me some advice, it would be much apprecaited!
J