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