June 15, 2015

This directory includes all of the components (DNA, protein, peptide) and restraints to 
make the final dimerized HMG model.

"anneal-everything.inp"
Simulated annealing script for CNS 1.3 

directory "noe/"
perl scripts to make distance restraints (DNA-to-DNA), (protein-to-DNA),
and (protein-to-protein). 

directory "prelim/"
templates for all of the chains required to make the model 
two protein chains and two DNA chains
the generate-all scripts will make a compatible structure (.mtf) file

directory "tbl/"
angles.csh - quick script to make helical torsion angles
dd-angles.tbl - dimerization helix torsion angles
dd-noe.tbl - dimerization helix to HMG intermolecular restraints
dna-dna.tbl - intramolecular restraints to maintain B-DNA
helix-extra.tbl - a few more amide-amide restraints to help make a helix
plane.inp - DNA planarity restraints
prote-dna-noe.tbl - intermolecular protein-DNA restraints
prot-hbonds.tbl - helix enforcing restraints for the HMG domains
prot-prot-noe.tbl - intramolecular restraints to make the HMG domains

Logan Donaldson
logand@yorku.ca
