Coarse-grain Models of HIV-1 Nucleoids

These are PDB-format files that may be read by most molecular
graphics programs. The script JSmol.script will create a customized
view with appropriate radii, using JSmol. The PDB format is modified
in the following ways:
--coordinates are in nanometers
--RNA strands have atom name "P" and residue name "RNA"
--integrase subunits have atom name "CA" and residue name "IN"
--nucleocapsid subunits have atom name "N", and residue names
  "NCO" for experimentally-observed positions and
  "NCR" for randomly-placed positions

Each file contains 25 instances of the nucleoid model.
Each model includes 2 gRNA strands, 2000 nucleocapsid subunits, and 140/0 integrase subunits.
Nine models are included in this release, exploring two types of variables:
1) Three types of starting models: 
   "selfavoidingGag" assumes that the RNA forms a non-overlapping random walk on
     the lattice of gag proteins in the immature virion
   "overlappingGag" assumes a similar random walk, but the RNA strands may overlap
   "random" assumes that RNA is released from gag and randomly fills the interior of
     the virion before condensation 
2) Three assumptions about integrase interaction:
   35 integrase tetramers, 70 integrase dimers, and no integrase

More information is available at:
http://ccsb.scripps.edu/latticenucleoid/HIVnucleoid