MANIFEST

src_tbosutinib_c4+d2_refine_waters_tls_38.pdb - original structure from Nick
  Two protein copies per unit cell
  chain A: Src 
  chain B: Src (described in paper; the one to model)
  chain C: ligands (resn DB8 resi 1-2; resi 1 goes with chain A, resi 2 with chain B)
  chain S: crystallographic waters (resi HOH, O atoms only, resi 1-284)
  
  To include in modeling:
  - Src: chain B
  - bosutinib: chain C and resi 2
  - crystallographic waters: chain S within 6 of chain B 

process.pml - Pymol script to process initial PDB structure to generate inputs for MODELLER, LEaP, and antechamber
  Run in PyMOL with '@process.pml'
  Generates:
    protein.pdb - protein (incomplete)
    ligand.pdb - ligand (without protons)
    waters.pdb - crystallographic waters with 6 A of protein or ligand (oxygens only)
    system.pdb - all of the above (protein, ligand, waters)

src-seqres-AB.txt - Manually-constructed PDB DBREF, SEQADV, and SEQRES blocks for chains A and B
src-seqres-B.txt - Manually-constructed PDB DBREF, SEQADV, and SEQRES block for chain B
src_tbosutinib_c4+d2_refine_waters_tls_38-seqres.pdb - Nick's structure with SEQRES block manually added.

model_src.py - generate Src model after processing by PyMOL output along with SEQRES data (currently BROKEN)

closewater.pdb - Pymol-extracted water within 5 A of chain B of Nick's structure (selection: "chain S within 5 of chain B")

modelPDB.py - MODELLER driver module (from mmtools)
modelPDB2.py - updated MODELLER driver module to allow addition of extra template structures
modelPDB3.py - updated MODELLER driver module to allow addition of extra template structures, ligand HETATMs, and water molecules (currently BROKEN)

output.pdb - modelled structure

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MODELLING PROCEDURE

Protein chain B was extracted from the crystallographic structure [src_tbosutinib_c4+d2_refine_waters_tls_38.pdb] to 
model in residues unresolved in the X-ray density.  Modeling of missing residues was performed using MODELLER 9v8 by 
copying over atomic coordinates from the crystallographic structure and annealing missing coordinates with MODELLER, 
using the 3LCK structure as a template for these unresolved regions.  Ligand atoms and waters from the X-ray structure 
within 6 A of protein were included during the modeling procedure to ensure the resulting structure was free of steric
clashes.  Only heavy atoms were modeleding during this phase.

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TODO FOR FUTURE

* Build complete ligand and water coordinates before modeling?