
Refinement of Lysozyme using NMR and SAXS data

1) calculate the SAXS chi^2 to the X-ray structure.

  % calcSAXS -fit -numQ 100 -expt saxswaxs.dat 193L_prot.pdb > 193L.pdb.saxs

  chi^2 and fit parameters are printed

2) view calculated and experimental SAXS curves.

  % ./plotLog.py saxswaxs.dat 193L.pdb.saxs:1:2:-

3) examine results of precalculated refinement calculations
 [ refinement of pdb entry 1E8L, model 49, using NMR data from pdb entry 
   1E8L and saxs data provided by Alex Grishaev. ]

  refine0_*: refinement using NMR data only
  refine_*: refinement using NMR and SAXS/WAXS data


  % emacs precalc/refine*stats

  (all metrics better for refine - SAXS/WAXS data has lead to better 
   convergence)

4) compare regularized average structures with ``reference'' PDB entry 193L.
 
  [backbone RMSD]

  % targetRMSD -diffSeq -selection "name C or name N or name CA" 193L.pdb \
         precalc/refine0_ave.pdb

  % targetRMSD -diffSeq -selection "name C or name N or name CA" 193L.pdb \
         precalc/refine_ave.pdb

  % targetRMSD -diffSeq -selection "name C or name N or name CA" 193L.pdb \
         precalc/analyze_1E8L_ave.pdb


  [visualization]

  % vmd-xplor -noxplor precalc/refine*_ave.pdb 193L.pdb

  within vmd-xplor:
    a) *Molecule --> Drawn --> drawing method --> NewCartoon
    b) *Molecule --> Drawn --> edit
         the edit form is opened. In the bottom of this window, choose
            fit to 
              [select] --> set to 193L.pdb
                by
                  [all] --> set to CA
                    select
                      *do it




5) compare experimental w/ calculated saxs curves

  % ./plotLog.py saxswaxs.dat:1:2:3 -suffix 1:2:- precalc/refine0_*saxs

  % ./plotLog.py saxswaxs.dat:1:2:3 -suffix 1:2:- precalc/refine_*saxs


Files:

NMR restraints from PDB entry 1E8L:
  dihedral.tbl
  hbond.tbl
  noe.tbl
  rdc1.tbl
  rdc2.tbl

SAXS/WAXS data from A. Grishaev. Data in format q, I(q) delta I(q):
  saxswaxs.dat

Lysozyme PDB entries:
  193L.pdb                  - crystal structure yielding good SAXS/WAXS fit
  precalc/193L.pdb.saxs     - corresponding saxs curve
  193L_prot.pdb             - protonated version of 193L.pdb
  1HWA.pdb                  - older NMR structure
  precalc/1HWA.pdb.saxs     - corresponding saxs curve
  1E8L.pdb	            - more recent NMR ensemble
  1E8L_ave.pdb 	            - corresponding (unregularized) average structure
  precalc/1E8L_ave.pdb.saxs - corresponding saxs curve

disulfide distance restraints - not used in the protocols here:
  disulfide.tbl


structure determination scripts:
  refine0.py
  refine.py
  anneal0.py
  anneal.py

directory containing previously calculated results:
  precalc/

convenience scripts:
  splitPDB        - for a PDB file, extract all ensemble members into separate 
                    files.
  plotLog.py      - helper to make semilog plots of SAXS curves.
  analyze_1E8L.py - analyze fit to each MODEL of 1E8L- NMR and SAXS data




