Simple simulated annealing of gb1 from extended structure

1) start the structure calculation.

% xplor -smp 2 -py -o anneal_nordc.out anneal_nordc.py

     [ takes about 10 minutes ]

( how to run in parallel? use the -smp # or -parallel option.)

2) view initial structures with randomized torsion angles

% vmd-xplor -noxplor *.init

  within vmd-xplor:
     to quit, choose 
       *Main --> Control --> Quit --> xplor and vmd
	

3) view precalculated final structures

% vmd-xplor -noxplor `getBest precalc`

  within vmd-xplor:
    a) display only backbone traces of structures
      *Molecule --> Drawn --> set selection
         type: backbone
    b) fit all structures to the first using Ca coordinates.
      *Molecule --> Drawn --> edit
         the edit form is opened. In the bottom of this window, choose
            fit to 
              [select] --> set to anneal_nordc_8.sa
                by
                  [all] --> set to CA
                    select
                      *do it

view NOE restraints visualized given a structure
  *Main --> NOE 
     opens the NOE form
       set Molecule1 to 
          anneal_nordc_11.sa
       set NOE constraint filename to
          noe_sum_3.tbl
       then select
        *load

4) structure statistics on the lowest energy structures

   - energy, rmsd, violations statistics
   - most violated restraints
   - list of lowest energy structures w/ rmsd to ave. struct.

% more precalc/anneal_nordc_##.sa.stats

5) per-structure analysis

% more precalc/anneal_nordc_19.sa

to sort structures by noe rmsd:

% grep noe precalc/anneal_*.sa | grep summ | sort -n -k 5

details of each restraint term
                      
6) compute accuracy to known structure

% targetRMSD -selection "(name C or name CA or name N) and (resid 1:56)" \
	g_xray.pdb `getBest precalc/*.stats` 


7) complete file listing

Python scripts
  anneal_nordc.py - structure calculation from extended random structure
  refine_nordc.py - structure calculation from ave. struct calculated using
  		    anneal_nordc.py

input tables
  dihed_g_all.tbl     - dihedral restraint table
  hbda.tbl            - h-bond table
  jna_coup.tbl        - J-coupling table
  noe_sum_3.tbl       - NOE table
  protG.seq           - gb1 sequence.


output files
  precalc/anneal_*.sa - precalculated structures
  g_xray.pdb          - comparison X-ray structure
