
PASD automatic NOE assignment structure determination

To run: execute the script runPASD- 
This is specialized to run under the PBS queue system

  Reads chemical shift and NOE peak position tables, match them 
up, and write them to a PASD restraints files.

   % xplor -tcl initMatch3dC.tcl
   % xplor -tcl initMatch3dN.tcl
   % xplor -tcl jointFilter.tcl

This step performs prefiltering:

  - stripe filter - adjusts chemical shift assignment so NOE stripes
                    line up
  - network analysis - topological distance restraint connectivity map -
                     set likelihoods based on these
  - primary sequence filter - if an intra-residue assignment exists, 
                              set likelihoods of other possible
                              assignments to zero

Look at high-likelihood assignments as a network map:

   % ./makeContactMap.py precalc/jointFilter.tcl.out

perform simulated annealing with linear distance restraint energy,
multiple assignments per peak and active inverse NOEs

   % xplor -tcl sa_pass2.tcl
   % xplor -tcl summarize_pass2.tcl

perform simulated annealing with quadratic distance restraint energy
and one assignment per peak

   % xplor -tcl sa_pass3.tcl
   % xplor -tcl summarize_pass3.tcl
  
   [pass 1 is called pass2 for historical reasons.  ]

Note that interesting comments are at the top of each .peaks and 
.shiftAssignments file, showing the state of the calculation at 
the start of each pass. Look at 

  cvn_3dc_final.peaks 
  cvn_3dc_final.shiftAssignments
    notice this entry: (NOE coverage)
      Number of high-likelihood long range peaks/residue in defined region

There are also interesting comments at the top of each cvn_pass*avg.pdb,
showing the state of the calculation at the end of each pass.

For comparison, the hand-done NMR structure is in cvn_reference.pdb

residue-by-residue analysis
  % xplor -tcl resByRes.tcl 

Convert the final PASD NOE restraints table to 
XPLOR format, removing all the low-likelihood peak assignments along the way:

  % xplor -tcl convert_restraints_to_xplor.tcl

The resulting cvn_xplor_noes.tbl file can now be used by other Xplor-NIH
scripts for further structure refinement.

Perform refinement (using a Python script)

 % xplor -tcl talos2cdih.tcl 
 % xplor -py -parallel -o refine.py.out refine.py 

Compare computed structures with the reference structure

 % targetRMSD -selection "name CA" cvn_reference.pdb precalc/cvn_pass2_avg.pdb
 % targetRMSD -selection "name CA" cvn_reference.pdb precalc/cvn_pass3_avg.pdb
 % targetRMSD -selection "name CA" cvn_reference.pdb precalc/ave.pdb



Summary of all files

scripts
  initMatch3dC.tcl - gen. initial 3D C assignments from shift, NOE tables.
  initMatch3dN.tcl - gen. initial 3D N assignments from shift, NOE tables.
  jointFilter.tcl  - combine initial C, N assignments, generate
                     initial likelihoods based on network and primary
                     sequence filters
  sa_pass2.tcl	      - run pass1 structure calculation
  summarize_pass2.tcl - summarize pass1, generate pass2 likelihoods
  sa_pass3.tcl	      
  summarize_pass3.tcl - summarize pass2, generate final assignments
  convert_restraints_to_xplor.tcl - convert PASD restraints into XPLOR 
                                    restraints, for further refinement.
  refine.py         - refinement script
  runPASD           - run all scripts in the proper order. 
                      Configured for the PBS queuing system.

data tables
  cvn_c13noe.shifts  - shift tables
  cvn_n15noe.shifts
  3dc_capp_def.PCK   - NOE peak tables
  3dn_capp_def.PCK                 
  cvn_disulfides.tbl - weak disulfide bond restraints
  cvn_talos_pred.tab - talos dihedral predictions

Output files
  cvn_reference.pdb          - reference X-ray structure
  precalc/cvn_pass1_noes.tbl - input table for pass1
  precalc/cvn_pass1_avg.pdb  - average structure after pass1
  precalc/cvn_pass2_noes.tbl 
  precalc/cvn_pass2_avg.pdb    
  precalc/cvn_pass3_noes.tbl 
  precalc/cvn_pass3_avg.pdb  - final average structure
  precalc/cvn_final_noes.tbl - final assignments
  precalc/cvn.psf            - cvn psf file
  precalc/cvn_nmr.pdb        - known NMR structure
  precalc/cvn_xray.pdb       - known xray structure
  precalc/*.pdb              - final ``good'' structures
  precalc/refine*            - output of final refinement

