/ATTO/hermans/dowser/bin/sgi-mips4
/ATTO/hermans/dowser/bin
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
*                                                           *
*  DOWSER: A program to place water molecules in cavities   *
*          inside protein molecules.                        *
*                                                           *
* Developed by the Computational Structural Biology group   *
* at the Univ. of North Carolina at Chapel Hill.            *
* Authors: Li Zhang, Xinfu Xia, Jan Hermans, Dave Cavanaugh *
* Revised February 1998                                     *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
*  
* CLEAN UP FILES
* execute: cleanup_dowser
*  
* REFORMAT THE INPUT PDB FILE and EXTEND WITH POLAR HYDROGEN ATOMS
* execute: reformatPDB -pdbin 1BPI.pdb  -pdbout reform.pdb
*
* DOWSER - default, no HETATM records will be used
* Input pdb file contains 620 atoms
* Reformatted and extended pdb file contains 568 atoms
*
* EXTRACT WATER MOLECULES FROM THE INPUT PDB FILE
* Execute: grep ^HETATM.*HOH 1BPI.pdb > xtal_o.dow
* The input file contains 167 crystallographic water molecules
*  
* CALCULATE THE ENERGIES OF XTAL WATERS
*    a. REMOVE EXTERNAL WATERS FROM THE XTALWAT SET (creating xtal_o.pdb)
*       execute: drain reform.pdb xtal_o.dow xtalsurf.dow xtal_o.pdb
*       Of the crystallographic waters 3 are internal
*
*    b. PLACE HYDROGENS ON XTAL WATERS IN THE MOST ENERGETICALLY FAVORABLE ORIENTATION (creating xtal_hoh.pdb)
*       execute: placeWat reform.pdb xtal_o.pdb rotate > place_xtal_o.dow
...
*  
*    c. REFINE XTAL WATER ORIENTATIONS by rotation only (with mutual interaction) 
*       execute: RefineWat reform.pdb place_xtal_o.dow rotate > xtal_hoh.pdb
*       Performed 2 iteration(s) for refinement
*
* COMPUTE THE MOLECULAR SURFACE
*    a. CONVERT PDB to MS format, eliminate H atoms and create file ms.rad
*       execute: pdb2ms reform.pdb ms.dow
*
*    b. RUN THE QMS program
*       PROBE RADIUS for QMS program is 0.20000
* execute: qms ms.dow 454 ms.rad 5 0.20000 > xms.dow
*
*       The MS program has produced 467 surface points
*
*    c. CONVERT OUTPUT FROM MS
*       execute: ms2pdb < xms.dow > pdbms.dow
*
* SORT SURFACE INTO BURIED AND EXPOSED
* execute: drain reform.pdb pdbms.dow surface.wat intsurf.pdb
* Of the surface points 22 are internal
*
* REDUCE THE NUMBER OF INTERNAL POINTS with 1 Angstrom separation
* execute: ReduceIntSurf intsurf.pdbx tmp 1
* Reduce the number of internal surface points before running PlaceWat
* Separation between internal surface points will be 1.000000
* Number of surface points in  input = 22
* Number of surface points in output = 10
*
* ADD the internal XTAL waters to the internal surface sites
*
* COMPUTE ENERGIES FOR BEST WATER PLACEMENT FOR EACH INPUT XYZ
* execute: placeWat reform.pdb intsurf.pdb both > placewat.dow
............. 
*
* SORT WATER MOLECULES BY ASCENDING ENERGIES and ELIMINATE
* OVERLAPPING WATERS
* execute: chooser placewat.dow chooser.dow distance
* There are 4 waters remaining
*
* REFINE THE FINAL WATER POSITIONS - DOWSER WATERS NOW INTERACT WITH EACH OTHER
* execute: RefineWat reform.pdb chooser.dow both > dowserwat.dow
* Performed 4 iteration(s) for refinement
*
* SORT WATER MOLECULES BY ASCENDING ENERGIES and ELIMINATE
* OVERLAPPING and HIGH ENERGY WATERS
* execute: chooser refine.dow dowserwat_all.pdb both
* There are 9 remaining water molecules
*
* DRAIN AWAY EXTERNAL DOWSER WATERS
* execute: drain reform.pdb dowserwat_all.pdb junk.dow dowserwat.pdb
* There are 9 remaining water molecules
*
* Compare the locations of the dowser and xtal waters
* execute: CompareWat dowserwat_all.pdb dowserwat.pdb xtal_o.dow xtal_hoh.pdb
*

* Find nearest xtal water for each dowser water
     Dowser water         energy  distance       nearest xtal water
# 1  31.81   7.23   1.71  -25.20   0.08 A  # 62  31.77   7.22   1.78
# 2  32.39   7.61   4.44  -23.48   0.22 A  # 61  32.58   7.51   4.39
# 3  33.53   4.42  10.67  -17.97   0.19 A  # 60  33.45   4.29  10.78

* Find nearest dowser water for each internal xtal water
   Internal xtal water     energy distance       nearest Dowser water
# 60  33.45   4.29  10.78  -17.88   0.19 A  # 3  33.53   4.42  10.67
# 61  32.58   7.51   4.39  -25.27   0.22 A  # 2  32.39   7.61   4.44
# 62  31.77   7.22   1.78  -23.82   0.08 A  # 1  31.81   7.23   1.71
*
* Place a REMARK to identify original pdb file in each output pdb file
*
* Remove intermediate files
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * *