WATPEAK (CCP4: Supported Program)

NAME

watpeak - selects peaks from peakmax and puts them close to the respective protein atoms

SYNOPSIS

watpeak XYZIN foo_in.pdb PEAKS peaks_in.pdb XYZOUT foo_out.pdb
[Keyworded input]

DESCRIPTION

Select atoms from one coordinate set (PEAKS, e.g. from PEAKMAX) which lie close to atoms in another coordinate set (XYZIN, e.g. your molecule). This is used to choose peaks from a difference map which are candidates as water molecules belonging to the molecule you are building (as opposed to belonging to neighbouring molecules in the cell).

KEYWORDED INPUT

Available keywords are:

BFACTOR, CELL, CHAIN, DISTANCE, END, HETATOMONLY, SYMMETRY, TITLE|REMARK.

TITLE | REMARK

Anything on these lines is just echoed to the output PDB file. A TITLE line is also echoed to the log file.

DISTANCE <dmin> <dmax>

Maximum distance for a peak to be accepted (default = 5.0Å). Minimum distance for a peak to be accepted (default = 0.1Å).

BFACTOR <Bfactor> [<occupancy>]

Values to set Bfactor & occupancy to, default = 30.0, 1.0 Note the input peak list may have the peak height in the occupancy column (see example). If this command is omitted, the Bfactor & occupancy will be left as input.

CHAIN <Chain_id>

Set chain id for output (default blank).

HETATOMONLY

Toggle switch to only match Oxygen or Nitrogen from the XYZIN file to a new peak in the PEAKS file. Default: accept close contacts to any atom.

CELL <a> <b> <c> [<alpha> <beta> <gamma>]

Must be given if cell is not specified in either PDB file. If this is the case NCODE will be assumed to be 1. If the CRYST1 card is supplied then the cell and ncode from PEAKS must be the same as XYZIN. See RWBROOK for more information about the orthogonalisation parameter ncode. Defaults alpha=90.0, beta=90.0, gamma=90.0

SYMMETRY

This card is COMPULSORY and can be given as the spacegroup number, name or as symmetry cards e.g. 

     SYMM 19
     SYMM x,y,z * -x,-y,-z
     SYMM P21

END

End input.

INPUT AND OUTPUT FILES

Input:

XYZIN
molecule to test against (Brookhaven format).
PEAKS
peak list. The peak height (for printing only) is assumed to be in the occupancy slot, as from PEAKMAX with option OUTPUT BROOKHAVEN.

Output:

XYZOUT
all atoms from PEAKS within DISTANCE of any atom from XYZIN (Brookhaven format).

NOTES

The different rejection criteria are explained below.

  1. The number of symmetry rejected waters; any water or its symmetry equivalent closer than dmin to a previously accepted water. Note that if dmin is set to zero then no symmetry equivalent waters will be rejected.
  2. The number of waters with near contacts; any water with one or more contacts closer than dmin to the protein. Note that the protein includes any atoms in XYZIN.
  3. The number of waters too far from the protein; any water with all its contacts greater than dmax.

Examples

    peakmax  mapin  c40_fo-fcx xyzout c40_peaks.pdb << eof-1
    numpeaks 100
    threshold 0.2
    eof-1
    
    watpeak  xyzin a95_40.pdb peaks c40_peaks.pdb xyzout waters_40.pdb <<eof-2
    title Possible waters from C40 DelF
    distance 4.0
    symm 19
    eof-2