WATPEAK (CCP4: Supported Program)
NAMEwatpeak - selects peaks from peakmax and puts them close to the respective protein atoms
SYNOPSISwatpeak XYZIN foo_in.pdb PEAKS peaks_in.pdb XYZOUT foo_out.pdb
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).
Available keywords are:
BFACTOR, CELL, CHAIN, DISTANCE, END, HETATOMONLY, SYMMETRY, TITLE|REMARK.
Anything on these lines is just echoed to the output PDB file. A TITLE line is also echoed to the log file.
Maximum distance for a peak to be accepted (default = 5.0Å). Minimum distance for a peak to be accepted (default = 0.1Å).
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.
Set chain id for output (default blank).
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.
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
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
The different rejection criterions are explained below.
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