RWCONTENTS (CCP4: Supported Program)
- Count atoms by type, and other analyses
The program reads and analyses a PDB file. Information given includes
numbers of atoms by type, theoretical number of hydrogens, molecular weights,
and Matthews Coefficient.
If the NHOH keyword is specified, the number of water molecules expected to be
determined by PX at the given resolution and temperature is reported, as
estimated by the statistical analysis of Carugo & Bordo, Acta Cryst D,
55, 479 (1999). This estimation is based on an analysis of structures deposited
at the Protein Data Bank. Only models having less that 3% heteroatom content
other than water were considered in this analysis. The predicted number
of crystallographic waters is meant only as a guide, and is not a substitute
for correct evaluation of electron density maps.
- Input coordinates in CCP4 PDB format.
NHOH <reso> [ ROOM | LOWT ]
Evaluate the number of water molecules expected to be determined by PX, as
estimated by the statistical analysis of Carugo & Bordo. This is determined
by the resolution <reso> which must be given. The subkeyword
ROOM or LOWT specifies whether the expression for room temperature
or low temperature results is used (default ROOM).
(Optional) Specifies the end of keyworded input and starts RWCONTENTS running.
Originator : Eleanor Dodson
Modifications : Martyn Winn
Sample Unix input using toxd:
rwcontents XYZIN $CEXAM/toxd/toxd.pdb << eof
nhoh 2.3 lowt
The output contains the following information derived from the coordinate data:
- a count of the number of amino acid residues, e.g.
Number of amino-acids residues = 59
- estimates for the theoretical numbers of hydrogens for the protein and for
the waters, e.g.
A rough estimate of the theoretical number of Hydrogens for the protein is 489.
A rough estimate of the theoretical number of Hydrogens for the waters is 118.
- the number of atoms of each type in the PDB file (taking account of partial
Number of atoms of each type in PDB file (except hydrogens).
(Partial occupancies are taken into account.)
Atom number and type - number of atoms 6 C 295.00
Atom number and type - number of atoms 7 N 93.00
Atom number and type - number of atoms 8 O 95.00
Atom number and type - number of atoms 16 S 9.00
- number of waters 59.00
- the total number of atoms including hydrogens, e.g.
Total number of protein atoms (including hydrogens) 966.00
Total number of atoms (including hydrogens) 1158.00
- the number of water molecules expected to be determined by PX, as
estimated by the statistical analysis of Carugo & Bordo, e.g.
Total number of protein atoms (excluding H) = 477.0
Expected number of crystallographic waters = 39
Associated standard error of this estimate = 4
Expected range at 99% confidence level: 30 to 48
Actual number of waters in model = 59.0
- cell volume, molecular weight of protein and of all atoms, e.g.
Cell volume: 66488.688
Molecular Weight of protein: 7139.000
Molecular Weight of all atoms: 8201.000
- the Matthews coefficient, and estimates of the solvent content and of
the percentage of the unit cell which is empty, e.g.
The Matthews Coefficient is : 9.31
Assuming protein density is 1.34, the solvent % is: 86.69
If atom volume ~ 10, % of cell without protein is: 85.47
If atom volume ~ 10, % of cell without atoms is: 82.58