RWCONTENTS (CCP4: Supported Program)

NAME

rwcontents - Count atoms by type, and other analyses

SYNOPSIS

rwcontents xyzin foo_in.xyz
[Keyworded input]

DESCRIPTION

The program reads and analyses a PDB file. Information given includes numbers of atoms by type, theoretical number of hydrogens, molecular weights, Matthews Coefficient the sum of the atomic formfactors, F000, and the sum of the square of the atomic formfactors, ie I000.

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 AND OUTPUT FILES

XYZIN: Input coordinates in CCP4 PDB format.

KEYWORDED INPUT

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).

END

(Optional) Specifies the end of keyworded input and starts RWCONTENTS running.

AUTHORS

Originator : Eleanor Dodson

Modifications : Martyn Winn

EXAMPLES

Sample Unix input using toxd:


  rwcontents XYZIN $CEXAM/toxd/toxd.pdb << eof 
  nhoh 2.3 lowt
  end
  eof

PRINTER OUTPUT

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.
 (including Haems).

 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 occupancies), e.g.


 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

 I000 - SIGMA - Sum(fi_squared)  Protein only:          23049.000

 I000 - SIGMA - Sum(fi_squared)  All Atoms:             26825.000

 F000 - SIGMA - Sum(fi)          Protein only:          3325.000

 F000 - SIGMA - Sum(fi)          All Atoms:             3797.000

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