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PROVE
 
PROVE
PROVE is a software to assess the quality of the atomic model of a macromolecule structure [Pontius et al., 1996]. It is based on the calculations of atomic volumes. If the volumes of buried atoms in your protein are significantly different than equilvalent residues in the PDB, then PROVE will indicate this by a Z-score that greater or lesser than 3. A negative Z-score means that the atom has a smaller than average volume, whereas a positive score indicates that an atom has a larger than average volume. The expected average Z-score is zero. 
Features

    * the volume of an atom is defined by the atom's radius and the planes separating it from other atoms
    * a single Z-score to evaluate your structure.

PROVE runs on Linux machines s; the executable is:
/joule2/programs/lx_bin/prove or just type "prove -p mycoordinates.pdb"

The program is installed in /joule2/programs/prove:

The documentation is available from /joule2/programs/prove/linux/PROVE2.5.1/README

The program is available from http://www.ucmb.ulb.ac.be/UCMB/PROVE/

There is no tutorial :

Reference:
Pontius J., Richelle J. & Wodak S.J. (1996) Deviations from standard atomic volumes as a quality measure for protein crystal structures J. Mol. Biol. 264(1): 121-136 http://www.idealibrary.com/links/doi/10.1006/jmbi.1996.0628/pdf



Example command file for automatic molecular replacement: 
syntaxis for PROVE/SURVOL Version 2.5.1, November 14, 2000:

prove [args] -p pdbfile [pdbfile ...]
  -p pdbfile []    name(s) of PDB file.
  -rad             using the radical planes method
  -dna             exclude DNA in calculations
  -het             exclude hetero atoms in calculations
  -hoh             exclude water in calculations
  -ranges name     name of file containing ranges of standard volumes
  -dssp name       name of file containing dssp output for structure
                   default is "tapeout"
  -res  float      value of resolution for use in postscript plotting programs.
                   default is 2.0 angstroms

  -rprobe float    select size of probe (in angstroms)  default is 1.5 angstroms
  -vdw             enable the option to manually assign chemical type and
                   radii to atoms that are undefined in vdw.noth.
                   WARNING: VOLUMES CALCULATED USING THE RADICAL PLANES
                   METHOD ARE STRONGLY DEPENDENT ON ATOMIC RADII.
                   CALCULATING VOLUMES USING THE RADICAL PLANES METHOD
                   AND RADII OTHER THAN THOSE IN THE ORIGINAL
                   FILE vdw.noth WILL RENDER THE SCORES ASSIGNED BY
                   PROVE MEANINGLESS
  -survol          prove will be used simply as a front-end for
                   SurVol; no further validation computation is
                   performed, only the output file with the results
                   from SurVol will be produced.
  -H               display this help text