RAMPAGE (CCP4: Supported Program)

NAME

rampage - Ramachandran plots using the Richardsons' data.

SYNOPSIS

rapper $CCP4/share/rapper/params.xml rampage --pdb filename --rampage-postscript filename --rapper-dir directoryname
[Keyworded input]

DESCRIPTION

RAMPAGE is an offshoot of RAPPER which generates a Ramachandran plot using data derived by the Richardsons and coworkers. It is recommended that it be used for this purpose in preference to PROCHECK, which is based on much older data.

The Ramachandran diagram plots phi versus psi dihedral angles for each residue in the input pdb file. The diagram is divided into favoured, allowed and disallowed regions, whose contouring is based on density dependent smoothing for 81234 non-Glycine, non-Proline and non-preProline residues with B < 30 from 500 high-resolution protein structures. Regions are also defined for Glycine, Proline and preProline.

INPUT/OUTPUT FILES

--pdb filename

(Compulsory) Input pdb file name.

--rampage-postscript filename

Output postscript file name.

KEYWORDED INPUT

-rapper-dir directory name

Name of the directory containing the data library. This should normally be set to $CCP4/user/share.

REFERENCES

1. S.C. Lovell, I.W. Davis, W.B. Arendall III, P.I.W. de Bakker, J.M. Word, M.G. Prisant, J.S. Richardson, D.C. Richardson, Structure validation by Calpha geometry: phi,psi and Cbeta deviation. Proteins: Struct. Funct. Genet. 50 437-450 (2003).

AUTHORS

Nicholas Furnham, Paul de Bakker, Mark DePristo, Reshma Shetty, Swanand Gore and Tom Blundell.

SEE ALSO

RAPPER