pdb_extract / PDB Validation Suite

To use either program in the core type:

setup pdb_validation

pdb_extract

pdb_extract is used to extract statistical information from the output files produced by many software for protein structure determination using Xray Crystallography and NMR methods. pdb_extract merges all the information into two mmCIF (macromolecular Crystallographic Information File) files. One mmCIF file contains structure factors and the other contains atomic coordinates and statistics from the steps of structure determination. These two mmCIF files are ready for PDB deposition.

The assembled two mmCIF files by pdb_extract should be uploaded to the ADIT server. Enter any additional information into ADIT and submit your files directly from there.

PDB Validation Suite

The PDB Validation Suite is a set of applications programs that create validation reports about 3D structure data. It is designed to work with files in mmCIF or PDB format.

This is the same software used in the Validation step of ADIT (AutoDep Input Tool) at the RCSB PDB.

USAGE:
validation -f file_name -o [0, 2]

Option -o 0 is used to create reports for a file in PDB format.
Option -o 2 is used to create reports for a file in mmCIF format.

For example, to create reports for a file in PDB format named proteina.pdb run validation -f proteina -o 0

OUTPUT:
The names of the output file begin with the root identifier <ID>, which is followed by an extension that indicates the file type.

For a PDB format file, the program converts the file name without extension into uppercase for the <ID>.
For mmCIF format file, the program uses data block identifier as the <ID>.

The application creates the following files:

1. <ID>.letter: a text file that contains a summary validation report.

2. <ID>.ps: a PostScript file that contains pictures of structure. If the structure contains nucleic acids, it also contains histograms of the geometrical features of the nucleic acids generated from the program NUCHECK.