MakeTNT-toolkit User Documentation previous next


Copyright © 2004-2008 Global Phasing Limited

All rights reserved.

This software is proprietary to and embodies the
confidential technology of Global Phasing Limited (GPhL).
Possession, use, duplication or dissemination of the software is
authorised only pursuant to a valid written licence from GPhL.

Author: (2004-2008) M. Brandl


General Information

PDB2TNT is a Java-based command line tool to generate TNT-restraints from a PDB-file. In more recent versions, PDB2TNT can also be used to generate dictionaries for Refmac and O.

Command Line Switches and Arguments

Conversion Mechanism:

Atom-specific covalent radii are used to convert the PDB-file into a graph, which is the basis for deriving TNT - Restraints. Target values for restraints are taken from the 3D-coordinates. If present the positions of H-atoms are used to improve the quality of the restraints (this can be suppressed by the -HPOS option). As Buster-TNT presently does not support the refinement of hydrogen atoms, they are removed from the final restraint file.

If an atom has three neighbours bonded to it, an improper torsion is measured between those four atoms and if its value is close to 0 or 180 degrees a TRIGONAL restraint is created, otherwise an IMPROPER torsion restraint is generated. IMPROPER torsion restraints are also generated for atoms surrounded by four (or more) neighbours.

Planar torsion restraints are put out if two bonded atoms (of elements with double/triple bond potential) are in planar coordination (based on their bond angles) and all torsion angles around this bond are planar as well. If the bonded atoms are in planar conformation, but at least one torsion angle is not, no restraints are not formed and a message to the user is written instead.

The different options for the -size argument are:


Using PDB2TNT in its default mode, the following output files are written into the working directory: With the -CCP4 flag, two files are generated: If you choose the -Odict option, you will obtain: If you choose -Odict, -ODB <O-database>:


Example input files (TXL.pdb_tnt, TXL.pdb) can be found in the samples/maketnt/PDB2TNT subdirectory of your MakeTNT-toolkit installation. Please also check the messages provided by PDB2TNT.
Maria Brandl,<>
Last modification: 02.02.07