2007.06.07 -- This application has been archived. Local users, see a CSB staff member for help if you need to run this program in the Core.

TNT

TNT is a general purpose refinement package used in the solution of macromolecular structures using X-ray crystallography. It is normally used to optimize a model to X-ray diffraction data while maintaining proper stereochemistry using least-squares function-minimization techniques. It can restrain a model to bond length, bond angles, dihedral angles, pseudorotation angles, planarity, and non-bonded "close" contacts (including symmetry related contacts).

TNT was written by Dale E. Tronrud.

Documentation for TNT is available on-line.

To use TNT in the CSB core, first set some variables by typing:

setup tnt (or source /srv/local/setup/tnt.set)

You then have the full complement of TNT executables available.

For a worked example enter the following commands from a dirctory in which you have write permission:

cp /srv/local/tnt/tnt5f_osf/doc/examples/bdna/* .
tnt 1 20 | tee standard.log

This refines a dodecamer of DNA with 20 cycles of least squares refinement, from R=0.208 to R=0.148. The progress of refinement will display on the screen. You should end up with 20 new coordinate files and a "standard.log" file which documents the refinement progress.

You can also analyse the refined coordinate files with commands such as:

geometry cyc20
rfactor cyc20

Or make 2fo-fc.dsn6 and fo-fc.dsn6 maps with the following:

make_maps cyc20

Or make a PDB file from a refined structure:

to_pdb cyc20

Or pick peaks from a map:

pekpik cyc20

A similar example using a protein-inhibitor complex may be found in /srv/local/tnt/doc/examples/phrm/