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

EditTNT is a Java-based interactive tool for editing and visualization of TNT-restraints. All types of restraints are supported. You can modify existing restraints or delete them and add new ones. Visualization is carried out by JMOL. Provided with a PDB-file (see below: How to start EditTNT), EditTNT can call Gelly (O.Smart) to optimize the PDB-file with the parameters chosen (including the inversion of chiralities by sign change of the corresponding improper torsion angles).

How to start EditTNT

EditTNT can be used to visualize restraints in PDB, MDL and Tripos-MOL2-files
% EditTNT [TNT-dictionary-file] [structure-file]

Argument Description Note
TNT-dictionary-file TNT-style-restraints-file  
structure-file name of PDB, MDL, or Tripos Mol2-file matches up with the TNT-dictionary file

See also

% EditTNT -h

for a list of command line arguments. For examples, please refer to the Tutorial section of this documentation.

How to Use EditTNT



If you click on Save Table on the menu, the table will be saved into a file with the extension ".user". If you have chosen to optimize a structure with Gelly, the latest update of the table will be saved into a file with the extension ".gelly", the optimized structure will be saved into a file with the extension ".opt.pdb" and a file "gelly_refine.log" will show you the course of the gelly - optimization and its final agreement with the restraints chosen by you.


1. Setup

Please copy the folder samples/maketnt of your MakeTNT-toolkit distribution over:

% cp -pri $BDG_home/MakeTNT/samples/maketnt .

This will create a local copy of the examples that we provide. In this folder you will find restraint files generated by Corina, the Libcheck program (part of Refmac and CCP4) and xplo2d (XPLOR option), as well as the corresponding TNT-dictionary files converted by MakeTNT. For details of MakeTNT usage, please refer to the MakeTNT-documentation.

2. Restraints from Corina

To look at TNT-restraints generated for the compound taxotere by Corina and converted into TNT-format by MakeTNT, please go to the maketnt/CORINA directory and type:

% EditTNT taxotere.dic TXL.mol

This will start the interface as shown above. Please select PLANE in the tab-header section. Click on an atom to highlight the planar restraints it is involved in. A count of restraints found for this atom will appear in the text window towards the bottom of EditTNT. You can also use the mouse keys to scroll up and down the list of plnar restraints.

Looking at the table you will find, that for this molecule all PLANE restraints are computed in a very satisfactory way, as is usually the case when using Corina-derived parameters. In the next sections, we will learn how to edit and - if necessary - modify restraints generated by other sources.

3. Restraints from Libcheck/Refmac

To view TNT-restraints derived from a Libcheck/Refmac descriptions, please go to the maketnt/Refmac directory and type:

% EditTNT adenosinetriphosphate.dic ATP.pdb

Select the PLANE-table again and look at the only entry, which describes the planarity of the ATP-purine ring. If you wish to add the N6 atom to this list, double click on the cell with the Header Atoms. It will change colour and you can scroll to either end of the list using the arrow keys on your keyboard. You can delete text in the cell using the backspace key and add text by just typing it into the cell. To add the "N6" atom to the list, go to the end of it and type ", N6".

Alternatively, click on "Duplicate Restraint" to start a new table with the same atom atoms. To change the selection of atoms, either

Once you are happy with your new restraint, insert it into the main table by pressing the respective button and remove the original restraint from there.

A similar mechanism can be used to add new restraints using the "Add Restraint" button.

To save the new restraint list, select Save Table. The TNT-dictionary file will be saved using the original name with the extension ".user". Before saving the list, please press "Enter" to make sure that all the latest changes are included.

4. Restraints from xplo2d (XPLOR): adding/removing restraints

For a demonstration of TNT-restraints derived from xplo2d (XPLOR-format), please go to the maketnt/XPLOR directory and type:

% EditTNT rosiglitazone.dic BRL.pdb

Please select the PLANE-table again. You will see four different PLANE-restraints generated for rosiglitazone. The first restraint describes the planar thiazolidinedione group and is correct, as are restraints 2 and 4 (for the benzyl and pyrdinyl group, respectively). However, the third restraint (4 atoms) is derived from a particular conformation rather than from a chemical rule. If you are interested in refining rosiglitazone in conformations different to the one in the structure shown, you probably want to remove that restraint. To do so, simply select it and click on the Remove Restraint - button. This removes the restraint in the table, but not in the underlying file. To make the change permanent, please save the new restraints by clicking on Save Table.

5. Restraints from PDB2TNT: using Gelly to invert the chirality around an atom

To find out how to use gelly interactively within EditTNT, please enter the maketnt/PDB2TNT directory and type:

% EditTNT TXL.dic TXL_tnt.pdb
Now, let's assume you would like to invert the chirality around the C34 atom. To do that, you enter the IMPROPER card in EditTNT, select the 8th restraint from the top, change its value from -30.7 to 30.7, press the ENTER key on the keyboard and then press the "Run Gelly" button on the interface. You will get a message that gelly has started running. Once optimization is complete (<10s), you will be notified by an EditTNT-message. Simultanously, a button for loading the new structure into EditTNT/JMOL will become active. Another button will take you back to the original structure. The "Run-Gelly" button could be modified by an option to specify parts of the molecule to be fixed during the optimization. Please let us know whether such an option would be useful to you.

Maria Brandl, <>
Last modification: 10.07.08