EditTNT

Contents

• General
• How to start EditTNT
• How to use EditTNT
• Output
• Tutorial
  1. Setup
  2. Restraints from Corina
  3. Restraints from xplo2d (XPLOR): adding/removing restraints

General Information

How to start EditTNT

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

• The main table
• Click on the tab BOND, ANGLE, TORSION, etc. to view a table of restraints of the given kind
• Use the mouse to select the first restraint you want to visualize in the table
• Scroll up and down the table with the arrow keys to search for restraints
• NEW in MakeTNT2.1.1: Click on an atom in the Jmol-window to highlight the restraints it is involved in



• Double click on a cell in order to edit restraints
• The display will update as soon as you press ENTER or move to another cell
• For planarity restraints atom counts will automatically update upon the modification of atom records
• Check the display before you save the table
• NEW in MakeTNT2.1.1: Interactive Addition/Duplication of Restraints

• Click on the "Add Restraint" or "Duplicate Restraint" - button in the main window
• Click on atoms in the Jmol-display to select atoms for the new restraint, they will show up in the extra table
• Click on a selected atom (NO DOUBLE CLICK) to remove it again
• Insert the new restraint into the main table by clicking on "Add Restraint To Table"

• Gelly optimization:
  • Click on "Run Gelly" to optimize your structure to the restraints chosen (only possible if pdb-file was submitted)
  • Once the optimization is complete (< 10s), switching to the optimized conformation (and back) will become available
  • Optimization will always start from the original pdb-file
  • If you would like an optimization to start from a previous gelly run, please restart EditTNT with the gelly-output PDB-file and the modified dictionary (*.gelly)
  • Please also notice the messages provided by EditTNT
  • To use gelly for changing chiralities, check the example below

Output:

Tutorial:

1. Setup

% 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

% 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

% 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

• click on the atom in the JMOL display window, this will
• selected atoms
• deselect selected atoms
or
• double click in the atoms cell to edit, a single click outside this cell, but inside the table will re-enable selection from the molecular viewer

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

% 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

% 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.