ADT

Introduction

Ligand

Grid

Docking

Run

Analyze

The docking simulation can be carried out using several different search methods, involving many possible parametric refinements.  Preparation of the molecules also depends on various sets of parameters.

To simplify the setting up of an AutoDock run,  we have developed a graphical user interface called AutoDockTools.  This leads the user through the preparation of the input files, helps to start the various programs, and helps to analyze the results.  AutoDockTools, or "adt", consists of five modules which build on the Python Molecular Viewer, "pmv". AutoDockTools can be started from the Unix prompt using the command:

> adt

To get started with adt,  the user needs to know a few basic things about pmv...
 

Pmv Basics

Starting pmv opens a Molecular Viewer which is composed of two or more menu bars at the top, a viewer in the center and a message box at the bottom.

 

	-	- Menu bars
	-	- Viewer window
	-	- Message box

The Menu Bars

The menu bars contain a collection of menu buttons with labels such as `File', `Display', `Color', etc. These menu buttons give the user access to menus of commands or to check buttons for specialized uses. The menus can be `torn off' by selecting the dashed line at the top. Some entries in the menus give access to a second list of commands via cascading menus.  This is indicated by a small triangle on the right.  Torn-off menus can be closed with the right mouse button.

`PyShell', a check-button located at the left of the lowest menubar, opens a Python interpreter.  The `PythonShell' opens automatically with an error message when an illegal operation occurs.  Users familiar with the Python debugger, pdb, can use it to get useful information about what may have caused the problem.

Menu buttons for the five adt modules are loaded into a tan menubar, and are labelled `Ligand', `Grid', `Docking', `Run' and `Analyze'.

Viewer Basics

The DejaVu Viewer-object is a fully functional visualization application providing control over a  variety of rendering parameters such as: depth cueing, rendering modes (points, lines, polygons), shading modes (flat, Gouraud), multiple light sources, arbitrary clipping planes etc.  Geometries to be visualized can be handed to a viewer object to be displayed and transformed.  More information about these advanced properties may be obtained from the DejaVu Tutorial.

The viewer has default key-stroke bindings which allow the user to reset, normalize and center the scene.  The user must press these keys while the cursor is over the viewer, to have the desired effect.

 

Useful Key-Strokes in the Viewer Window.

Key	Operation
R	Reset:  reset the rotation, translation and scale transformations of the objects in the scene.
N	Normalize:  normalize the size of all the visible objects to roughly fill the viewer.
C	Center:  set the center of rotation to the center of gravity of all the visible objects.
D	Depth-cue:  Toggle on and off depth-cueing.


 

The viewer has default mouse bindings for the trackball object, which allow the user  to rotate, translate or scale objects in the scene; the effect of each mouse button is also modifed by the <Shift> keys:
 
 

Rotations, Translations and Scaling in the Viewer Window.

Modifier Key	Left Mouse Button	Middle Mouse Button	Right Mouse Button
(None)	Pick	Rotate.	XY-Translate.
Shift	Set the center of rotation.	Scale.	Z-Translate.

 
Owing to perspective, the Z-translation may appear like a scaling operation, but it is not.  You can tell the difference by doing a Z-translation away from you: hold down the <Shift> key and the right mouse button, and move the cursor to the left or downwards in the viewer window. If you have depth-cueing turned on (press the <D> key), you will see the object not only shrink, but also fade into the dark fog.

You can set the rotation center of the current object by picking on any vertex in the scene with the left mouse button, while holding down the <Shift> key.
 

The Current Selection

Most pmv commands operate on the set of objects the user has currently selected.  Selection is performed using the `Select' menu.  By default, the selected vertices are indicated by yellow crosses.  An example of the use of the selection is shown in the image at the top of thispage.  To make the small molecule more distinct,  it was selected  using the `Select : Direct Select : Molecule List...' option.  Then its display was changed using `Display : SticksAndBalls'.

Self-Logging

The user should note that all actions in adt log themselves in the message area below the viewer, and also in a file.  Scripts may be built using these log files, and sourced in adt using the `File : Source' command, in order to replay a sequence of commands.  By default, each session writes a log file of all the commands used in the molecular viewer into a file called `mvAll.log.py'. To prevent this from being over-written in a subsequent session, the user should save this by copying or moving this to a different filename.

Commands Executed at Start-Up

Sequences of commands, which the user wishes to be executed every time the adt is used, may be kept in a `.pmvrc' file which Pmv will access on starting. This is normally stored in the user's home directory.

Loading Other Functions

Also, Pmv is modular, customizable and extensible.  This means that the user is able to add new functions to the viewer while working.  For example, the `measure' module is not routinely loaded when adt is started.  If the user wanted to measure the distance between two atoms, this module can be loaded using the `File : Load Module' command.  Likewise, individual commands may be added using the `File : Load Command' option.  Macros, such as `showHideDejaVuGui', one of four macros in `DejaVuMac.py' which gives the user access to the advanced viewer properties mentioned above, can be loaded using `File : Load Macros.'

ADT

Introduction

Ligand

Grid

Docking

Run

Analyze