about Aqva

Aqva is a molecular graphics program designed for the interactive visualization and analysis of molecules such as proteins, nucleic acids and lipids. Aqva runs on all major Unix platforms and Apple Mac OS X.


List of features:

  • Molecular Visualization
    Aqva is a general application for displaying molecules containing any number of atoms and is similar to other molecular visualization programs in its basic capabilities.

  • Visualization of molecular trajectories
    Aqva can load atomic coordinates trajectories in the CHARMM, XPLOR dcd format. Trajectories can be used to animate molecules on screen or the generate movies.

  • Interactive molecular dynamics simulations
    Aqva has a built-in molecular dynamics engine that can be used to compute energies, minimize or run short interactive simulations. Aqva has support for various CHARMM and AMBER force fields.


Subsections:


Loading a molecule

Aqva can load molecules in PDB format. Files can be compressed with gzip or bzip2.

Load Molecules into Aqva:

  1. Click on the Open button in the MainWindow ToolBar or use the File->Open menu entry.
  2. Enable Molecules.
  3. Select the appropriate file.

Using the mouse

When the mouse is in the OpenGL graphics window it may be used to perform the following actions:

  • Rotate, translate, z-rotate or scale the representation of the displayed molecules.
  • Center a selected atom.
  • Perform an action on a molecule.

The mouse of the graphics window is always in one of four modes:

  • Rotate Mode This mode is activated by pressing the 'r' key on the keyboard. When the mouse is in rotate mode, holding the left mouse button down and moving the mouse rotates the molecules about axes (X and Y) parallel to the screen.
  • Translate Mode This mode is activated by pressing the 't' key on the keyboard. When the mouse is in translate mode, holding the left button down allows you to move the molecules parallel to the screen plane (left, right, up, and down). To move the molecule towards or away from you, hold the middle button down and move the mouse right or left, respectively.
  • Z-Rotate Mode This mode is activated by pressing the 'z' key on the keyboard. When the mouse is in rotate mode, holding the left mouse button down and moving the mouse from left to right will rotate the molecules about the Z axis perpendicular to the computer screen.
  • Scale Mode This mode is activated by pressing the 's' key on the keyboard. When the mouse is in rotate mode, holding the left mouse button down and moving the mouse will sacle the apparence of the molecules.

A double-click on the left mouse button will activate a context menu wich contains a list of atoms, resp. molecules, which are below the pointer. By selecting an atom all molecules will be translated to make selected the new center of rotation. By selecting an entry corresponding to a molecule name an other menu will apper with all the actions that can be applied to the current selection.

Representations

Each molecules is drawn in the OpenGL graphics window as a collection of several representations. A molecule can have any number of representations. When a molecule is first loaded, it is given a `default' view, which will draw all the atoms as lines and points, coloring each atom by what kind of element it is.

  • Points Draws atoms as ... points.
  • Lines The default representation is `Lines', which is also known as `wireframe'. It draws a line between each atom and the atoms to which it is bonded. Both atoms have to be selected before the bond will be drawn. The first half of each bond is colored appropriately for the first atom, while the color of the final half corresponds to the second atom.
  • Tube The tube representation draws a smooth cube through the CA positions of the backbone of a protein.
  • Ribbon The Ribbon representation is similar to the Tube, the only difference beeing that in the Ribbon representation segments are drawn sith a shape that encodes the secondary structure.
  • Sphere Draws atoms as ... spheres.

Analysis

Several analysis algorithms can be applied to molecule directly using the Aqva Gui. A double-click on the name of a molecule or molecules collections activates a context menu that will display a list of all available actions.


Andrea Cavalli
Last modified: Mon Jul 21 17:41:41 CEST 2008

Copyright © 1999-2009 Andrea Cavalli