Tools

tools 1 tools 2
Move All 		tools 3

The most useful tools are located at the top of the display window, but some other functions are only accessible via the "Tools menu".

The tools are divided into three groups:

  • First group: change main window characteristics

    tools 1

    • This tool allows to change the Offscreen size in order to produce bigger than screen images.
      You can also change the slab depth, the density of dots to draw van der Waals surfaces, as well as the distance in pixels for the stereo separation.

 

  • Second group: move molecule

    tools 2

    • Translate
    • Enlarge
    • Rotate

    Once the proper tool has been selected, you can act on the molecule with the mouse. See the Move & Rotate section to know all the details, and learn how to affect all the protein or only some residues.

  • Third group: general usage tools

    tools 3

    • Distance between two atoms.
    • Angle between three atoms.
    • By default, gives a measure of omega, phi and psi angles of the picked amino-acid (you can pick any atom of the aa). But when this tool is invoked with the "control" key, it will prompt you to pick 4 atoms, which allows to measure the torsion angle of any specific bond.
    • Provenance of an atom (will give the name of the molecule, group, chain, and atom).
    • Display/Undisplay groups that are/aren't at a certain distance from an atom.
    • Center the molecule on one atom (using this tool will automatically switch to world coordinates).
    • Fit a molecule onto an other (available only when two or more molecules are loaded). In this case, you will be prompted to pick three corresponding atoms of molecule to fit. Note that there are other better ways to superpose two proteins available from the tool menu.
    • Mutation tool.
    • Torsion tool.

    All these functions will ask you to pick atoms in the display window.
    Follow the instructions that appear in red under the tools; the results will be given at the same place as well as directly on the molecule.
    Note: if "caps lock" is down, you can measure several distances or angles successively. To exit the "repeated" measurement mode, you can either depress "caps lock" or hit "esc".