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
- 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
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
- 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
- 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
- Mutation tool.
- Torsion tool.
All these functions will ask you to pick atoms in the
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".