Other display modes are available, as will be described below.
The simplest operations are those involving moving the structure about on screen using the mouse. Each operation is achieved by holding the relevant mouse button down (with or without either the shift- or control-keys) and moving the mouse.
The different operations that can be performed are:-
|Left mouse button||Rotate x-y|
|Right mouse button||Translate x-y|
|Shift-key + left mouse button||Zoom in/out|
|Shift-key + right mouse button||Rotate z|
|Control-key + left mouse button||Slab plane|
The various colours are:-
Only the first of these is of interest here, GIF, which saves the image as a GIF file which you can then incorporate into your Web page.
Through the command window you can enter a wide range of interactive commands, each typed at the "RasMol>" prompt. Each command must be given on a separate line. Keywords are case insensitive and may be entered in either upper or lower case letters. All whitespace characters are ignored except to separate keywords and their arguments.
The full list of commands is given in the Operating Manual, referred to above. Only a selection will be described here.
For example, the command
RasMol> wireframe on
displays all currently-selected atoms in wireframe mode.
Conversely, the command
RasMol> wireframe off
switches off any wireframe bonds amongst the currently-selected atoms.
Some of the on/off commands also have an alternative version in which a number can be entered in place of the on/off. For example, the wireframe command can be entered as:-
RasMol> wireframe 0.2
This switches the wireframe mode on, but makes all the bonds 0.2Å thick (ie it gives the bonds a stick-like appearance).
The on/off commands include the following:-
|wireframe on/off||Display wireframe|
|wireframe 0.2||Display stick bonds of radius 0.2|
|backbone on/off||Display CA backbone only|
|backbone 0.2||Display CA backbone as sticks of radius 0.2|
|spacefill on/off||Atoms as spacefill spheres|
|spacefill 1.0||Atoms as spheres of radius 1.0|
|ribbons on/off||Display molecule ribbons|
|ribbons 1.0||Display molecule ribbons, width 1.0|
|cartoon on/off||Display protein cartoon|
|dots on/off||Display dot-surface about all atoms|
|dots 10||Display low-density dot-surface|
|hbonds on/off||Display hydrogen bonds|
|hbonds 0.1||Display hydrogen bonds, radius 0.1|
|set axes on/off||Display coordinate axes|
|set boundbox on/off||Display bounding box|
Selection is performed by the command:-
RasMol> select [atom-expression]
[atom-expression] defines the atoms required.
Atom expressions come in several varieties. These include:-
select 3 select 3,6,9 select 12-25
These three commands select: a single residue, three individual residues, and a range of residues, respectively.
Residues can also be selected using the full residue name:
selects all residues in chain A.
selects all the atoms in the structure.
When any group of atoms/residues has been selected all subsequent operations affect only these selected atoms.
For example, if you enter:-
RasMol> set picking distance
and then click on two atoms, RasMol will calculate the distance between them, and display it in the command window.
RasMol> set picking angle
RasMol> set picking torsions
calculate angles and torsion angles between 3 and 4 successively clicked atoms, respectively.
Other useful picking commands are:-
RasMol> set picking centre- which allows the whole molecule to be rotated about the next atom that is clicked on.
RasMol> set picking ident - which shows the name of
each atom clicked on (this is the default setting).