Controls the display of cartesians axes with origin at the center of the bounding box.
Atom expressions are used to select atoms. The selection of bonds is controled by the bondmode setting. When set to 'and', the default, a bond is selected only if both atoms are selected. When set to 'or' a bond is selected if either atom is selected.
You may want to select bonds in order to control their color (color bonds <color>) or their size (wireframe 32).
Controls the display of double and triple bonds. When the setting is off then all bonds are shown as single bonds.
Note that there are several factors which control rendering of multiple bonds. 1) Whether or not the file contains bond connection information. 2) whether or not Jmol calculates multiple bonds 3) whether or not the bond setting is on or off (this setting) 4) the size of the bonds.
Item 4 needs a little more explanation. RasMol only shows multiple bonds if the radius of the bonds is <= 32 RasMol units (32/250 = 0.128 Angstroms). Presumably this is done because multiple bonds would look ugly if they were larger. Jmol currently respects this for backward compatibility with existing scripts.
Controls rending of the bounding box which completely encloses the molecule. The bounding box is defined by the minimum and maximum coordinate values of the centers of the atoms along each of the x, y and z axes.
RasMol does not hilite or change colors on selected atoms. You can 'set display selected' to go to some wild color scheme. Jmol implements this by using 'halos' around the selected atoms. 'set display normal' turns off the halos.
This is a problem area for us and we would like feedback from experienced users on how this should behave. We want to maintain compatibility with existing RasMol/Chime scripts, but we think that the visual feedback of selection halos is good during script development. We also think that new/inexperienced users would benefit from using the halos. Any suggestions/ideas/feedback would be appreciated.
Sets the fontsize used for atom and monitor labels.
Jmol extension: A value of 0 specifies the Jmol default size. The Jmol default size is calculated as a function of the atom size. So small atoms use a small font and large atoms use a large font.
This is another area where we would like user feedback on how we can extend the functionality while maintaining backward compatibility with existing RasMol/Chime scripts.
Controls the default selection behavior of heterogenous atoms in protein molecules in .PDB files. When turned 'on' the command 'select all' will include heterogenous atoms that are included in the .PDB file.
See also: the predefined set 'hetero' and the 'set hydrogen on | off' command.
Controls the default selection behavior of hydrogen atoms in protein molecules in .PDB files. When turned 'on' the command 'select all' will include hydrogen atoms that are included in the .PDB file.
See also: 'set hetero on | off' command.
(But .PDB files do not usually include hydrogen atoms?)
In RasMol terminology, a 'monitor' is a distance measurement. These are called 'measurements' in the Jmol menus. This command controls the display of the numeric labels (for distance, angle, or dihedral angle). That is, with 'set monitor off' the lines will still be drawn, but the measurement values will not be shown.
See also: monitor command