To select atoms
This is not a command, but a keyword for an "atom expression". Typically used in the select command.
It refers to the set of atoms identified by Jmol to be part of a protein (due to their chemical structure containing the key atom names).
This is also a keyword for an atom expression. Typically used in the select command.
"Ligand" is the set of atoms that
Be cautious; it will not always select what you may think are "ligands". For example, monoatomic ions (Ca2+) are part of the ligand set, while isolated nucleotides like GMP will be identified as nucleic and hence not ligand.
An essential command, as any style of rendering that you want will apply only to the set of atoms that is selected at that moment.
Most frequently employed as part of a select command. It has several variants or uses; among them:
combination: and, or, not
To specify rendering style
Applies a color to the selected atoms, their bonds and other graphic elements attached to them.
Sets the thickness of a stick representing a bond (in angstroms; needs a decimal point).
spacefill or cpk
Sets the diameter of the sphere representing an atom (most usually in percent, relative to Van der Waals radius)
A schematic rendering that is relevant only to protein and nucleic acid chains.
display and hide
Reversibly removes part of the molecule from view (without changing the assigned rendering style). Note that its action is not cumulative, but exclusive.