Editing MotiveValidator:Terminology (section)

=Motif / Fragment=
With respect to the chemistry of biomolecules, the term ''motif'' is used to refer to a well defined distribution of structural elements in a biomolecule or biomolecular complex, with characteristics 
generally associated with a specific function. Within the '''MotiveValidator''' environment, a ''motif'' is generally a fragment of a biomacromolecule, biomacromolecular complex or ligand, made up of 
one or more residues or parts of residues. A ''motif'' can in principle be any fragment of a biomolecule. Nonetheless, '''MotiveValidator''' is focused on the validation of residues, thus here ''motif'' generally 
refers to a fragment made up from the residue under study, together with its surroundings (i.e., atoms from neighboring residues). Note that the terms ''fragment'' and ''motif'' are used as synonyms in this manual.

We can generally say that, within the '''MotiveValidator''' environment, all ''residues'' can be thought of as ''motifs''. Therefore, different ''instances of the same residue'' (such as multiple arginine residues throughout the sequence of a protein, or copies of the same ligand in different monomers) can be considered and processed as different ''motifs'', making their identification straightforward and unambiguous.

We use the term model residue (or simply model) to refer to a particular structure that is known to be correct. This structure will then be used as reference template in the validation process, whereby a query residue with the same name (3-letter code) as the model will be compared to the model. Within the '''MotiveValidator''' environment, a model contains one residue. The origin of the model can be the wwPDB chemical component dictionary accessible via LigandExpo, or a custom model provided by the user.