Although MOZYME will normally recognize all the elements in a PDB file, the
possibility exists that an element or entity will be defined in a PDB file
in an unusual way, and as a result it will not be recognized. To allow for this,
the keyword PDB(text) is provided. The text is composed of a series
of entries of form 'Chemical-symbol:Atomic number', separated by commas.
Thus if a PDB had some hydrogen atoms represented by the symbol J, and
a bromine atom represented by QW, then these symbols would be correctly
recognized by MOZYME if PDB(J:1,QW:35) were specified on the keyword line.
Entities which do not correspond to elements can be excluded by assigning them
the atomic number zero, e.g. PDB(LP:0) would exclude any explicitly
defined lone-pairs.