Use quotation marks to set off nicknames if it’s appropriate to indicate the informal name: Katherine “Kate” Smith. In many circumstances, it’s acceptable to use a nickname or a more familiar version of a first name on first reference, but defer to the preferences of the person being referred to.
Use periods and spaces for initials standing for given names: E. B. White; do not use periods for an entire name replaced by initials: JFK. But again, take into account the individual’s preferences.