There's currently no "real" definition for this in ISOLDE, but I find the following works for all but the worst density:
- deprotonate the cysteine residues (i.e. delete their HG atoms). If histidine residues are involved, make sure they're deprotonated on the zinc-facing nitrogen (select the His, and do "isolde mod his sel {ND|NE|both}" where the last argument defines the protonated nitrogen(s)). If your density is remotely reasonable I'd suggest giving it a try after doing just this.
- if it's still recalcitrant, try adding distance restraints. Ctrl-click on the ZN, ctrl-shift-click on an adjacent sulfur or nitrogen, and use the Simple Distance Restraints widget to add a restraint (set the target distance to 2.35 A for sulfur, 2.05 for nitrogen). Consider increasing the spring constant from the default 50 to 250 or so.
- if it still misbehaves after that (i.e. the local density is truly awful) then consider adding distance restraints between the coordinating atoms (i.e. sulfur-sulfur, sulfur-nitrogen etc.). I'm afraid ISOLDE doesn't currently implement manually-added angle restraints.
Hope this helps!
Tristan