I had the same issue. Make sure you are using pdb 3 nomenclature versions of Reduce and Probe. Current Mac versions are 212 and 313. The 313 reduce also requires a new HET dictionary file; reduce_wwPDB_het_dict.txt The het dictionary should be setup like this in your .cshrc setenv REDUCE_HET_DICT /Kinemage/reduce_wwPDB_het_dict.txt and then in your .coot file you need the lines (define *reduce-command* "/Kinemage/reduce313") (define *probe-command* "/Kinemage/probe212") note; I changed the probe and reduce file names
Mark
