I just tried that too along with removing the -oldpdb flag from "generic-objects.scm" so that it uses the pdb 3 nomenclature with the same result of drawing the clashes but listing them incorrectly.
==================================================== James M. Vergis, Ph.D. University of Virginia Molecular Physiology and Biological Physics MKWEINR 360A Snyder Building 480 Ray C. Hunt Drive PO Box 800886 Charlottesville, VA 22908-0886 phone: 434-243-2730 FAX: 434-243-8271 [EMAIL PROTECTED] ==================================================== -----Original Message----- From: Mailing list for users of COOT Crystallographic Software [mailto:[EMAIL PROTECTED] On Behalf Of Mark Collins Sent: Tuesday, October 14, 2008 11:08 AM To: [email protected] Subject: Re: [COOT] Coot molprobity problem in Version 0.5? 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
