I think there is a problem with the way coot parses the output from coot-molprobity/probes-dots.out for displaying the probe clashes and making the "Molprobity Probe Clash Gaps" window.
Using the reduce and probe versions in example #1 below, coot 0.5 will display the packing/clashes on the molecule but the "Molprobity Probe Clash Gaps" window where you can click on each residue doesn't display the information properly and will return a "not found error" and therefore not choose the residue. I think this is related to the extra space between the ":" and the "A" in the examples below. If I use the versions of reduce/probe that work fine in coot 0.4.1 in 0.5, the "Molprobity Probe Clash Gaps" window is empty and the clashes/packing are not drawn on the molecule. Running probe from the command line also results in these gaps(I hope all this makes sense). I have tried several combinations of reduce/probe (both compiled from source and downloaded binaries) and also tested this with a a pre-built binary to make sure my 64-bit version of coot 0.5 wasn't to blame. #1) PROBE-DOTS.OUT FROM VERSIONS OF REDUCE(3.03.070307)/PROBE(2.12.071128) MOSTLY WORK WITH COOT 0.5: ============================================================================ ======================== [EMAIL PROTECTED] coot-molprobity]$ more probe-dots.out :1->1:wc: A 1 GLY C : A 2 ALA O :0.364:0.443:-23.028:17.043:-10.447:0.000:0.0027:C:O:-23.028:17.043:-10.447: 17.30:13.75 :1->1:wc: A 1 GLY C : A 2 ALA O :0.364:0.429:-22.911:17.044:-10.195:0.000:0.0033:C:O:-22.911:17.044:-10.195: 17.30:13.75 :1->1:wc: A 2 ALA C : A 1 GLY O :-0.001:0.297:-22.934:16.874:-10.243:0.000:0.0152:C:O:-22.934:16.874:-10.243 :12.50:19.32 :1->1:wc: A 2 ALA C : A 1 GLY O :-0.001:0.261:-22.605:16.482:-10.261:0.000:0.0211:C:O:-22.605:16.482:-10.261 :12.50:19.32 :1->1:wc: A 2 ALA C : A 1 GLY O :-0.001:0.340:-22.339:16.228:-10.136:0.000:0.0098:C:O:-22.339:16.228:-10.136 :12.50:19.32 #2) PROBE-DOTS.OUT FROM REDUCE(3.03.070307)/PROBE(2.12.070727) THAT WORK WITH COOT 0.4.1 BUT NOT 0.5: ============================================================================ ======================= [EMAIL PROTECTED] bin]$ more coot-molprobity/probe-dots.out :1->1:wc:A 1 GLY C :A 2 ALA O :0.364:0.443:-23.028:17.043:-10.447:0.000:0.0027:C:O:-23.028:17.043:-10.447: 17.30:13.75 :1->1:wc:A 1 GLY C :A 2 ALA O :0.364:0.429:-22.911:17.044:-10.195:0.000:0.0033:C:O:-22.911:17.044:-10.195: 17.30:13.75 :1->1:wc:A 2 ALA C :A 1 GLY O :-0.001:0.297:-22.934:16.874:-10.243:0.000:0.0152:C:O:-22.934:16.874:-10.243 :12.50:19.32 :1->1:wc:A 2 ALA C :A 1 GLY O :-0.001:0.261:-22.605:16.482:-10.261:0.000:0.0211:C:O:-22.605:16.482:-10.261 :12.50:19.32 :1->1:wc:A 2 ALA C :A 1 GLY O :-0.001:0.340:-22.339:16.228:-10.136:0.000:0.0098:C:O:-22.339:16.228:-10.136 :12.50:19.32 ==================================================== 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] ====================================================
