Just a note to concur with this message. I'm getting this with 0.5, Ubuntu 8.04 32-bit. There was no problem with coot-0.5-pre-1-revision-1211 BTW.
I haven't figured out why, and would love to know. Mark 2008/10/14 James M. Vergis <[EMAIL PROTECTED]> > 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] > ==================================================== > -- Mark BROOKS Telephone: 0169157968 Fax: 0169853715 Institut de Biochmie et de Biophysique Moleculaire et Cellulaire UMR8619 - Bât 430 - Université de Paris-Sud 91405 Orsay CEDEX
