I'm on Mac 10.5.4 with Coot pre-5 1391 (but problem was same with pre-5 986).
I have
reduce and probe installed. I have .coot file setup as follows:
(set! *probe-command* "/sw/share/xtal/bin/probe")
(set! *reduce-command* "/sw/share/xtal/bin/reduce")
(set-find-hydrogen-torsion 1)
(set-do-probe-dots-on-rotamers-and-chis 1)
(set-do-probe-dots-post-refine 1)
(set-rotamer-lowest-probability 0.5)
Both probe and reduce execute when the command is issued.
If I do a real space zone refinement no molprobity dots are shown.
Yet I see in the log:
probe command "/sw/share/xtal/bin/probe" ("-mc" "-u" "-quiet" "-drop"
"-stdbonds" "-
both" "(file1 within 10.6 of 22.95, 63.74, 29.07, not water not (chainb
77)),file2" "file2"
"molprobity-tmp-reference-file.pdb" "molprobity-tmp-moving-file.pdb")
I also get a coot-molprobity directory with a probe-dots.out file
The probe-dots.out has many lines of
:1->1:wc: B 2 THR C : B 4 ASP OD1
:0.231:0.333:11.947:87.693:31.375:0.000:0.0106:C:O:11.947:87.693:31.375:151.85:159.
18
:1->1:wc: B 2 THR C : B 4 ASP OD1
:0.231:0.403:12.113:87.887:31.383:0.000:0.0047:C:O:12.113:87.887:31.383:151.85:159.
18
:1->1:wc: B 2 THR C : B 4 ASP OD1
:0.231:0.259:12.022:87.681:31.626:0.000:0.0213:C:O:12.022:87.681:31.626:151.85:159.
18
:1->1:wc: B 2 THR C : B 4 ASP OD1
:0.231:0.347:12.196:87.873:31.635:0.000:0.0091:C:O:12.196:87.873:31.635:151.85:159.
18
My question is why the molprobity not being displayed on the screen.
