There was some problems with the pythonic probe/reduce part of coot (and
hence Wincoot). This should be fixed now and be available from
pre-release version 1110.
N.B. this may equally be due to the use of probe version 2.12 please use
2.11 untill this is fixed.
Bernhard
> Hi all,
>
> I am having trouble displaying the probe dots generated by
> molprobity in coot. I am loading a single protein pdb file with no
> maps.
> If I run probe from the validation menu, the hydrogens are
> generated and
> displayed for my molecule. A small gui pops up which is titled:
> Molprobity probe clash gaps, but it is blank. No probe dots are
> visible
> on the main coot gui either. If I instead run probe(0) via coot's
> python
> scripting, I get more information about the error. I have included
> the
> tail end of the probe output in the attached .txt file. The last
> line,
> however, claims:
>
> TypeError: 'type' object is not iterable
>
> The generated hydrogens are again visible, but there are no probe
> dots.
> Machine/installation info:
>
> Mac OSX 10.4.11
> coot 0.4.1
> molprobity is from January 9, 2008
>
>
> The following is set in my .coot file in my home directory
>
> (define *probe-command* "/Applications/molprobity/bin/macosx/probe")
> (define *reduce-command* "/Applications/molprobity/bin/macosx/reduce")
> (set-find-hydrogen-torsion 1)
> (set-do-probe-dots-on-rotamers-and-chis 1)
> (set-do-probe-dots-post-refine 1)
>
> The following are the contents of my .bashrc file
>
> export HISTIGNORE="&:ls:[bf]g:exit"
> source /usr/local/ccp4-6.0.2/bin/ccp4.setup
> export CCP4I_TCLTK=/usr/local/bin
> source /Applications/cns_solve_1.2/cns_solve_env.sh
> alias xemacs='/Applications/Aquamacs\
> Emacs.app/Contents/MacOS/Aquamacs\
> Emacs'
> shopt -s dotglob
> function coot {
> COOT_REFMAC_LIB_DIR='/usr/local/coot/share/coot/lib'
> PATH=/usr/local/coot/bin:$PATH /usr/local/coot/bin/coot "$@" ; }
> export PATH=$PATH:/Applications/molprobity/bin/macosx
>
***************************************************
Dr. Bernhard Lohkamp
Div. Molecular Structural Biology
Dept. of Medical Biochemistry and Biophysics (MBB)
Karolinska Institutet
S-17177 Stockholm
Sweden
phone: (+46) 08-52487698
fax: (+46) 08-327626
email: [EMAIL PROTECTED]
