Thanks for the info Bernhard. I will try to switch to the 2.11 version
of probe. I still have one more question though for the group at large.
I am running this on a Mac 10.4.11. It seems that all the pre-release
versions are for linux or windows only. Should I just try to install
from source code when 1110 comes out?
-Jennifer
Bernhard Lohkamp wrote:
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]
