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
I don't know if it is a permissions problem, installation problem, or
what, but thanks in advance for the help.
Jennifer Doebbler
Argonne National Lab
Processing set: A 1 LYS N [4]: A 40 THR OG1 [3]
permutations: 12
Computing dot scores
Num optimizations problems to be solved for this clique: 1
Beginning Optimization
Dynamic programming succeeded to fully optimize hypergraph
Optimal score following low resolution optimization: 2.180
> : 2.457
Optimal score following high resolution, local optimization: 2.457
Found 0 hydrogens (0 hets)
Standardized 0 hydrogens (0 hets)
Added 991 hydrogens (0 hets)
Removed 0 hydrogens (0 hets)
Adjusted 24 group(s)
If you publish work which uses reduce, please cite:
Word, et. al. (1999) J. Mol. Biol. 285, 1735-1747.
For more information see http://kinemage.biochem.duke.edu
BL INFO:: run probe as /Applications/molprobity/bin/macosx/probe -u -stdbonds
-mc "ALL ALL" coot-molprobity/probe-in.pdb > coot-molprobity/probe-out.pdb
probe: version 2.12.071107, Copyright 1996-2007, J. Michael Word
density: 16, probe radius: 0.25, maxBonded: 4
regular HB cutoff: 0.6, charged HB cutoff: 0.8
Dot gap bins: low to -0.4, -0.4 to 0, 0 to 0.25, 0.25 to high, & Hbonds
C=O carbon VDW scaled by 0.943 to a radius of 1.65 A
Score Weights: gapWt=0.25, bumpWt=10, HBWt=4
draw spike, len: 0.5
Excluding water-water interactions
Limiting dots from bumps to max non-bump cap
Coloring dots by gap (& list color by atom)
pattern 1: (all and all)
>>name:pat:type:srcAtom:targAtom:min-gap:gap:spX:spY:spZ:spikeLen:score:stype:ttype:x:y:z:sBval:tBval
SelfIntersect
If you publish work which uses probe, please cite:
Word, et. al. (1999) J. Mol. Biol. 285, 1711-1733.
For more information see http://kinemage.biochem.duke.edu/
(handle-read-draw-molecule-with-recentre "coot-molprobity/probe-in.pdb" 0)
Reading coordinate file: coot-molprobity/probe-in.pdb
PDB file coot-molprobity/probe-in.pdb has been read.
Spacegroup: P 43 21 2
Cell: 78.715 78.715 38.234 90 90 90
Symmetry available for this molecule
Molecule 3 read successfully
BL DEBUG:: handle_dots with coot-molprobity/probe-out.pdb 3
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/usr/local/coot/share/coot/python/coot_gui.py", line 723, in
interesting_things_gui
interesting_things_with_fix_maybe(title, baddie_list)
File "/usr/local/coot/share/coot/python/coot_gui.py", line 790, in
interesting_things_with_fix_maybe
for baddie_items in baddie_list:
TypeError: 'type' object is not iterable
