Hey Paul,
That totally worked! Thanks for the quick response!!!
Terry
On 5/25/2011 3:04 PM, Paul Emsley wrote:
On 25/05/11 21:20, Terry Lang wrote:
Hey Everyone,
I am having some problems running Probe Clashes on WinCoot. I
am running phenix.refine to obtain the pdb file and then WinCoot for
manual building. I have the following installed:
WinCoot (6.0.1), probe (2.12.110413) and reduce (3.14.080821)
REDUCE_HET_DICT points to a valid location for reduce_wwPDB_het_dict.txt
When I ran things originally, I got this error:
"BL WARNING:: reduce didnt run ok, so stop here!"
Some googling got me to this posting:
http://www.proteincrystallography.org/ccp4bb/message14548.html
I manually applied the fix. As a result, reduce runs without any
apparent error, but returns 1 which causes the probing process to exit.
Indeed, I recently had occasion to make this fix in the scheme
version. It is not clear to me why there is an exit status of 1 - as
you say, reduce seems to work properly.
I have also tried modifying generic_objects.py to ignore the error
and continue on
with the reduced.pdb file that reduce outputted, I end up getting this
error:
Traceback (most recent call last):
File "<string>", line 1, in<module>
File "E:\WinCoot\share\coot\python\generic_objects.py", line 236, in
probe user_mods_gui(imol_probe, reduce_out_pdb_file)
File "E:\WinCoot\share\coot\python\coot_gui.py", line 4399, in
user_mods_gui no_adj_buttons = make_no_adj_buttons(flips[1])
File "E:\WinCoot\share\coot\python\coot_gui.py", line 4345, in
make_no_adj_buttons chain_id = atom_spec[1]
NameError: global name 'atom_spec' is not defined
run_generic_script (probe, 0)
Comment out this:
# show the GUI for USER MODS
if using_gui():
user_mods_gui(imol_probe, reduce_out_pdb_file)
in WinCoot\share\coot\python\generic_objects.py.
Paul.
--
Paula Therese Lang
Postdoctoral Scholar
Alber Lab
UC Berkeley/QB3
