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:
> 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
> 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)
> File "E:\WinCoot\share\coot\python\coot_gui.py", line 4345, in
> make_no_adj_buttons chain_id = atom_spec
> NameError: global name 'atom_spec' is not defined
> run_generic_script (probe, 0)
Comment out this:
# show the GUI for USER MODS