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
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