[phenixbb] Prime and switch crashing

[Terwilliger, Thomas C]

Hi Oliver,
I'm glad that the work-around gets by this problem.  Even so, Might you possibly be able to send me off-line a set of inputs and commands that fails so that I can fix the bug?
Thanks a lot!
-Tom T

On Jun 13, 2014, at 5:57 AM, Oliver Clarke wrote:

> Never mind, it works using autobuild (phenix.autobuild data=data.mtz solvent_fraction=0.58 model=model_rs6_refine_001.pdb ps_in_rebuild=true maps_only=true) so this doesn’t really matter.
> 
> Best,
> Oliver.
> On Jun 13, 2014, at 7:42 AM, Oliver Clarke <olibclarke at gmail.com> wrote:
> 
>> Hi all,
>> 
>> I’m getting an error running phenix.prime_and_switch_map that I can’t figure out. It crashes shortly after F(model) initialization. The last part of the log and traceback is appended below - if anyone can figure out what I’m doing wrong I’d be very grateful! 
>> 
>> I’m running dev-1702 on a Mac (not sure whether this is a mac specific issue though). This happens with multiple different pdb/mtz combinations, so I don’t think it is something specific to my files. 
>> 
>> Best,
>> Oliver.
>> 
>> Command: phenix.prime_and_switch_map model_rs6_refine_001.pdb model_rs6_refine_001.mtz debug=true
>> 
>> Error:
>>                 ----------F(model) initialization----------
>> 
>> Twinning will be detected automatically.
>> |--(resolution: 3.00 - 71.59 A, n_refl.=26875 (all), 5.48  % free)------------|
>> |                                                                             |
>> | r_work= 0.2683 r_free= 0.3402 coordinate error (max.-lik. estimate): 0.58 A |
>> |                                                                             |
>> | x-ray target function (ml) for work reflections: 5.858242                   |
>> |-----------------------------------------------------------------------------|
>> 
>> End of input processing
>> Traceback (most recent call last):
>> File "/Applications/PHENIX-dev-1702/Contents/phenix-dev-1702/build/mac-intel-osx-x86_64/../../phenix/phenix/command_line/prime_and_switch_map.py", line 160, in <module>
>>   run(sys.argv[1:])
>> File "/Applications/PHENIX-dev-1702/Contents/phenix-dev-1702/build/mac-intel-osx-x86_64/../../phenix/phenix/command_line/prime_and_switch_map.py", line 68, in run
>>   map_coeffs = fmodel.electron_density_map().map_coefficients(
>> TypeError: electron_density_map() takes exactly 2 arguments (1 given)
> 
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