[phenixbb] Prime and switch crashing

Oliver Clarke olibclarke at gmail.com
Fri Jun 13 04:42:04 PDT 2014

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. 


Command: phenix.prime_and_switch_map model_rs6_refine_001.pdb model_rs6_refine_001.mtz debug=true

                  ----------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>
  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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