[phenixbb] phenix refinement of cryoEM data
a.malay at riken.jp
Thu Apr 16 23:47:20 PDT 2015
I am a relative newcomer to Phenix. I have a large multimeric protein structure docked into an electron density map, and I would like to further refine it by rigid-body refinement using Phenix. Is this a realistic strategy?
I have made some attempts, first by converting the .mrc map file to .mtz as outlined here:
Then I tried to refine using rigid body refinement in Phenix. However, the program quits but doesn’t really tell me why. Here’s the last part of the log file:
Number of unique models: 24
Time building chain proxies: 36.85, per 1000 atoms: 0.26
Number of scatterers: 142296
At special positions: 0
Unit cell: (342, 342, 342, 90, 90, 90)
Space group: P 1 (No. 1)
Number of sites at special positions: 0
Number of scattering types: 4
Type Number sf(0)
S 264 16.00
O 27720 8.00
N 25872 7.00
C 88440 6.00
sf(0) = scattering factor at diffraction angle 0.
Writing MTZ file:
Can anyone give me any ideas as to what went wrong? Also, is there a better way to do this?
Thanks very much in advance!!
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