[phenixbb] phenix refinement of cryoEM data

Ali Malay a.malay at riken.jp
Thu Apr 16 23:47:20 PDT 2015

Dear all,

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:
https://www.phenix-online.org/documentation/reference/map_to_structure_factors.html <https://www.phenix-online.org/documentation/reference/map_to_structure_factors.html>

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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