[phenixbb] Specify space group with phenix.map_to_structure_factors?

Oliver Clarke olibclarke at gmail.com
Mon Feb 15 11:49:40 PST 2016

Hi, I frequently use phenix.map_to_structure_factors to generate mtz files
from EM maps for use in Coot - it is by far the best tool I have found for
this purpose.

For convenience (so I can easily build and refine one protomer of a
four-fold symmetric entity), I often convert these mtz files from the
default P1 to P4 spacegroup using CCP4, and I wonder if  it would be
possible to include an option to specify the output spacegroup directly in
map_to_structure_factors (or perhaps it is there and I have missed it?)?

Even better would be if there were a way to check the symmetry and refine
the orientation of the input volume such that the map is centered in the
unit cell and the symmetry axis of the volume is appropriately aligned -
often I have aligned the input volume to another reference volume in
Chimera, and if the alignment is not perfect the symmetry axis of the
volume might be slightly misaligned from what would become the fourfold
axis of the output.

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