[phenixbb] Refine pixel size of map (for EM data)?

Oliver Clarke olibclarke at gmail.com
Mon Feb 8 01:28:44 PST 2016


I wonder whether it would be possible to add an option for
phenix.real_space_refine to allow refinement of the pixel size of the map
(or the unit cell dimensions - just an overall size scale factor), and
write out the altered map at the end of refinement.

Although we try to calibrate this as best as we are able at the time of
data collection, it is never perfect - for example, in one case I have
dealt with, our nominal pixel size out of the scope is 1.19 Å, but the
pixel size calibrated based on a crystal structure of a fragment of the
protein is 1.25 Å. This is not a huge difference, but it is sufficient I
think to have a substantial impact on refinement, particularly as regards
clash assessment and H-bond/sec struc restraints.

In cases where one does not have a solved crystal structure to use for
calibration, perhaps refining the pixel size in conjunction with the
geometry might be of some use?

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