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

Edward A. Berry BerryE at upstate.edu
Mon Feb 8 07:46:11 PST 2016

I think the option to refine cell would be useful for x-ray structures as well.

One of the checks in whatcheck is (or at least was) to suggest corrections to cell
based on bond length deviations along the direction of each axis.

Unfortunately it seems the ideal bond lengths in whatcheck were slightly
different from those in CNS which we used for refinement, so after refining
with the corrected cell and running whatcheck again, it would suggest
another correction of about the same magnitude in the same direction.
Cycling several times we ended up with quite different cell parameters
with relatively little change in R (I didn't look at bond deviations,
and this was a low-resolution, high R structure).

Of course the camera length and xray wvelength should be known
to high precision, in which case this would be just a fudge factor,
but with only 3-6 parameters it shouldn't affect the refinement much.
After all it is fairly standard during spot integration to refine
camera length (at least for HKL users), and if that is in doubt
then so are the cell parameters.


On 02/08/2016 04:28 AM, Oliver Clarke wrote:
> Hello,
> 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?
> Cheers,
> Oli
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