[phenixbb] Re: Refine pixel size for EM map?

Hi Oli, I think this has come up before, but as far as I know the only current method to refine pixel size in Phenix is by using the refine_cell_scale option in phenix.voyager.em_placement. This requires you to have a placed (or at least dockable) model that is on the right scale (i.e. hasn’t been refined against the map of interest). These days, the high-confidence subset of an AlphaFold model would probably be sufficient to give a good correction for the magnification factor. In tests I’ve done, it has a pretty high convergence radius. What you probably want is something that will correct a model that may already have been refined against the map of interest. This is a feature that Pavel Afonine and I have discussed before, and I think Pavel did at least some preliminary experiments in phenix.real_space_refine. Like you, I think it should be possible to use the geometric restraints to get the refinement engine to correct the pixel size to make it compatible with good geometry. However, this may not be trivial to get to work robustly and might require things like taking account of second derivative terms relating the positional and pixel size (or magnification factor) parameters. Pavel might have more to say on this. Best wishes, Randy

On 3 Jun 2025, at 08:19, Oliver Clarke wrote:

Hi,

I remember asking about this some time ago, but I am not sure if it was ever implemented.

Is there a way to refine just pixel size for an EM map in phenix.real_space refine (or another phenix utility)? Even just automatically rigid-body fitting a crystal structure and calculating the pixel size with max correlation would be handy. We do this at the moment using Chimera/ChimeraX, but an automated way to do it in phenix would be handy.

In the absence of a crystal structure, I wonder if directly refining pixel size during real space refinement would be possible/reasonable at higher resolution (<2Å)?

Cheers Oli _______________________________________________ phenixbb mailing list -- [email protected] To unsubscribe send an email to [email protected] Unsubscribe: phenixbb-leave@%(host_name)s

----- Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: +44 1223 336500 The Keith Peters Building Hills Road E-mail: [email protected] Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk