[phenixbb] Automated estimation of voxel size using reference pixel size in phenix?

[Randy John Read]

Hi Oli,

The relatively new EM_placement docking tool (phenix.voyager.em_placement) has an option to refine the voxel size as part of the likelihood-based rigid-body refinement step, and it seems to work pretty well. At the moment, this has to be done as part of a docking search, but I’m planning to implement a rigid-body refinement option for previously-placed models, which might be useful in some circumstances.

Best wishes,

Randy

> On 13 Nov 2023, at 13:42, Oliver Clarke <olibclarke at gmail.com> wrote:
>
> Hi,
>
> In cryoEM, the pixel size is often not known with certainty, and we need to calibrate it by measuring the real space correlation of a reference crystal structure of a component at different nominal pixel sizes.
>
> Currently we do this manually, using `fitmap` in UCSF Chimera, but given the sophisticated set of tools in Phenix for fitting atomic models and analyzing real space correlations, I was wondering if a tool in Phenix already exists to do this, or whether there would be any interest in adding such a tool at some point?
>
> Cheers
> Oli
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-----
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: rjr27 at cam.ac.uk
Cambridge CB2 0XY, U.K.                              www-structmed.cimr.cam.ac.uk