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

[Oliver Clarke]

Is that the option "refine_cell_scale"? Or is there another option I am overlooking

Cheers
Oli

> On Nov 13, 2023, at 10:41 AM, Oliver Clarke <olibclarke at gmail.com> wrote:
> 
> Oh wonderful, that is exactly what I was looking for, I will test it now! Thanks Randy!
> 
> Cheers
> Oli
> 
>> On Nov 13, 2023, at 10:30 AM, Randy John Read <rjr27 at cam.ac.uk> wrote:
>> 
>> 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
>> 
>