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

[Randy John Read]

Yes, that’s the right option!

It doesn’t allow you to specify a starting scale value, which defaults to 1. That might be a useful option for cases where the initial docking fails because the scale is too far from the correct value. My impression is that this used to be a bigger problem in the past, but that microscopes are generally calibrated reasonably well these days.

Best wishes,

Randy

> On 13 Nov 2023, at 15:45, Oliver Clarke <olibclarke at gmail.com> wrote:
>
> 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
>>>
>>
>

-----
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