[phenixbb] Automated estimation of voxel size using reference pixel size in phenix?
Oliver Clarke
olibclarke at gmail.com
Mon Nov 13 07:41:59 PST 2023
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
>
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