[phenixbb] Automated estimation of voxel size using reference pixel size in phenix?
Oliver Clarke
olibclarke at gmail.com
Mon Nov 13 07:45:15 PST 2023
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
>>> _______________________________________________
>>> phenixbb mailing list
>>> phenixbb at phenix-online.org
>>> http://phenix-online.org/mailman/listinfo/phenixbb
>>> Unsubscribe: phenixbb-leave at phenix-online.org
>>
>> -----
>> 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
>>
>
More information about the phenixbb
mailing list