[phenixbb] Fourier_shell_correlation_(FSC)_in_cryo-EM_refinement Takanori Nakane

[Pavel Afonine]

Oh I'm sorry, I thought Takanori Nakane answered your question!
Ok, here is my version of the answer:

> But I could not find FSC (e.g. FSC average) quality metrics in the refinement log.

I afraid I don't know what "FSC average" is. This perhaps explains why 
we don't calculate it (just yet!).

You can calculate map-model FSC, as well as several others FSC using 
phenix.mtriage that is available in the GUI or CL, or using 
phenix.map_model_cc.

All the best,
Pavel

P.S.: Still, I'm happy to help you with the issue you mentioned in your 
previous email if you send us relevant information!


On 1/18/18 19:15, oleg at quantumbioinc.com wrote:
> I appreciate if somebody would answer my original question about FSC in the cryo-EM refinement.
>
> -----Original Message-----
> From: "Pavel Afonine" <pafonine at lbl.gov>
> Sent: Thursday, January 18, 2018 10:06pm
> To: oleg at quantumbioinc.com, "Takanori Nakane" <tnakane at mrc-lmb.cam.ac.uk>
> Cc: phenixbb at phenix-online.org
> Subject: Re: [phenixbb] Fourier_shell_correlation_(FSC)_in_cryo-EM_refinement
>
> This is good to know, thank you. It would be particularly helpful if you
> supply the error message and provide files that lead to the failure.
>
> All the best,
> Pavel
>
> On 1/18/18 19:01, oleg at quantumbioinc.com wrote:
>> phenix.model_vs_map crashes with a Python exception.
>>
>>
>> -----Original Message-----
>> From: "Takanori Nakane" <tnakane at mrc-lmb.cam.ac.uk>
>> Sent: Thursday, January 18, 2018 10:44am
>> To: oleg at quantumbioinc.com
>> Cc: phenixbb at phenix-online.org
>> Subject: Re: [phenixbb] Fourier_shell_correlation_(FSC)_in_cryo-EM_refinement
>>
>> Hi Oleg,
>>
>> Do you mean FSC between a model and a map?
>> You can calculate it with phenix.model_vs_map.
>>
>> Best regards,
>>
>> Takanori Nakane
>>
>>> I started to do some refinements of cryo-EM structures. But I could not
>>> find FSC (e.g. FSC average) quality metrics in the refinement log. Is it
>>> because of the real space refinement methodology or some features need
>> to
>>> be activated? Please advise
>>> Thanks
>>> Oleg ?
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>>
>>
>>
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>