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, [email protected] wrote:

phenix.model_vs_map crashes with a Python exception.

-----Original Message----- From: "Takanori Nakane" Sent: Thursday, January 18, 2018 10:44am To: [email protected] Cc: [email protected] 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 ? _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]

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, [email protected] wrote:

I appreciate if somebody would answer my original question about FSC in the cryo-EM refinement.

-----Original Message----- From: "Pavel Afonine" Sent: Thursday, January 18, 2018 10:06pm To: [email protected], "Takanori Nakane" Cc: [email protected] 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, [email protected] wrote:

...

phenix.model_vs_map crashes with a Python exception.

-----Original Message----- From: "Takanori Nakane" Sent: Thursday, January 18, 2018 10:44am To: [email protected] Cc: [email protected] 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 ? _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]