[phenixbb] Validation_cryoEM Calculation the FSC model-map

Marta Martinez mmmtnez at cnb.csic.es
Wed Feb 5 02:39:19 PST 2020

Dear all,

we are wondering how the mask and unmasked values of the FSC model-map  
have been computed and how the mask is defined when the phenix tool  
phenix.validation_cryoem ("Comprenhensive Validation (cryo-EM)") is  

The motivation of this question comes from the results that we get  
when we have big maps (e.g. some viruses) and the atomic structure is  
determined only for the asymmetric subunit. We usually compute the  
validation considering both the whole map, and a fraction of the map  
that only contains the atomic structure of the asymmetric subunit (the  
atomic model is the same in both cases, the asymmetric subunit). We  
would expect the same results, as it happens for the validation  
statistics, but the FSC model-map values are different, especially  
when we talk about masked values. Recently we have checked that we  
have the same kind of results when we use small maps, so it doesn't  
seem to be due to the size of the map.

Can you kindly explain the reason of these results and what we should  
expect in general. Is there any restriction when a fraction of the  
whole volume is selected?

Thank you very much in advance.



Marta Martinez Gonzalez

Biocomputing Unit (Lab B13)
National Center for Biotechnology-CSIC
Darwin, 3. Campus de la Universidad Autonoma de Madrid
28049 Madrid. Spain
Tel:+34 915854510 Fax:+34 913720112
E-mail: mmmtnez at cnb.csic.es

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