[phenixbb] Mask used for map-to-model FSC

Pavel Afonine pafonine at lbl.gov
Mon Oct 19 10:12:42 PDT 2020

Hi Yang,

map-to-model FCS uses the mask that is calculated as described here:


The parameters of the mask calculation have set physical meaning and 
altering them does not seem to be a good idea. This is the reason why 
they are not exposed to users.

Also, you can extract a box with map and model around the region you 
have modeled and get statistics for it.


On 10/19/20 07:50, Yang Shi wrote:
> Hi all,
> Does anyone happen to know how to control the tightness of a mask for
> map-to-model FSC calculation? I have tried the "atom radius" in
> Map/Model CC tab of "Comprehensive validation (cryo-EM)", but it was
> not working for me.
> The reason I am asking this question is that I can only model a small
> region in the cryoEM map, the rest is unknown to me.  Then the CC in
> low-frequency was  0.4-0.6 in the FSC curve, while the overall masked
> cc was 0.85. I would like to find an easy way to make the FSC curve
> look better.
> Any suggestions would be appreciated!
> Best wishes,
> Yang
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