Hi Pavel, Many thanks for your reply. A masked map helps. Best wishes, Yang

On Oct 19, 2020, at 18:12, Pavel Afonine wrote:

Hi Yang,

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

http://scripts.iucr.org/cgi-bin/paper?S2059798318009324

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.

Pavel

...

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