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

Yang Shi yshi.cam at gmail.com
Mon Oct 19 17:20:24 PDT 2020

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

> On Oct 19, 2020, at 18:12, Pavel Afonine <pafonine at lbl.gov> 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
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