Hello,

Is it possible to generate a map to show local agreement between cryo-EM map and the model generated using the same map? If I am not wrong, the supplementary figure S5 had accomplished the job (using Chimera), but I don't understand how to generate a similar figure for my project. Is it possible to do with phenix?

http://emboj.embopress.org/content/28/6/755

have a look at "Phenix tool to compute a difference map for cryo-EM" article here:

http://phenix-online.org/newsletter/CCN_2017_01.pdf#page=8

Is that what you are looking for?

We can discuss this more, if needed.

Pavel