Dear Phenix people, In "New tools for the analysis and validation of cryo-EM maps and atomic models” (ActaD 2018), it is reported that "map sharpening can affect d99 (Fig. 9g) but it is rather insensitive to masking (Fig. 9h).” I have a case where d99 increases a lot with masking, as shown in the screenshot below (from Mtriage). On the other hand, FSC decreases. What does this mean? Can it be attributed to the fact that there is a strong scatterer in the molecule (a heavy atom) that strongly influences the intensity of the map? Are there other possible explanations (preferential orientation for example)? What is the best way to handle such maps? Thank you for the attention. Best, Roberto.  Roberto Battistutta Associate Professor Department of Chemical Sciences University of Padua via Marzolo 1, 35131 Padova - ITALY tel. +39.049.827.5262 fax. +39.049.827.5829 [email protected]
