Hi Rakesh,   I don't understand what you mean by "length normalized by masking".  Chimera can compute cross-correlation using the Fit in Map panel.  If you are fitting an atomic model to the map it needs to simulate a map from the atomic model  since correlation is between two maps.  You do that using the "Use map simulated from atoms" option in the Fit in Map panel Options pane.     Tom On 12/6/2021 4:00 PM, Rakesh Ramachandran wrote:

Hi Tom,    I am using Chimera Fit in Map for EM fitting. Though it does fit well, I want to calculate a cross correlation score based on the model map size, that is the cross correlation should be length normalized by masking the rest of the map.

-- Regards Rakesh Ramachandran