Dear Chimera Users,

I am new to Chimera and cryoEM. For my project, I would like to create a single map (which will be used as a mask) for six 3D classes. To achieve that, I have aligned all my six maps using Chimera 'Fit in Map' and used vop maximum (vop maximum #0,#1,#2,#3,#4,#5) to generate a new map that is supposed to 'cover' all the other maps.

My question is, when I look at the vop output map (green map in the file attachment), why do we still see some densities from input maps (salmon color) outside the vop output map? I have also adjusted the contour level of all map to 0.04 (volume all step 1 level 0.04). I hope someone could help me to clarify my understanding of vop maximum.

Thank you for your help.

Best wishes,

Reyhan