Hi Xiaoyan, Tom Goddard had provided some useful hints when I asked a similar question last month. This has worked really well, though does require fitting a set of coordinates into each map that you want to compare. After following the suggestion set the focus always to all (or some element) of the aligned model for a consistent view across a set of maps. see http://www.cgl.ucsf.edu/pipermail/chimera-users/2016-October/012767.html