Hi Reza, If I understand correctly, you are coloring the reconstruction surface by a second map that has the local resolution values. At least from some experiments I just now tried, in ChimeraX if you already have clipping before you use the “color” command, the planar surface where the clipping occurs is also colored automatically. You can move the clipping plane after coloring as long as it was already clipping when the coloring command was used. If you recolor to change what values go with what colors, make sure the clipping is in effect beforehand. I tried it for both the “Side View” near/far clipping and the adjustable-angle front/back clipping that can be shown with the “clip” command. I tried both “color sample” to color by map value and “color radial”. <http://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#map> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

On Jun 15, 2018, at 2:51 PM, Reza Khayat <rkhayat@ccny.cuny.edu> wrote:

Hi, I’m coloring a cryo-EM image reconstruction based on its local resolution. Thus, the image reconstruction will contain multiple colors. Is it possible to color the clipping plane the same as the underlying image reconstruction? Thanks. Best wishes, Reza