Hi Shuo, The threshold is not in the data file, it is only a display setting. To keep the threshold that you set, you would instead save and restore a ChimeraX session. There is a "save" command option as to whether the map should be saved in the session file or kept as a separate file, and you could do it either way, but the threshold information is in the session, not the map. <http://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#session> If you don't want to save a session file, the alternative is to write down the threshold level and either restore it manually in the Volume Viewer or with a command (which could be made into an alias if you have to repeat it often), e.g. volume #1 level 0.312 I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

On Sep 3, 2020, at 9:00 PM, Shuo <leyannihao@163.com> wrote:

Hi,

When I open an .mrc map, Chimera will show the map with an initial threshold. But the initial threshold is not so good, so I changed it to high value with the scale bar in Volume Viewer. I want to save the map, so that when I open the map again, the initial threshold will be the high value, not the lower one. How could I do this?

Best, Shuo