[Chimera-users] how to set initial threshold when opening a mrc

[Elaine Meng]

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 at 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