[chimerax-users] coloring a map by local resolution

[Elaine Meng]

> On Apr 13, 2021, at 4:17 PM, William.H.McCOy.IV at cgl.ucsf.edu wrote:
> 
> I can't get the following from relion 3.1 to work: The output is a file called LocalRes/polished/relion_locres.mrc that may be used in UCSF chimera to color the Postprocess/polished/postprocess.mrc map according to local resolution.  # This is done using Tools -> Volume data -> Surface color, and then select by volume data value and browse to the resmap file.

Dear William,
We have a mailing list that is recommended for asking questions, chimerax-users at cgl.ucsf.edu (CC'd on this message).
<https://www.rbvi.ucsf.edu/chimerax/docs/contact.html>

Coloring by local resolution is a fairly common task and I don't know of any reason it wouldn't work.  It is not clear what you mean by not working.  If you are more specific with your question, we can give more targeted answers.

First you have to open both mrc files in ChimeraX.  Say you opened the map that you want to show as a surface as model #1 and the map with locres values for coloring as model #2.  Then in Volume Viewer, you can adjust the isosurface level of map #1 and hide the isosurface of map #2 (or you can hide it using Model Panel, same thing).   In Surface Color you would choose the (already open) models: the surface to color is model #1, you want to color it by "volume data value," and the map with values to use for coloring is #2.  You can see the help for the tool by clicking its Help button, or view the copy on our website here:

<https://rbvi.ucsf.edu/chimerax/docs/user/tools/surfacecolor.html>

I hope this helps,
Elaine
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Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco