[Chimera-users] split map based on resolution or surface color

Elaine Meng meng at cgl.ucsf.edu
Mon Jun 3 09:34:56 PDT 2019

Hi Shu-hao,
One idea is to show the resolution map as isosurfaces, and then use the resolution isosurfaces to mask the density map.

The resolution map used for coloring can be shown as surfaces using Volume Viewer or the “volume” command.  Then, you could adjust the isosurface level to the resolution value you want either by moving the vertical bar on the histogram in the Volume Viewer dialog, or with the “level” option of the volume command.  For example, to show the resolution map (let’s say it is model #3) as pink isosurfaces at resolution 4.5, use command:

volume #3 show style surface level 4.5 color pink


Then, you could use the “mask” command to use these surfaces in combination with the original density map model to make new map models with zeroes inside or outside the surfaces.  For example, if the original density map is #2, command:

mask #2 #3 [… other options …]

see <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mask.html>

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

> On Jun 2, 2019, at 1:06 PM, Shu-Hao Liou <shu-hao.liou at einstein.yu.edu> wrote:
> Hi Chimera User,
>     Is that possible to split a density map base on its resolution? That means I have a surface color file contained all local resolution distribution through a density map.
> Best,
> Shu-hao

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