[Chimera-users] to color EM map

Elaine Meng meng at cgl.ucsf.edu
Wed Jun 3 09:00:09 PDT 2015


Hi Smith,
Well, you could first color the atomic structure (protein) subunits the four colors, then select the atoms, then use Color Zone (in the Volume Viewer menu: Tools, or the main Chimera menu under Tools…Volume) to color the EM isosurface to match the nearby atoms.  The same thing can be done with the zone option of command “scolor”.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/colorzone/colorzone.html>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/scolor.html#zone>

Another way would be to try to segment the map into the four parts and then color the segmentation surfaces as desired, but since you already fit the structure the first way is probably easier.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/segger/segment.html>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Jun 3, 2015, at 1:45 AM, Smith Liu <smith_liu123 at 163.com> wrote:

> Dear All,
> Suppose I have an EM map for a protein complex of 4 subunits. I have fitted them in chimera. Will you please tell me how to give each part of the map a different color based on the subunits? For example, for subunit A, B,C, D part of the EM map, how to color the map accordingly in blue, red, yellow and purple?
> Smith




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