[Chimera-users] scolor filament (geometry cylindrical)

Elaine Meng meng at cgl.ucsf.edu
Fri Jun 8 12:55:42 PDT 2018

Hello René,
Since the axis is only the direction, you probably also need to specify the center, say something like:

scolor #0 geometry cylindrical axis sel center sel cmap 5,gold:10,red:15,blue


Although it would make sense for the center to automatically fall on the axis, it is my understanding that you have to specify it explicitly.
I hope this helps,
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Jun 8, 2018, at 11:01 AM, René Frank <rawf2 at mrc-lmb.cam.ac.uk> wrote:
> Hello People,
> I would like to surface colour a filament within an EM map using cylindrical geometry (scolor geometry cylindrical). 
> However, the electron density of the filament does not lie perfectly on the x, y or z axis. Is there a way of using two marker points placed at each end (on the longitudinal axis) of the filament to define the orientation of the cylindrical geometry and scolor the filament accordingly?
> My attempts to do this whilst executing the following command didn’t seem to work:
> scolor #0 geometry cylindrical axis sel cmap 5,gold:10,red:15,blue
> Many thanks for any suggestions/help,

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