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 <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/scolor.html#cylindrical> 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 ----- 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@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,