[Chimera-users] spheres chimera

Elaine Meng meng at cgl.ucsf.edu
Wed Mar 18 15:39:45 PDT 2020

Hi Giulia,
(For next time), please send questions to chimera-users at cgl.ucsf.edu instead of me individually. I CC'd that address here.

There is no option like that for the interactive spheres display, sorry. It is only available for molecular surfaces.

However, for a non-movable display that is like that, you can try using the "conic" command for rendering to show spheres as solid when they are clipped.  You have to first move the structure, then use conic; for example, a Chimera command that works for me on a Mac is:

conic -o ~/Desktop/myfile.png -s

... which will then draw a non-movable image of the current position and create the specified output file.  There are other options to this command, see these pages for details:

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

> On Mar 18, 2020, at 3:03 PM, Galotto, Giulia <ggalotto at wpi.edu> wrote:
> Hi, 
> I am writing to ask a question about a chimera representation. I am representing the protein as VDW spheres, but I would like the spheres to be filled, not hollow. This is because I am going to do per model clipping and slice the protein in two. When I slice it I see the empty spheres, and I would like the see them filled instead. 
> Is there a way to do this? 
> Thank you so much!
> Best, 
> Giulia Galotto
> Worcester Polytechnic Institute

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