Thanks for all of your help. I came out with dome nice figures


On Fri, May 30, 2014 at 11:16 AM, Thomas Holder <thomas.holder@schrodinger.com> wrote:
On 30 May 2014, at 14:05, Takanori Nakane <tn290@cam.ac.uk> wrote:
> However, showing intact spheres above the clip plane for the surface
> can be difficult. I am not sure if it is possible to set different
> clipping planes to each object.

no this is not possible, but has been requested many times. Maybe that would be a nice PyMOL Open-Source Fellowship project?

--
Thomas Holder
PyMOL Developer
Schrödinger, Inc.


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