How to make a script that is as fast as molviewer to show 3D all atom structures using surf in Matlab?

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Hello, I am writing my own GUI for 3D molecular viewing and so far it has been working great. I use Sphere and Surf to plot every atom and I use cameratoolbar to be able to zoom in and orbit pretty well. This works very very well up to 1000 atoms or so. When I try to open larger structures, Matlab is having a hard time moving the structure around. The same structures can easily be opened with molviewer and moved around with no effort. I have tried everything I can to speed up the surf plot. I am using OpenGL and I have taken off the edges of the spheres and even reduced the number of polygons per sphere but there is no comparison between molviewer and surf/figure. Is there a way to make it faster? Or what makes molviewer so fast in comparisson? Thanks

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