I thinkI have found a way to resolve this issue, although it's definitely a software bug that needs to be fixed by the Vesta team.
On my good computer, a 4 years old Surface Laptop 2 with the latest windows 10 updates and OpenGL 4.6.0, I also get these partial spheres when exporting vector images. Furthermore, the colour of atoms and wave function isosurfaces in my output files have significant dark shades as compared to how they look in the raster exports.
The problem seems to be with OpenGL or Intel display driver for windows machines; the newer they are, the more significant the problem.
In contrast to my Surface, on my 10 years old Lenovo X220t running Windows 10 and OpenGL 3.2.0, I was able to export vector images that look like
kkmwo...@gmail.com's vector image. No lighting effect but at least the atoms are complete and the dark shades are not present.
When I disable the intel display driver from device manager, so that the emergency/windows-built-in display driver kicks in, and the OpenGL version becomes 1.1.0, I was able to get my exported vector images to look like
kkmwo...@gmail.com's raster image, with the lighting effect present.
On my wife's iMac Late 2015, all I can manage is what I get with OpenGL 3.2.0; not sure how to solve this there though.
I'm not sure if this method will work for cases other than mine, but I hope it will help steer the discussion towards what seems to be the right direction and hopefully lead to a bug fix from the vesta team.
Regards