Until version 4.0, the basic rendering options of Swiss-PdbViewer was a custom wireframe mode, without depth sorting. It was mainly to circumvent the computing/rendering limitations of computers at that time (1995). A second mode was introduced at the same time with Quickdraw3D, and then OpenGL. From version 4.1, the custom wireframe mode has been abandonned, and the default rendering is now done with OpenGL (enable the 'Display:Render in 3D' option, or use Pov-Ray.
To give you a better idea of the kind of images that were generated, have a look at a legacy page containing the same scene rendered with each renderer.
Open GL can generate very good images fairly quickly, and it is hardware accellerated on nowadays graphic cards.
You can modify some rendering parameters such as the bonds radius, the atom radius, the rendering smoothness, and so on... with the '3D Rendering' menu items of the Preferences menu.
Increasing the smoothness will only divide a sphere with more facets, which improves the look of your image, but also dramatically increases the rendering time. Therefore, a good idea is to set-up your scene with low resolution controls, and increase the rendering parameters only when everything is ok.
Note that at this point, you may also want to render in background while working in an other application. You should be able to work without even noticing that an image is calculated since I have assigned a very low priority to the rendering process.
Note that you don't necessarily need a high number of facets to describe a good-looking sphere, provided you enable the "use meshes" options.
If you want a better image quality than the default view or the OpenGL rendering can provide, you can export a POV scene description of the current view. You will get Ray-traced quality images (it means you can add reflections, refractions and transparencies and shadows to your views). Of course, Ray-tracing is quite expensive in computationnal time, so it would be a good idea to use the other modes to set-up the view.