For quite some time now, we have ourselves experienced and continued to receive complaints regarding graphics artifacts and other glitches with ATI/AMD Radeon “HD” graphics chips on multiple platforms. Though we haven’t had time to investigate everything to our satisfaction, it is worth noting that such issues are conspicuously absent from those using recent nVidia and Intel graphics chips, and that they also do not occur with older ATI chips -- only the newer “HD” –branded models.
Therefore, if you are given a choice with a new purchase today, we strongly recommend going with nVidia-based graphics chips for running PyMOL. Intel chips work fine too though they aren’t typically as fast.
Just to be clear, we don’t know for certain yet whether the fault lies with PyMOL, with the OpenGL drivers, or with the ATI graphics chips themselves. but if you simply buy nVidia, then you can entirely avoid having to deal with AMD/ATI-specific OpenGL problems. Eventually these problems will likely be worked out – the chips are just glitchy, not DOA – but there is a lot to be said for deliberately avoiding problematic scenarios altogether.