Ray trace mode 1 (normal colour with a black outline) is great for creating images for publication. However, when you use this mode with a mesh representing electron density, it looks really bad - this mode puts a black outline around every line of electron density, making them thick, black lines about 3x the needed thickness.
You can get around this by setting it to ray trace mode 0 (no black outlines) but the cartoon and stick portions look better with the outline. It would be great if we could put the black outline around everything except meshes.
The outlining algorithm is pixel & depth-based so there's no easy way of separating out different types of geometry. Image compositing is probably the only way one could get a result such as this, so perhaps PyMOL should have a built-in compositing capability?
MAIIAIHARQIFDSRGNPTVEVDLKTAKGLFRAAVPSGASTGVHEALELRDTNSKAYMCKGVLTAVSNVNNIIAPALLKKQIPVTNQSEVDQFMIELDGKENKGNLGANAILGVSLAVCKAGAAELNLPLYRYIAKLAGHKDVIMPVPAFNVINGGSHAGNKLAMQEFMILPTGASSFTEAMQMGSEVYHNLKAVIKREFGLDACNVGDEGGFAPNIQDNMKGLQLLEEAIKIAGYTGKV
EIGMDCAASEYYKKGKYDLDFKNPQSAESHWLSPDEMANVYKEMIQKYPIVSIEDPFDQDDWDAWPKLTASTNIQIVGDDLTVTNPKRIEKAIKVKACNCLLLKVNQIGSITESIEACKMAQKAGWGVMVSHRSGETEDNFIADLVVGLCTGQIKTGAPCRSERLAKYNQLLRIEEELGSTAKYAGKHFRHPQI