I can't answer your general questions. There's too much stuff in there. However, this caught my eye:
[helper release];
[renderer.helper release];
PDBHelper *aHelper = [[PDBHelper alloc] initWithContentsOfFile:pdbToLoad];
helper = [aHelper retain];
renderer.helper = [aHelper retain];
[aHelper release];
I think this stuff possibly leaks. It doesn't make sense anyway.
If renderer.helper is a retain or copy property, do not release it. It already has code that releases old values when it is assigned new values. Also do not retain objects you assign to it.
You have alloc'd aHelper, so there's no need to retain it again. The above code should be rewritten something like:
[helper release];
helper = [[PDBHelper alloc] initWithContentsOfFile:pdbToLoad];
renderer.helper = helper;
Also, I think your helix malloced arrays should probably be instance variables. As things stand, if you have more than one ES1Renderer, they are sharing those variables.
JeremyP
2010-07-29 08:16:40