Hi, > I want to align two structures (worked fine in pymol) then generate symmetry related molecules for each to compare crystal packing contacts (did not). Both structures are for same dna each with different ligand. One structure has one molecules/AU (generates symmetry fine). The other 2/AU (does not work; messed up symmetry whereby half of original is superimposed by half of symmetry related). The latter generates symmetry fine in coot. Problem with coot: can't align. Any ideas?
If you align before generating symmetry-mates in your 2/AU structure, then you may be getting incorrect generated molecules, because the coordinates have changed but your symmetry operators have not (this is probably something you're already aware of, and are avoiding, but it could be an issue). On the other hand, you could have problems if you generate symmetry-mates before alignment, because you presumably only want to align the original models, not the packing mates (which again, you're probably aware of). One way to work around this would be to get the transformation matrix for the alignment of the original models, generate unaligned symmetry-mates in coot (or pdbset, or another program that doesn't give you problems...I havne't had any problems w\ symexp in pymol, but you may be using a different spacegroup), and apply the alignment matrix to the symmetry-mates. Good luck, Pete Pete Meyer Fu Lab BMCB grad student Cornell University
