On Thu, Nov 6, 2014 at 5:20 PM, Oliver Clarke <[email protected]> wrote:
> I wonder if a solution might be to create new residues containing alkyl > chains of various lengths, named something like U01, U02, U(n), where N is > the length of the alkyl chain that fits the density. Sort of similar to the > way one might leave UNK residues in a peptide of unidentified sequence. Or > maybe there is a better way of doing this? Would appreciate any suggestions. > This would be "UNL", which is a catch-all for unidentified ligands. The best example I can think of is PDB ID 3arc, which is a relatively high-resolution structure of Photosystem II containing a number of partially ordered mystery lipids. This is a bit of a mess because they're a mix of unbranched alkyl chains and branched esters, so the chemistry is not internally consistent, but at least the scattering types are defined and the UNL designation makes the ambiguous identity explicit. I think this is the generally accepted convention. I wouldn't worry too much about nomenclature; you can just generate restraints for a generic ligand of this type with as many carbon atoms as you need - for instance, using a SMILES string like this: CCCCCCCCCCCCCCCCCCCCCCCCCCC and hopefully that will be sufficient for all of the fragments in your structure. -Nat
