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On 29/11/10 16:17, Nathaniel C. Gilbert wrote: > I have arachidonic acid soaked into my crystal structure and want to model it. The phenix.refine is allowing my cis double bonds to distort to a gauche or trans form. Is it the cif file or the refinement restraints in the program that I need to correct. > It is not entirely clear to me what you are asking - I'd say that "the cif file" and "the refinement restraints" are pretty much synonymous. I suggest that you clear up (by using idealization and checking the starting conformer) whether the "bad" resulting conformation is due the the restraints or the density. Incidentally arachidonic acid is in the PDB (and CCP4's copy of SBase). I took that idealized structure and fed it into Prodrg, the resulting torsion restraints look good to me. If you want to brute-force/hand-edit the restraints, make sure that the torsions across the double bonds (C5-C6, C8-C9, C11-C12 and C14-C15) have a value_angle of 0 and a period of 1. (The torsions from the (rather old) version of libcheck I have here (generated from a SMILES string) were not great and seem to be consistent with your question.) Paul.