Nathaniel I made a small mod to eLBOW (which will be available in the next nightly build) that allows you to get an all cis ACD from a SMILES string. I have attached the result. Note that the name of the file has ZZZZ for the four cis (zusammen) configurations. As Paul suggested, the torsion value is 0. and the period is 1.
Nigel On Mon, Nov 29, 2010 at 9:29 AM, Paul Emsley <paul.ems...@bioch.ox.ac.uk> wrote: > 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. > -- Nigel W. Moriarty Building 64R0246B, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : nwmoria...@lbl.gov Fax : 510-486-5909 Web : CCI.LBL.gov
acd_ZZZZ.cif
Description: Binary data
