Nathaniel The atom names in the file I sent have the correct atom names as defined by the PDB for ACD. Naturally, the atom names in your PDB file and the restraints CIF file should match and given that you need the correct names to deposit your structure into the PDB, then I would recommend doing it sooner later than later. PHENIX has a number of tools to do this for you and we can talk off-line about them.
Nigel On Tue, Nov 30, 2010 at 8:16 AM, Nathaniel C. Gilbert <ngil...@lsu.edu> wrote: > I appreciate the input Paul and Nigel. The cif dictionary file you sent me > doesn't have matching restraint definitions for 53 atoms in the ACD file. I > opened the cif file you sent and extracted the SMILES code for ACD. Then I > ran it in phenix.elbow to have it generate a pdb of the ACD. Then i would use > the cif file you sent and import it into coot or phenix.refine, but it would > not match the cif and pdb. I can wait for the new nightly build to come out, > but I was wondering why this process wouldn't work. > > Paul, I'm not as familiar with the CCP4 suite. Refmac5 doesn't give me as > many new Fo-Fc peaks to build more model into as does phenix.refine even > though Rfree numbers are comparable. > -- 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
