Phenix should also work nicely: phenix.elbow inputfile.smi --opt
Inputfile can be one of many different file formats (ie: smiles, sdf, pdb, etc.) The --opt flag runs an AM1 geometry optimization that usually produces superior restraints as compared to running without it. Cheers, Jim On Tue, Jun 23, 2015, 10:27 AM Tim Gruene <t...@shelx.uni-ac.gwdg.de> wrote: > Dear Sean Fanning, > > you could try the grade server (grade.globalphasing.org). I don't know > its size limit. It recognizes the ligand YJD from 2YJD and produces > restraints for it. > > In your case you may need to generate the mol2 file or SMILES string. I > think openbabel could generate the mol2 file from the PDB file, I > haven't tried. > > Best, > Tim > > On 06/23/2015 05:17 PM, Sean Fanning wrote: > > Dear CCP4 Users, > > I have a structure containing a synthetic alpha helical peptide (similar > to > > the one found in PDB: 2YJD) for which I need to generate the restraints > > (.cif). I have the PDB coordinates for the peptide but need the .cif for > > refinement/fitting. Does anyone have any suggestions on how I could > > generate this file? > > Thank you very much, > > Sean Fanning > > > > -- > -- > Dr Tim Gruene > Institut fuer anorganische Chemie > Tammannstr. 4 > D-37077 Goettingen > phone: +49 (0)551 39 22149 > > GPG Key ID = A46BEE1A > > >
