You can also do it using ReadySet! which makes all the calls to eLBOW. phenix.ready_set 2yjd.pdb
phenix.geometry_minimization 2yjd.updated.pdb 2yjd.link.edits 2yjd.ligands.cif Cheers Nigel --- 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 On Tue, Jun 23, 2015 at 11:13 AM, Jim Fairman <fairman....@gmail.com> wrote: > 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 >> >> >>
