Gerado John is correct that you can modify the restraints model to include a covalent bond. Also in more recent version of Phenix, if the input geometry is approximately correct, the bond can be automatically linked.
If you send me the input file, I'll take a closer look. Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : [email protected] Fax : 510-486-5909 Web : CCI.LBL.gov On Thu, Dec 7, 2017 at 9:51 AM, Tanner, John J. <[email protected]> wrote: > You can add a covalent bond by modifying this part of the PHENIX .def file > via the gui: > > geometry_restraints.edits { > excessive_bond_distance_limit = 10 > bond { > action = *add delete change > atom_selection_1 = None > atom_selection_2 = None > symmetry_operation = None > distance_ideal = None > sigma = None > slack = None > } > > John J. Tanner > Professor of Biochemistry and Chemistry > Chair, Biochemistry Department Graduate Admissions Committee > Department of Biochemistry > University of Missouri-Columbia > 117 Schweitzer Hall > 503 S College Avenue > <https://maps.google.com/?q=503+S+College+Avenue+%0D+Columbia,+MO+65211&entry=gmail&source=g> > Columbia, MO 65211 > Phone: 573-884-1280 <(573)%20884-1280> > Fax: 573-882-5635 <(573)%20882-5635> > Email: [email protected] > http://faculty.missouri.edu/~tannerjj/tannergroup/tanner.html > Lab: Schlundt Annex rooms 3,6,9, 203B, 203C > Office: Schlundt Annex 203A > > On Dec 7, 2017, at 11:40 AM, Eleanor Dodson <0000176a9d5ebad7-dmarc- > [email protected]> wrote: > > Is that format correct? > Eleanor > > On 7 December 2017 at 17:32, gerardo andres <0000130afa955101-dmarc- > [email protected]> wrote: > >> Hi everyone. I´m trying to make a covalent bond between a cystein residue >> of a protein and its ligand, but always that I do the refinement by Phenix, >> the ligand is placed outside of its electronic density. I edited the PDB >> file like this: >> LINK SG CYS A 215 C02 LIG C 1 , but this is >> not working. Someone has some idea to address this problem? >> >> Thanks, >> >> Gerardo >> > > >
