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
Columbia, MO 65211
Phone: 573-884-1280
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Email: [email protected]<mailto:[email protected]>
http://faculty.missouri.edu/~tannerjj/tannergroup/tanner.html
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Office: Schlundt Annex 203A
On Dec 7, 2017, at 11:40 AM, Eleanor Dodson
<[email protected]<mailto:[email protected]>>
wrote:
Is that format correct?
Eleanor
On 7 December 2017 at 17:32, gerardo andres
<[email protected]<mailto:[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
