Thanks Eleanor, John and Nigel for your tips. Actually it seems to be a problem
of geometry restraints.
Nigel, let me edit the .def file as John recommended and then I'll contact you.
Best regards
Gerardo Andrés Libreros
Laboratório de Biologia Estrutural Aplicada
Universidade de São Paulo
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
---
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
Is that format correct?
Eleanor
On 7 December 2017 at 17:32, gerardo andres <
130afa955101-dmarc-requ...@jiscmail.ac.uk> 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
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
how to make covalent
bond between ligand and protein residue by using CCp4 package
On 14/07/10 12:56, Vandana Kukshal wrote:
how to make covalent bond between ligand and protein residue by using
CCp4 package
JLigand
http://www.ysbl.york.ac.uk/~pyoung/JLigand/JLigand.html
p.s. Don't Reply if you are not following the same thread - doing so
causes confusion to threaded
Better link with nice tutorial from Andrey is:
www.ysbl.york.ac.uk/mxstat/
In the JLigand section there are some tutorials from Andrey to
demonstrate how covalent links can be generated and used.
Garib
On 14 Jul 2010, at 14:35, Paul Emsley wrote:
On 14/07/10 12:56, Vandana Kukshal wrote:
