[phenixbb] ligand refinement
Pavel Afonine
PAfonine at lbl.gov
Thu Feb 21 18:49:16 PST 2008
Hi Christine,
I think you need to do this (Ralf please correct me if I'm wrong):
1) Run phenix.elbow to create a cif file for your ligand (if you don't
have one):
% phenix.elbow model.pdb --do-all
elbow will go though your pdb file and create a dictionary file for
whatever is not present in the standard library. One of the output cif
files with "all" (xxx_all.cif) in its name is the file that you need to use.
2) Now you need to tell phenix.refine that your ligand is covalently
bonded to the macromolecule:
% phenix.refine model.pdb data.mtz xxx_all.cif may_params.par
where may_params.par defines the bond and contains these lines, for example:
refinement.geometry_restraints.edits {
bond {
action = *add
atom_selection_1 = chain X and resname HIS and resid 117 and name NE2
atom_selection_2 = resname LIG and resid 98 and name C
distance_ideal = 1.45
sigma = 0.02
}
}
You can also define an angle. Look "Definition of custom bonds and
angles" in phenix.refine manual for more information:
http://www.phenix-online.org/documentation/refinement.htm
Please let us know if you have any questions.
Pavel.
On 2/21/2008 5:52 PM, Christine Gee wrote:
> Dear Phenix developers
> I have a covalently bound ligand in my structure and I would like to
> use phenix to refine the structure. The ligand is bound to the
> sulfur of a cysteine. What is the best method for defining the
> ligand. Should I generate a cif file for the whole amino acid and
> the ligand, or can I make one for just the ligand and add in some
> restraint somewhere which tells phenix to make a bond between the
> ligand atom and a nearby sulfur in a cysteine. If I generate a cif
> file with the whole amino acid and ligand, I assume I will I have to
> follow some convention in atom naming so that the main chain bonds
> and angles will form and refine OK?
> Regards
> Christine
>
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