An alternative way of doing this..

You can make a file with a content like this

refinement {
geometry_restraints.edits {
    bond {
      atom_selection_1 = chain A and resseq 123 and name CA
      atom_selection_2 = chain Z and resseq 321 and name N
      distance_ideal = 1.3
      sigma = 0.02
    }
    angle {
      atom_selection_1 = chain A and resseq 123 and name CA
      atom_selection_2 = chain A and resseq 321 and name N
      atom_selection_3 = chain A and resseq 234 and name O
      angle_ideal = 120.
      sigma = 2.5
    }
    bond {
      atom_selection_1 = chain A and resseq 1 and name CA
      atom_selection_2 = chain Z and resseq 2 and name N
      distance_ideal = 1.3
      sigma = 0.02
    }
    angle {
      atom_selection_1 = chain A and resseq 1 and name CA
      atom_selection_2 = chain A and resseq 2 and name N
      atom_selection_3 = chain A and resseq 3 and name O
      angle_ideal = 120.
      sigma = 2.5
    }
}

and load it with all the other files in the GUI or provide in the command line, whichever you use.

It is true that many non-standard links can be created automatically or by specialized stand-alone tools. However, these tools use a lot of heuristics and are highly reliant on input model geometry.

To make sure a particular bond was created, try to find it in .*geo file that refinement always outputs. If it is there -- you all good!

Don't use graphic programs to check if a particular bond was used in refinement. Why? Here is the answer:

http://phenix-online.org/newsletter/CCN_2016_01.pdf#page=10

Pavel

On 4/15/20 03:44, Xavier Brazzolotto wrote:

2 solutions that I use

A first one consists in designing your residue linked to your ligand (under ChemDraw / MarvinSketch) then prepare the restraints under eLBOW (from smiles for examples). You will have to modify some atom names into the generated cif file (C, O, CA, N, CB, etc… depending of the modified residue) and above all change the nature of this molecule to L-peptide. Then you can use it in coot as a modified residue and use the modified cif file in Phenix. You can adjust the modification by tuning the occupancy of the atoms corresponding to the ligand and keep the occupancy to 1 for the atoms of the residue. Here you will have a nice covalent bond.

The second solution would be to restrain the distance between the atom of your residue and the atom of the ligand to a covalent bond (C-C distance or whatever it is). Certainly, angles should be restraint too.

Le 15 avr. 2020 à 00:59, Muhammad Bashir Khan <[email protected]> a écrit :

Hi All;

I have a protein molecule and a ligand structure. I want to make a covalent bond between the ligand and protein molecule, could somebody explain to me how I can do that using phenix.

I used the

" phenix.ligand_linking pdb_file_name" commond

It creates

apply_link.def

and

data_link.cif

I did refine the structure again giving the above file as well but did not see any covalent bond created between the protein and ligand.

Thanks for your help

Bashir
--

------------------------------------------------------
Muhammad Bashir Khan, Ph.D.
Research Associate
Department of Biochemistry
Medical Science Bldg.
Lab 3-27
University of Alberta
Edmonton AB, T6G 2H7

Phone: 780-492-4577-
e-mail: [email protected]

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Xavier Brazzolotto, PhD

[email protected]

Département de Toxicologie et Risques Chimiques

Unité Neurotoxiques

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