[phenixbb] covalently linked ligand

[Pavel Afonine]

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 <mbk at ualberta.ca 
>> <mailto:mbk at ualberta.ca>> 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: mbk at ualberta.ca <mailto:cbrooks1 at ualberta.ca>
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>
> Xavier Brazzolotto, PhD
> xavier.brazzolotto at chemdef.fr <mailto:xavier.brazzolotto at chemdef.fr>
>
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