Examples

Selecting the active site of a protein

The 1BSX pdb file is a structure that contains a dimer of the thyroid hormone receptor-beta bound to the ligand T3. Here we select all residues of chain A, which is one of the monomers, that within 3.5$\AA$ of the ligand:

julia> using PDBTools

julia> atoms = wget("1BSX", "chain A"; format="PDB");

julia> protein = select(atoms, "protein");

julia> ligand = select(atoms, "resname T3");

julia> active_site_atoms = Atom[]
       for residue in eachresidue(protein)
           if distance(residue, ligand) < 3.5
               append!(active_site_atoms, atom for atom in residue)
           end
       end

julia> length(active_site_atoms)
56

julia> resname.(eachresidue(active_site_atoms))
6-element Vector{InlineStrings.String7}:
 "PHE"
 "ARG"
 "LEU"
 "ASN"
 "LEU"
 "HIS"

Note

The Atom[] creates an empty vector of PDBTools.Atom objects, and we append to this array the list of atoms of each residue.
We opt here to download the file in the "PDB" format, because the chain identifier in the mmCIF deposited file does not include the ligand in chain A.

Storing partial charges

Here we exemplify the use of a custom field to store partial charges for all atoms in a protein:

julia> using PDBTools

julia> ats = wget("1BSX", "protein");

julia> charges = ones(length(ats));

julia> ats_with_charges = add_custom_field.(ats, charges); # charges in custom field

julia> ats_with_charges[1].custom
1.0