Some auxiliary functions to quickly retrieve some data
Get the protein sequence
To obtain a list of the residue names of the protein with three- and one-letter codes, use
julia> using PDBTools
+
+julia> getseq(PDBTools.SMALLPDB)
+3-element Vector{String}:
+ "A"
+ "C"
+ "D"Use getseq(atoms,code=2) to get the sequence as three-letter residue codes, or code=3 to get full natural-aminoacid names, like "Alanine", "Proline", etc:
julia> using PDBTools
+
+julia> getseq(PDBTools.SMALLPDB, code=2)
+3-element Vector{String}:
+ "ALA"
+ "CYS"
+ "ASP"
+
+julia> getseq(PDBTools.SMALLPDB, code=3)
+3-element Vector{String}:
+ "Alanine"
+ "Cysteine"
+ "Aspartic acid"If there is some non-standard protein residue in the sequence, inform the getseq function by adding a selection:
julia> using PDBTools
+
+julia> atoms = readPDB(PDBTools.SMALLPDB);
+
+julia> for at in atoms
+ if resname(at) == "ALA"
+ at.resname = "NEW"
+ end
+ end
+
+julia> getseq(atoms, "protein or resname NEW"; code=2)
+3-element Vector{String}:
+ "NEW"
+ "CYS"
+ "ASP"By default the selection will only return the sequence of natural amino acids.
The getseq function can of course be used on an Atom list, accepts selections as the last argument, as well as the reading and writing functions:
julia> using PDBTools
+
+julia> atoms = readPDB(PDBTools.SMALLPDB);
+
+julia> getseq(atoms, "residue > 1")
+2-element Vector{String}:
+ "C"
+ "D"Distance between sets of atoms
The distance between atoms, or sets of atoms, can be computed with the distance function. This function returns the minimum distance between the atoms of the sets involved. For example:
julia> using PDBTools
+
+julia> model = wget("1BSX");
+
+julia> protein = select(model,"protein");
+
+julia> ligand = select(model,"resname T3");
+
+julia> distance(protein,ligand)
+2.7775834820937417Closest atoms and their distance
A function similar to the one above is closest, which returns the shortest distance between atoms but also the identity of the atom or pair of atoms that satisfy that shortest distance:
julia> using PDBTools
+
+julia> model = wget("1BSX");
+
+julia> protein = select(model,"protein");
+
+julia> ligand = select(model,"resname T3");
+
+julia> closest(ligand,protein)
+(43, 3684, 2.7775834820937417)
+
+julia> ligand[43]
+ 4037 O1 T3 B 2 512 -22.568 81.625 3.159 1.00 36.59 1 - 4041
+
+julia> protein[3684]
+ 3684 NE2 HIS B 435 472 -21.539 82.145 5.686 1.00 44.44 1 - 3686
+
+julia> distance(ligand[43],protein[3684])
+2.7775834820937417Obtain arrays with coordinates
Use the coor function:
julia> using PDBTools
+
+julia> atoms = readPDB(PDBTools.SMALLPDB);
+
+julia> coor(atoms[1])
+3-element StaticArraysCore.SVector{3, Float64} with indices SOneTo(3):
+ -9.229
+ -14.861
+ -5.481
+
+julia> coor(atoms[1:2])
+2-element Vector{StaticArraysCore.SVector{3, Float64}}:
+ [-9.229, -14.861, -5.481]
+ [-10.048, -15.427, -5.569]The coor function accepts selections:
C$\alpha$ coordinates:
julia> using PDBTools
+
+julia> atoms = readPDB(PDBTools.SMALLPDB);
+
+julia> coor(atoms, "name CA")
+3-element Vector{StaticArraysCore.SVector{3, Float64}}:
+ [-8.483, -14.912, -6.726]
+ [-5.113, -13.737, -5.466]
+ [-3.903, -11.262, -8.062]The coordinates are output as arrays of static arrays (more specifically, as a Vector{SVector{3,Float64}}, from StaticArrays).
Maximum and minimum coordinates of the atoms
Use maxmin(atoms), or maxmin(atoms,"resname CA"), for example:
julia> using PDBTools
+
+julia> atoms = readPDB(PDBTools.SMALLPDB);
+
+julia> maxmin(atoms, "residue > 1")
+ Minimum atom coordinates: xmin = [-6.974, -16.785, -10.863]
+ Maximum atom coordinates: xmax = [-1.94, -9.552, -3.844]
+ Length in each direction: xlength = [5.034000000000001, 7.2330000000000005, 7.019]m is a structure containing the three vectors with minimum and maximum coordinates, and lengths.
Residue tick labels for plots
The functionality of the residue_ticks as described requires PDBTools version 1.6.0 or greater.
The residue_ticks function provides a practical way to define tick labels in plots associated to an amino-acid sequence:
residue_ticks(
+ atoms (or) residues (or) residue iterator;
+ first=nothing, last=nothing, stride=1, oneletter=true
+)The input structure can be provided as a vector of atoms (type Vector{Atom}) a residue iterator (obtained by eachresidue(atoms)) or a vector of residues (obtained by collect(eachresidue(atoms))).
The function returns a tuple with residue numbers and residue names for the given atoms, to be used as tick labels in plots.
first and last optional keyword parameters are integers that refer to the residue numbers to be included. The stride option can be used to skip residues and declutter the tick labels.
If oneletter is false, three-letter residue codes are returned. Residues with unknown names will be named X or XXX.
Example
Here we illustrate how to plot the average temperature factor of each residue of a crystallographic model as function of the residues.
julia> using PDBTools, Plots
+
+julia> atoms = wget("1UBQ", "protein");
+
+julia> residue_ticks(atoms; stride=10) # example of output
+([1, 11, 21, 31, 41, 51, 61, 71], ["M1", "K11", "D21", "Q31", "Q41", "E51", "I61", "L71"])
+
+julia> plot(
+ resnum.(eachresidue(atoms)), # x-axis: residue numbers
+ [ mean(beta.(res)) for res in eachresidue(atoms) ], # y-axis: average b-factor per residue
+ xlabel="Residue",
+ xticks=residue_ticks(atoms; stride=10), # here we define the x-tick labels
+ ylabel="b-factor",
+ xrotation=60,
+ label=nothing, framestyle=:box,
+ )Produces the following plot:
Alternatively (and sometimes conveniently), the residue ticks can be obtained by providing, instead of the atoms array, the residue iterator or the residue vector, as:
julia> residue_ticks(eachresidue(atoms); stride=10)
+([1, 11, 21, 31, 41, 51, 61, 71], ["M1", "K11", "D21", "Q31", "Q41", "E51", "I61", "L71"])
+
+julia> residue_ticks(collect(eachresidue(atoms)); stride=10)
+([1, 11, 21, 31, 41, 51, 61, 71], ["M1", "K11", "D21", "Q31", "Q41", "E51", "I61", "L71"])