pdbdistplot

Visualize intermolecular distances in Protein Data Bank (PDB) file

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    Syntax

    pdbdistplot(PDBid)
    pdbdistplot(PDBid,Distance)
    pdbdistplot(___,Name=Value)

    Description

    pdbdistplot(PDBid) retrieves the structure specified by PDBid from the PDB database and creates a heat map showing inter–residue distances and a spy plot showing the residues where the minimum distances apart are less than 7 angstroms. If multiple chains are present in PDBid, separate plots are created.

    example

    pdbdistplot(PDBid,Distance) specifies the threshold distance shown on a spy plot. Default is 7.

    pdbdistplot(___,Name=Value) specifies additional options using one or more name-value arguments. Use any arguments from the previous syntaxes.

    example

    Examples

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    Open Live Script

    Display a heat map of the inter-residue distances and a spy plot at 7 angstroms of the protein cytochrome C from albacore tuna.

    pdbdistplot("5CYT");

    Figure contains an axes object. The axes object with title Chain R: Inter-atomic distances contains an object of type image.

    Figure contains an axes object. The axes object with title Chain R: Residues less than 7.00 Angstroms apart, xlabel nz = 2251 contains a line object which displays its values using only markers.

    Display a spy plot at 10 angstroms of the same structure.

    pdbdistplot("5CYT",10);

    Figure contains an axes object. The axes object with title Chain R: Inter-atomic distances contains an object of type image.

    Figure contains an axes object. The axes object with title Chain R: Residues less than 10.00 Angstroms apart, xlabel nz = 4104 contains a line object which displays its values using only markers.

    Input Arguments

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    PDB structure, specified as one of these values:

    • Character vector or string specifying a unique identifier for a protein structure record.

    • Name of a variable for a MATLAB structure containing PDB information for a molecular structure, such as returned by getpdb or pdbread.

    • Name of file containing PDB information for a molecular structure, such as created by getpdb with the ToFile property.

    Note

    Each structure in the PDB database is represented by a four-character alphanumeric identifier. For example, 4hhb is the identification code for hemoglobin.

    Data Types: char | string

    Threshold distance in angstroms shown on a spy plot, specified as a number.

    Data Types: double

    Name-Value Arguments

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    Specify optional pairs of arguments as Name1=Value1,...,NameN=ValueN, where Name is the argument name and Value is the corresponding value. Name-value arguments must appear after other arguments, but the order of the pairs does not matter.

    Example: Model=5,Hetero=true

    Chains to consider, specified as one of these values:

    • Character vector or string specifying the chain ID to consider.

    • Cell arrays of character vectors or string vector specifying the list of chain IDs to consider.

    This value is case-sensitive. By default, all chains included in the model are considered.

    Data Types: char | string

    PDB structural model to consider, specified as a positive integer.

    Data Types: double

    Control to include hetero atoms in the plot of residue interactions, specified as true or false.

    Data Types: logical

    Version History

    Introduced before R2006a

    See Also

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