Documentation

pdbdistplot

Visualize intermolecular distances in Protein Data Bank (PDB) file

Syntax

pdbdistplot(PDBid)
pdbdistplot(PDBid, Distance)

Arguments

PDBid

Any of the following:

  • 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.

Distance

Threshold distance in angstroms shown on a spy plot. Default is 7.

Description

pdbdistplot displays the distances between atoms and amino acids in a PDB structure.

pdbdistplot(PDBid) retrieves information for the structure specified by PDBid from the Protein Data Bank (PDB) database. Creates a heat map showing interatom distances and a spy plot showing the residues where the minimum distances apart are less than 7 angstroms.

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

Examples

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

pdbdistplot('5CYT');

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

pdbdistplot('5CYT',10);

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