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pdbdistplot

Visualize intermolecular distances in Protein Data Bank (PDB) file

Syntax

pdbdistplot(PDBid)
pdbdistplot(PDBid, Distance)
pdbdistplot(___,'Chain',ChainID)
pdbdistplot(___,'Model',ModelNum)
pdbdistplot(___,'Hetero',TF)

Arguments

PDBid

Any of the following:

  • Character vector 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.

ChainID

Any of the following:

  • Character vector specifying the chain ID to consider.

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

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

ModelNum

Positive integer specifying which model to consider. Default is 1.

Description

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

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.

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

pdbdistplot(___,'Chain',ChainID) specifies the chains to consider. By default, all chains included in the model are considered.

pdbdistplot(___,'Model',ModelNum) specifies which PDB structural model to consider. Default is 1.

pdbdistplot(___,'Hetero',TF) specifies whether to include hetero atoms in the plot of residue interactions. TF is logical, true or false. Default is false.

Examples

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');

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

pdbdistplot('5CYT',10);

Introduced before R2006a

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