molviewer

Display and manipulate 3-D molecule structure

Syntax

molviewer
molviewer(File)
molviewer(pdbID)
molviewer(pdbStruct)
FigureHandle = molviewer(...)

Input Arguments

File

Character vector or string specifying one of the following:

  • File name of a file on the MATLAB® search path or in the MATLAB Current Folder

  • Path and file name

  • URL pointing to a file (URL must begin with a protocol such as http://, ftp://, or file://)

The referenced file is a molecule model file, such as a Protein Data Bank (PDB)-formatted file (ASCII text file). Valid file types include:

  • PDB

  • MOL (MDL)

  • SDF

  • XYZ

  • SMOL

  • JVXL

  • CIF/mmCIF

pdbIDCharacter vector or string specifying a unique identifier for a protein structure record in the PDB database.

Note

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

pdbStructA structure containing a field for each PDB record, such as returned by the getpdb or pdbread function.

Output Arguments

FigureHandleFigure handle to the Molecule Viewer.

Description

molviewer opens the Molecule Viewer app. You can display 3-D molecular structures by selecting File > Open, File > Load PDB ID, or File > Open URL.

molviewer(File) reads the data in a molecule model file, File, and opens the Molecule Viewer app displaying the 3-D molecular structure for viewing and manipulation.

molviewer(pdbID) retrieves the structural data of a protein, pdbID, from the PDB database and opens the Molecule Viewer app displaying the 3-D molecular structure for viewing and manipulation.

molviewer(pdbStruct) reads the data from pdbStruct, a structure containing a field for each PDB record, and opens the Molecule Viewer app displaying a 3-D molecular structure for viewing and manipulation.

FigureHandle = molviewer(...) returns the figure handle to the Molecule Viewer window.

Tip

You can pass the FigureHandle to the evalrasmolscript function, which sends RasMol script commands to the Molecule Viewer window.

Tip

If you receive any errors related to memory or Java® heap space, try increasing your Java heap space as described at https://www.mathworks.com/support/solutions/en/data/1-18I2C/.

After displaying the 3-D molecule structure, you can:

  • Hover the mouse over a subcomponent of the molecule to display an identification label for it.

  • Spin and rotate the molecule at different angles by click-dragging it.

  • Spin the molecule in the x-z plane by clicking .

  • Spin the molecule in the x-y plane by pressing and holding the Shift key, then click-dragging left and right.

  • Zoom in a stepless fashion by pressing and holding the Shift key, then click-dragging up and down.

  • Zoom in a stepwise fashion by clicking the figure, then turning the mouse scroll wheel, or by clicking the following buttons:

    or

  • Move the molecule by pressing and holding Ctrl + Alt, then click-dragging.

  • Change the background color between black and white by clicking .

  • Reset the molecule position by clicking .

  • Show or hide the Control Panel by clicking .

  • Manipulate and annotate the 3-D structure by selecting options in the Control Panel or, for a complete list of options, by right-clicking the Molecule Viewer window to select commands:

  • Display the Jmol Script Console by clicking .

    Note

    There is a known bug with the Open button of the script editor that prevents loading a Rasmol script interactively. Instead use the evalrasmolscript function which sends RasMol script commands to the Molecule Viewer app. Also, you can copy and paste the script commands into the script console.

Examples

View the acetylsalicylic acid (aspirin) molecule, whose structural information is contained in the Elsevier MDL molecule file aspirin.mol.

molviewer('aspirin.mol')

View the H5N1 influenza virus hemagglutinin molecule, whose structural information is located at www.rcsb.org/pdb/files/2FK0.pdb.gz.

molviewer('http://www.rcsb.org/pdb/files/2FK0.pdb.gz')

View the molecule with a PDB identifier of 2DHB.

molviewer('2DHB')

View the molecule with a PDB identifier of 4hhb, and create a figure handle for the Molecule Viewer.

FH = molviewer('4hhb')

Use the getpdb function to retrieve protein structure data from the PDB database and create a MATLAB structure. Then view the protein molecule.

pdbstruct = getpdb('1vqx')
molviewer(pdbstruct)

Compatibility Considerations

expand all

Not recommended starting in R2020b

See Also

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Introduced in R2007a

Bioinformatics Toolbox Documentation

Support