Bioinformatics Toolbox™

molviewer - Display and manipulate 3-D molecule structure

Syntax

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

Arguments

File

String specifying one of the following:

File name of a file on the MATLAB search path or in the MATLAB Current Directory
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

pdbID

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.

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

Return Values

FigureHandle Figure handle to a Molecule Viewer window.

Description

molviewer opens a blank Molecule Viewer window. 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 a Molecule Viewer window displaying the 3-D molecular structure for viewing and manipulation.

molviewer(pdbID) retrieves the data for a protein structure record, pdbID, from the PDB database and opens a Molecule Viewer window 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 a Molecule Viewer window 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:

 http://www.mathworks.com/support/solutions/data/1-18I2C.html

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

Click-drag the molecule to spin, rotate, and view it from different angles.
Hover the mouse over a subcomponent of the molecule to display an identification label for it.
Zoom the plot by turning the mouse scroll wheel or clicking the following buttons:
or
Spin the molecule by clicking .
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 .

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.