Display and manipulate 3-D molecule structure
FigureHandle = molviewer(...)
String specifying one of the following:
The referenced file is a molecule model file, such as a Protein Data Bank (PDB)-formatted file (ASCII text file). Valid file types include:
|pdbID||String specifying a unique identifier for a protein structure record in the PDB database.|
|pdbStruct||A structure containing a field for each PDB record, such as returned by the getpdb or pdbread function.|
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.
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:
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:
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 .
View the acetylsalicylic acid (aspirin) molecule, whose structural information is contained in the Elsevier MDL molecule file aspirin.mol.
View the H5N1 influenza virus hemagglutinin molecule, whose structural information is located at www.rcsb.org/pdb/files/2FK0.pdb.gz.
View the molecule with a PDB identifier of 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)