Zoom: Size: Wireframe:

Select Molecule options

These options may allow selection of the entire molecule, subcomponent molecules (for example protein vs nucleic acid), or smaller molecular components (cofactors, carbohydrates, specific nitrogenous bases or amino acids, etc) of the model presented in the Jmol window.

Selecting a molecule so that it’s name heads the menu allows alteration of its appearance in the model.

A molecule can be hidden or revealed using the adjoining checkbox. Hiding a molecule will hide all components (atoms, bonds, ribbon, etc.) of the model associated with that molecule.

Display options

Display options determine how the selected molecule will be rendered in the model. The model may include atoms, bonds, a ribbon, trace, etc, which can be individually sized using the ‘Size’ buttons. The adjoining checkboxes can be used to hide or make visible different model components.

Atoms: Atoms can be rendered as solid spheres with a uniform radius in Angstroms, which together with bonds comprise a traditional ‘ball and stick’ projection. This is normally the default view. Note about hydrogen atoms: some models show hydrogen atoms but others do not.

vdW checkbox: toggles rendering of atoms between uniform diameters and percentage of the van der Waals radius of each element. The van der Waals Radius of an atom is the calculated radius when it is adjacent to but not bonded to another atom. Since the van der Waals radius of an element is related to the size of its electron cloud, elements with greater mass will have larger van der Waals radii.

Dots: This projects an array of small dots around the surface of atoms. Dots are a useful way to show a molecular surface while not obscuring other aspects of the molecular structure, such as a ball and stick rendering. If vdW is checked, the dots are drawn as a percent of the van der Waals radius.

Bonds: Covalent bonds are generally drawn as rods between the atoms. In some models single, double and triple bonds are distinguished (but this does not occur in all models).

H-bonds: The position of hydrogen bonds is calculated by the Jmol applet. This is performed between N-H and C-O groups of proteins and between nitrogenous bases of nucleic acids. Thus, not all hydrogen bonds may be rendered in a model.

Ribbon: A ribbon-like feature that follows the backbone of DNA and proteins. For nucleic acids, a ribbon will follow the sugar-phosphate linkages, and for proteins it follows the path of peptide bonds and alpha carbons. The flattened appearance of the ribbon highlights secondary structural features, such as the alpha-helices and beta-sheets of a protein.

Trace: Like a ribbon, a Trace follows the molecular backbone, but is rope-like in appearance. A Trace shows the path of the backbone while allowing other structural features to be emphasized.

IsoSurface: IsoSurface projects a surface to a molecule as it would appear to water molecules rolling along the perimeter. This is also referred to as the Sovent-excluded or Connolly surface. Follow this link for a more complete description of the rendering of molecular surfaces.

Color by options

Atoms, Ribbons and Traces can be colored to highlight structural features. Follow this link for a more complete description of colors.

Element: Atoms will be colored according to element type. The colors of the most common elements are:

H C N O P S Fe

1o Structure: different types of amino acids and nucleotides are given a unique color (according to the Jmol ‘shapely’ color scheme).

2o Structure: This differentiates regions of protein secondary structure:

α-helix β-sheet

4o Structure: This gives a different color to each peptide subunit of a multi-subunit protein and to each strand of a nucleic acid.



MolnQuiry is an educational site presenting the structural properties of biological molecules in an interactive, task-oriented learning environment.

Study Panel: A guided presentation of molecular structure.
Inquiry Panel: A task-oriented examination of molecular structure.

Intro to Molecular Models
BondsChemical groups
Proteins Nucleic acids
Carbohydrates Lipids
Membranes Immunology

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MolnQuiry uses the Jmol Applet, and much gratitude is expressed to the Jmol development team. Jmol resources can be found at the Jmol Home.

Dept of Biology & Environmental Science

Steven R. Spilatro
© 2008

Name: _______________________

Date: _______________________

Printing will show results for Inquiry Activities

Click here to load a model and learn about the image controls.

Click on Select Molecule, Display, and Color By to learn more about the options available.

Use the following molecule to practice manipulating model features and using the MolnQuiry menus.

Click here to show a model of the HTLV-1 RNA binding protein, which contains an associated RNA molecule.

a.In the Select Molecule menu, select RNA to make changes to this molecule.

b.In the Display menu, use the checkbox to display a ribbon along the RNA backbone. The ribbon shows the presence of:1 2 3 4 RNA chain(s).

b. In the Select Molecule menu, click the checkbox to hide the RNA, and then select Protein so that its appearance can be changed. In the Display menu select Atoms, and then use the size button to decrease the radius to around 0.5 angstroms; in the Color by menu, select 1o Structure, to color each type of amino acids uniquely. Return to the Display menu and add a Trace along the backbone of the ptorein, and then color it by 2o Structure. Zoom-in the molecule using the zoom buttons for a closer view. The amino acids at the ends of the peptide are: (click on each amino acid to see its identity)Proline and ArginineLysine and SerineMethionine and Prolineor Arginine and Lysine.

Attempts: Correct: