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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.

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What does a molecule look like?

Examine the following models to explore different ways in which molecules can be visualized. Change the appearance of the models as you wish. Instructions for rotating, moving and zooming the models can be found on the move? link.

1. Lewis Two-dimensional Projection

Atomic structures do not easily translate into visual depictions. In a classical 'Lewis' representation, we show molecules as a set of atoms, represented by their atomic symbol, connected by bonds, represented by lines (or multiple lines to show double and triple bonds). For example, the diagram to the right shows a traditional 2-dimensional representation of the sugar glucose. Click here to show this molecule in the Jmol window. In the Jmol molecular modeler different elements are assigned specific colors, which helps us to distinguish them.

Colors of Some Biologically Important Atoms
Atomic
number
Element, symbol & color
1Hydrogen - H
6Carbon - C
7Nitrogen - N
8Oxygen - O
11Sodium - Na
12Magnesium - Mg
15Phosphorus - P
16Sulfur - S
17Chlorine - Cl
19Potassium - K
20Calcium - Ca
26Iron - Fe

2. Three-Dimensional Models

Three-dimesional arrangement. In reality the atoms of a molecule do not exist in a flat plane; they are arranged within 3-dimensional space. Click here to reproject the model in three-dimensions. The three dimensional arrangement minimizes interactions between the atoms, and reduces the energy level of the molecule.

Ball and Stick Models. Atoms can be projected in different ways. Click here to show glucose as a 'ball and stick' model. In this type of projection, the size of the atoms is chosen somewhat arbitrarily and serves primarily to show their position.

Spacefill Projections. Alternatively, the size of atoms can reflect the van der Waals radius, which is related to the size of the electron cloud surrounding the nucleus, as shown here . Notice that the van der Waals radius is related to the atomic mass and differs among elements.

Dot projections. Unfortunately, a spacefill projection often hides the bonds. Projecting the electron cloud as an array of dots, as shown here , allows the bonds to be visible as well.

Molecular surface. Of course, atoms do not have individual colors, and the electron clouds will form a relatively smooth, though vaguely defined surface. We might, therfore, show glucose like this to depict the molecular surface with which other molecules would interact. The nuclei of the atoms are located well below the surface.


3. Other types of molecular projections

Some biological molecule are long chains of subunits, such as proteins which are made of amino acids, and nucleic acids (DNA and RNA) which are made of nucleotides.

Catalase is a protein conisting of 506 amino acids (in cells, the protein consists of four identical subunits). In this ball & stick model each amino acid is given a different color; however, the path of the amino acid chain within the protein cannot be perceived. By reducing the size of the atom spacefill projection allows addition of a Trace that follows and highlights the path of the amino acid chain. By combining different molecular representations, the position of other non-amino acid molecules associated with the protein, such the heme and NADPH cofactors shown here. can be highlighted.

Alternatively, the three-dimensional arrangement of molecular subunits can be shown with a Ribbon as shown here for DNA. The ribbon highlights the double helical arrangement of the two strands.

Dept of Biology & Environmental Science



Steven R. Spilatro
© 2008


Working with Molecular Models.

Clicking the right mouse button in the Jmol window will open the Jmol menu of commands for altering the appearance of the molecular model. You are encouraged to explore the options that are available -- fear not, no damage can be done! However, MolnQuiry provides a simplified interface through the "Select Molecule", "Display" and "Color by" drop-down menus, and the Zoom: up/down and Size: up/down arrows. Further explanations of these options can be accessed by clinking on the blue titles above the option boxes. The exercises below provide an introduction to basic molecule manipulations.

Name: _______________________

Date: _______________________

Results for Molecular Bonding Inquiry Activities

1. The following activities will give you experience changing the position of a molecular model. Click here to show the mitochondrial cytochrome B-C1 complex as positioned in a cell membrane (the surfaces of the membrane are shown by the red and blue layers). Rotate, zoom and move the model as instructed below.

a. Rotate the image around the X-axis by holding down the Left mouse button and dragging up/down.

b. Rotate the image around the Y-axis by holding down the Left mouse button and dragging left/right

c. Rotate the image around the Z-axis by holding down the Shift-key and Right mouse button, and dragging left/right.

d. Zoom the image by holding down the Shift-key and Left mouse button, and dragging up/down.

e. Move the image along the window X-axis by holding down the Control-key and Right mouse button, and dragging left/right

f. Move the image along the window Y-axis by holding down the Control-key and Right mouse button, and dragging up/down


2. The following activities will give you experience altering the projection of the molecular model. Click here to show a 'Lewis' model of the carbohydrate called sucrose, and then change the appearance of the model as instructed below.

a. Click here convert to a 3-D model.

b. Click here to convert to a Spacefill model.

c. Toggle on and off any of the molecular components. From the 'Display' drop-down menu, check and uncheck the option box for each component. This makes the component visible or hidden. Set the model with the atoms and bonds visible, but dots hidden. Clicking on the name of the component in the drop-down menu sets that component as the one altered by using the Size:up/down arrows. Select 'Atoms'.

d. Set the diameter of the atoms to approximately 0.64 Angstrom. (Depending upon your browser, you may not get this exact value.) The Size:up/down arrows will alter the component named in the 'Display' drop-down menu. It should presently show 'Atoms', so use the Size:up/down arrows to change the atom diameter.

d. Reduce bond diameter to 0.1 Angstrom. In the 'Display' drop-down menu, check the "Bonds" option box to make the bonds visible, and then use the Size:up/down arrows to change the bond diameter.

e. Set atom radius proportional to the Van der Waals radius. From the 'Display' drop-down menu, click on 'Atoms' and then check the "Vdw" option box. Notice that each atom type has a different diameter.

f. Display dots at approximately 100% of the Van der Waals radius. From the 'Display' drop-down menu, click the "Dots" option box, and then use the Size:up/down arrows to change the diameter.


3. The following activities will give you experience displaying other molecular properties. Click here to show a Protein-DNA complex. Change the appearance of the model as instructed below.

a. Give each nucleotide of the DNA molecule a different color. Under the "Select Molecule" drop-down menu, select "DNA". Under the "Color by" drop-down menu select "1O Structure".

b. Hide the atoms of the DNA molecule, and set the bonds to a diameter of 0.3 Angstrom. Do this as described in exercise #2 above.

c. Add a ribbon to the DNA molecule.From the 'Display' drop-down menu, check the ribbon checkbox, and then increase its size to a value of 400.

d. Give each amino acid of the protein a different color. Under the "Select Molecule" drop-down menu, select "Protein". Under the "Display" drop-down menu, select "Atoms". Under the "Color by" drop-down menu select "1O Structure".

e. Decrease the size of the atoms. Use the Size:up/down arrows to decrease the size of the atoms in the protein molecule to approximately 0.66 Angstrom.

As now shown, the model highlights the binding of particular amino acids into the major and minor grooves of the DNA double helix. Clicking on an amino acid of the protein or nucleotide of the DNA will show its identify.