5. Coloring

DeepView provides many different ways to color a model. Color is not a trivial matter in molecular modeling. Colors can reveal structural, chemical, and comparative features vividly, and can help you to keep your bearings during complex operations.

Select, display, and center the complete model, without side chains. Turn off the display of ribbons, H-bonds, or any other features except the wireframe backbone.

Color: Secondary Structure
DeepView colors helical residues red, beta sheet residues (strands) yellow, and all others gray. Notice that the color for each residue is displayed in a small square beside the residue in the right-hand column of the Control Panel. Notice also that Color menu commands colors all groups, regardless of what is selected (as you will see, there are ways to color only individual residues or selections, using the Control Panel).

Color: Secondary Structure Succession
DeepView colors helices and strands, but with this command, color reflects the order of each structural element in the overall sequence of residues. DeepView colors the first element of secondary structure violet, the last one red, and the ones in between with colors of the visible spectrum that lie between violet (400 nm) and red (700 nm). The result is that it is easy to follow the chain through the protein -- elements of secondary structure are colored from the N-terminal to the C-terminal end in the order violet, blue, green, yellow, orange, red. DeepView assigns as many shades as needed for the number of secondary-structural elements present. As before, DeepView assigns gray to all other residues.

Color: Chain
DeepView colors the entire model yellow. If there were more than one chain in this model, each chain would be shown in a different color. This color provides good contrast to the colors you will now add for sidechains.

Select: Group Property: non Polar
heading: side
This action adds side chains to selected (in this case, nonpolar) residues only.

On the Control Panel, notice that, next to the column heading colr, there are the letters BS. This indicates that coloring commands will change backbone and sidechain displays only. Now pull down the Color menu, and notice that the first line brings down a submenu of "act on" commands. This submenu determines which display elements (backbone, sidechain, ribbon, and so forth) will be changed by subsequent Color-menu commands. (On Macintosh, this submenu is also located below the col heading of the Control Panel. Find it by clicking the small black triangle below col.)

Color: act on Sidechains
Notice that the letters BS are now replaced by S, indicating that any subsequent Color commands will now change only the colors of side chain, which backbone color is unaffected.

Color: Type
This command recolors the side chains all residues according to chemical type. Note that it colored only the sidechains because the Color menu is set to sidechains only; mainchain residues remain colored by secondary structure. Nonpolar sidechains are now gray (other side chains are not shown because you selected and displayed nonpolars only). Look at the control panel to see the colors assigned to other types of residues. What are the colors for basic (positive), acidic (negative), and polar residues? Now look at the model. Notice that most of the gray side chains on display cluster in the heart of the molecule, as you would expect, because most hydrophobic side chains in a water-soluble protein like lysozyme are buried.

Select: Group Property: Acidic
<control> Select: Group Property: Basic
On the second command, press the control key first, and hold it down while pulling down the menu. Using control with a Select menu command adds groups to the selection, without un-selecting others. (Recall that the control key has a similar function in the Control Panel.)

Linux: Control key function may be missing.

heading: side
This adds side chains for selected groups, and removes all other side chains. Look around the model. Most of the red and blue side chains shown are on the surface, as you expect for charged side chains in a water-soluble protein. Note that the nonpolar side chains are no longer on display, because you did not hold down the control key during the Select: Group Property: Acidic command above.

Can you show only the polar sidechains on the backbone? To DeepView, "polar" means polar but not charged.

Again select, display, and center the complete model, with side chains.

Color: act on Backbone + Sidechains
This action resets the Color menu so that subsequent Color commands affect backbone and sidechain displays.

Color: Accessibility
This operation may take 10 or more seconds, depending on the speed of your computer. (During slow operations, DeepView shows a progress bar to let you know everything is all right.) After the calculation, you see the model in colors ranging from violet to orange. The color of each residue is based on the percentage of its surface area that is exposed (accessible) to the surrounding solvent. The least accessible (buried) residues are colored violet. To residues of higher accessibility, DeepView assigns colors of higher wavelength in the visible spectrum (the color violet is about 400 nm, and red is about 700 nm). So in this display, the colors of the rainbow reflect the exposure of the residue to solvent: violet residues are the least exposed, red residues the most exposed. Find tri-NAG (showing surface is a good way to find a group quickly). Which NAG residue is most accessible?

Also notice that the colors of the visible spectrum are used here in a manner that is common to coloring for many quantitative features: violet for the lowest values (in this case, % exposure to solvent), and red for the highest values, with intermediate values represented by colors between blue and red on the visible spectrum. (In Color: Secondary Structure Succession, the quantitative feature was residue number in the sequence).

Technical Note

To be more precise, the accessibility of each residue is computed as this ratio:

(exposed surface area) / (maximum possible exposed surface area)

The maximum for residue X is defined as the exposed surface area of residue X in the pentapeptide gly-gly-X-gly-gly in fully extended conformation. To make this calculation, DeepView adds 1.4 angstroms (approximate radius of a water molecule) to the radius of every atom, computes their surfaces, eliminates all overlapping surfaces, computes the exposed surface area for each residue, computes the ratio of that surface to the maximum possible, and assigns colors on this scale: 75% of maximum exposed: red; 37.5% exposed: green; 0% exposed: violet, with intermediate colors for intermediate values. You can see why even DeepView, which is a very fast program, takes a few seconds to carry out this calculation. (Well, that's what I said a few years ago—but as you can see, the calculation time is now less than one second, and no progress bar appears.)

Select and center TRP62 by option-clicking the residue in the control panel. With only TRP62 selected and the whole model shown, click on the surface header (small cluster of dots, with a v -- for van der Waals -- at its lower right) in the Control Panel. TRP62 is now shown with a dotted surface that represents the van der Waals radius of each atom. Zoom in so that you can see this residue and its surroundings clearly. Notice that it lies just below the surface of the enzyme, almost completely surrounded by other groups.

Linux: There may be no counterpart to the option key on the Linux keymap.

Notice that, just beneath the surface heading, there is a small black triangle. This is the handle for another pull-down menu. Click on the triangle to pull the menu down, and select accessible. Notice that the v becomes an a -- for accessible. Again, with the whole model on display, but only TRP62 selected, click on the surface heading. A small region of surface dots appears, outside the van der Waals surface. This surface is that portion of the surface of TRP62 that is solvent-accessible, or exposed to the surrounding medium or solvent. You can see that only a small fraction of the TRP62 surface is solvent-accessible, in keeping with the violet color assigned when you colored it by accessibility.

The van der Waals surface lies at a distance of the van der Waals radius from the center of the atom directly below its surface, and includes the full surface of all selected atoms, except where their surfaces overlap. In contrast, the solvent-accessible surface lies above each atom at a distance of the van der Waals radius plus 1.4 angstroms, and includes only the surface with which a spherical solvent molecule of radius 1.4 angstroms could come into contact. Any other part of the surface is hidden from the solvent by surrounding residues. Like coloring by accessibility, showing the accessible surface requires a lengthy calculation, and can take a long time for the entire molecular surface of a large protein model.

Turn off both the van der Waals and accessible surfaces. Center the model, still colored by accessibility.

NOTE: If the dots on van der Waals and accessible surfaces are too sparse for your liking, increase their density with Prefs: Display. Changes take effect the next time you move the model. I use 8 for both vdW and surface dot density.

Display: Slab
This command reduces the display to a thin slab centered at the middle of the molecule. DeepView shows only the groups that lie within this slab; the program hides groups that lie in front of or behind this slab. With this display of the molecule in cross section, you can see that residues in the heart of the molecule are not accessible to solvent (dark blue), while surface residues are accessible. Rotate the molecule to see that this is true for all the surface.

You can change the thickness of the display slab (to display a thinner or thicker section of the molecule) using the mouse. Hold down shift and left-click drag to the left or right. Moving to the left thins the display slab; moving right thickens it. You can also move the slab toward or away from you, keeping the same thickness of cross section, by holding down the shift key and left-click dragging the mouse forward or backward. Moving the mouse away from you pushes the slab farther away, revealing groups more distant from you; moving the mouse towards you pulls that slab forward, revealing groups in front. This works no matter which of the manipulation buttons -- rotate, translate, or zoom -- are currently selected. Zoom/center to return the slab to the center of the model. Then turn off slabbing by again selecting Display: Slab. Slabs are very handy for eliminating background and foreground groups and exposing the groups you want to study.

How can we color individual residues, or complex selections of residues? The small colored squares in the col column of the Control Panel provide a means to color individual residues, while the col heading at the top allows you to choose a color for all currently selected residues. Display the whole model with side chains, and select all groups except tri-NAG. (There are several ways to make this selection. One quick way is to select NAG 201-203 and then choose Select: Inverse Selection.)

Next you will change the color of the selected groups. Click to activate the Control Panel.

heading: col
You will see a standard Macintosh color wheel, and below it, a shade bar. If necessary, slide the pointer on the shade bar to give the wheel bright colors. Then click in the green region of the wheel. Click OK. Now the whole model, except for tri-NAG, which is not selected, is green.

Linux and other versions: Your familiar color picker should appear.

Next, color tri-NAG red, as follows. Select NAG 201-203.

heading: col
Set shade and color to a bright red that will show up well against the black background. Click OK. Now the green enzyme sports a red inhibitor.

You can also color any individual residue by clicking on its individual color box, regardless of whether it is part of the current selection. Try this by coloring LEU129, the C-terminal residue, yellow.

Do you see any other yellow bonds in the model? Identify these yellow structures. Center on one of them as follows:

Click the fourth icon from the right on the graphics window (it has an eye and 4 arrows on it). As instructed below the icons, click an atom -- choose one of the atoms connected by a yellow bond (in stereo, remember to click in the left image). The atoms you chose becomes the center of rotation and display. Zoom in to get a closer look -- slabbing might help.

Select: All
Color: CPK
This action returns all groups to standard or CPK colors: white for carbon, red for oxygen, blue for nitrogen, and yellow for sulfur. This color scheme will help you to identify the yellow bonds, which are the common disulfide cross-links between cysteine residues. Disulfides, which stabilize the three-dimensional structure of proteins, are found mostly in extracellular proteins like lysozyme. Life is rough outside the cell, and disulfides make proteins more rugged.

By the way, the way to color only selected groups CPK is to click col, and then click Cancel on the color wheel dialog.

Test your DeepView skills:

Make a model in which lysozyme is shown only as a ribbon, colored by secondary structure, and tri-NAG is shown in normal (CPK) colors with a dotted van der Waals surface. Your model should look like this (but in a different orientation):

Linux: Ribbons don't seem to be able to take up any kind of colour scheme. The closest approximation to the above picture is one with the wireframe coloured in a similar manner to the ribbons.





Take time to PLAY with the tools introduced in this section.

For more information about coloring, click on DeepView User Guide in the Contents frame (at left), go to the Display section, and click Color Menu in the third paragraph.

Next Section: 6. Measuring and Labeling

To The Molecular Level