VIDA User Manual

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• 5.9.1 Display Styles
• 5.9.2 Color
  • 5.9.2.0.1 Coloring Schemes
  • 5.9.2.1 Amino
  • 5.9.2.2 BFactor
  • 5.9.2.3 Carbon
  • 5.9.2.4 Chain
  • 5.9.2.5 CPK, CPKNew
  • 5.9.2.6 Element
  • 5.9.2.7 Formal Charge
  • 5.9.2.8 Group
  • 5.9.2.9 Partial Charge
  • 5.9.2.10 Reference
  • 5.9.2.11 Residue
  • 5.9.2.12 Shapely
• 5.9.3 Proteins
• 5.9.4 Monitors
• 5.9.5 Hydrogen Bonds

 
5.9 Molecular Visualization

This section describes the very powerful, versatile, and interactive molecular visualization capabilities of the 3D display. The interactive control of molecular visualization is typically performed using the Style Control (see Section 5.1.2) or through scripting commands (for more details on scripting see Chapter 10).

 
5.9.1 Display Styles

All of the standard display styles are available (Wireframe, Stick, Ball and Stick, CPK, and Stars) and can be seen in Figure 5.11.

Figure 5.11: Molecule rendering styles

[Wireframe] [Stick] [Fancy Ball and Stick] [CPK] [Stars]

By default, small molecules are drawn in Stick mode while large molecules are drawn in Wireframe mode. These defaults can be changed in the application preferences (see Chapter 11).

 
5.9.2 Color

By default, the atoms in a molecule are colored according to their element types and the bonds in a molecule are colored according to the element types of the two atoms defining that bond. There are two color palettes that specify the actual colors used for a given element, one for use with dark-colored backgrounds and the other for use with light-colored backgrounds. Both of these palettes can be viewed and modified in the application preferences (see Chapter 11). The dark-background atom color palette can be seen in Figure 5.12(a).

Figure 5.12: Dark background atom and residue color palettes

[Atom Color Palette] [Residue Color Palette]

5.9.2.0.1 Coloring Schemes

There are a number of molecule specific coloring schemes in addition to the standard element based coloring. The following schemes are discussed below: amino, bfactor, carbon, chain, cpk, cpknew, element, formal charge, group, partial charge, reference, residue, and shapely.

 
5.9.2.1 Amino

The amino color scheme is a protein specific scheme which colors atoms according to their individual residues. The residue colors are listed below.

 
5.9.2.2 BFactor

The bfactor color scheme is a protein specific scheme which colors atoms according to the bfactor value using a fixed blue-to-red gradient between 0 and 100.

 
5.9.2.3 Carbon

The carbon color scheme colors all of the carbon atoms in the current scope the same color which is specified by the user.

 
5.9.2.4 Chain

The chain color scheme is a macromolecule specific scheme which assigns a unique color to each of the macromolecular chains.

 
5.9.2.5 CPK, CPKNew

The CPK color scheme is an element specific scheme based on the colors used in the popular CPK plastic space filling models. The CPKnew color scheme is a variant on the CPK color in that it uses a slightly brighter version of some of the colors. The atom colors are listed below with the RGB values for CPK in the third column and the RGB values for CPKNew in the fourth column (if different).

 
5.9.2.6 Element

The element color scheme is the default color scheme used when coloring molecules. Colors are assigned according to atomic number. The actual colors used for a given element can be edited in the application preferences as seen in Figure 5.12(a).

 
5.9.2.7 Formal Charge

The formal charge color scheme colors atoms according to their formal charge using a fixed red-to-blue gradient between -4 and +4.

 
5.9.2.8 Group

The group color scheme is a macromolecule specific scheme which colors each atom according to its position in a macromolecular chain. The colors are assigned along a smooth rainbow spectrum from blue to green to yellow to orange to red.

 
5.9.2.9 Partial Charge

The partial charge color scheme colors atoms according to their partial charge using a red-to-blue gradient between -1.0 and +1.0.

 
5.9.2.10 Reference

The reference color scheme colors all of the carbon atoms in the current scope using the current Reference color which can be set in the application preferences. The default is green.

 
5.9.2.11 Residue

The residue color scheme is a protein specific scheme which colors atoms according to their individual residues. The actual colors used can be edited in the application preferences as seen in Figure 5.12(b). The default colors correspond to those used in the shapely color scheme.

 
5.9.2.12 Shapely

The shapely color scheme is a protein specific scheme which colors atoms according to their individual residues. This scheme is based upon Bob Fletterick's ``Shapely Models" [1]. The residue colors are listed below.

 
5.9.3 Proteins

In addition to the standard display styles, the two protein specific displays of C-Alpha Traces and Ribbons are supported. Examples of these display styles can be seen in Figure 5.13.

Figure 5.13: Different views of the same protein

[Wireframe] [C-Alpha Trace] [Ribbon]

Given that protein files often inevitably contain many extra components that are not necessarily of interest to the user (waters for example), the ability to hide the display of non-bonded atoms is provided to ease the viewing of proteins without having to manually edit the input file. An example of a protein displayed with and without waters can be seen in Figure 5.14.

Figure 5.14: Same protein with and without waters

[Protein with Waters] [Protein without Waters]

Figure 5.15: Same protein as a single molecule vs as multiple molecules

[Multimer displayed as a single molecule] [Multimer displayed as multiple molecules]

Another common scenario when working with proteins is that the input file contains a large multimer which as expected is interpreted as a single molecule. However, sometimes the ability to interact with the individual components is of particular value. The ability to split a molecule into separate components can be performed by selecting the ``Components" option in the From Split submenu in the New Molecule submenu in the top-level File menu. This function will then determine what the individual components of the Focused molecule are and create a new list containing a new molecule for each component. The original molecule is not changed or deleted. An example of this process can be seen in Figure 5.15. The From Split submenu also contains ``Selected" and ``Marked" options which will create new molecules from the original based on the selected or marked set of atoms.

It may also be of interest to put some of these components back together into a single molecule. This can be done by choosing one of the following options from the From Merge submenu in the New Molecule in the top-level File menu: ``Selected", ``Marked", ``Visible". Choosing any one of these options will create a new molecule which is composed of all the molecules that were either ``Selected", ``Marked", or ``Visible" at the time of the operation.

 
5.9.4 Monitors

The ability to display measurement monitors is a useful feature and is well supported. Access to these measurement facilities is available from the Mouse popup toolbar on the left hand side of the 3D display. There are three buttons which turn on Distance, Angle, and Torsion measurement respectively.

Figure 5.16: Different types of monitors

[Distance Monitor] [Angle Monitor] [Torsion Monitor]

When the mouse is put into one of these modes, the measurements are made based on the selected set of atoms. In Distance mode, the first atom selected is consider the ``anchor" atom. Once the anchor atom has been selected, a temporary distance monitor will be displayed to any other atom that the mouse passes over. Selecting another atom will create a permanent monitor and clear the anchor. In Angle mode, the first two atoms selected are considered the anchor atoms and a temporary angle monitor will be displayed to any other atom that the mouse passes over. Selecting a third atom will create a permanent monitor and clear the anchors. In Torsion mode, the first three atoms selected are considered the anchor atoms and a temporary torsion monitor will be displayed to any other atom that the mouse passes over. Selecting a fourth atom will create a permanent monitor and clear the anchor.

Monitors can be removed by performing a right-click operation in the 3D display and selecting the ``Delete visible monitors" option. Monitors are also displayed in the ``List Window" and can be deleted individually there (see Chapter 8). Examples of the three types of monitors can be seen in Figure 5.9.4.

 
5.9.5 Hydrogen Bonds

Both internal (intramolecular) and external (intermolecular) hydrogen bonds can be displayed. Hydrogen bonds are determined by typing all of the atoms as either acceptors, donors, both, or neither. Then the hydrogen bond energy is calculated between all acceptors and donors based on the ChemScore [2] scoring function which takes into account both interatomic distance as well as the coordination geometry. This function provides a relative score between 0 and 1.0 for the energy of the hydrogen bond. For all hydrogen bonds with an energy greater than 0, the bond is drawn as a dotted green line. The thickness of the line as well as the spacing between the dots correlates to the bond energy. Therefore, thicker more solid lines have higher energy than thinner more dotted lines. An example of both internal and external hydrogen bonds can be seen in Figure 5.17.

Figure 5.17: Hydrogen bonds in a protein active site

[External Hydrogen Bonds] [Internal Hydrogen Bonds]

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				VIDA User Manual

Previous: 5.8 Display Widgets Up: 5. 3D Display Next: 5.10 Grid Visualization

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Documentation released on 23 May 2007.