Chime tut

B8: How to select a sub-set.

Chime commands, such as Color and Display, operate on the entire molecule by default. It is possible to modify this behavior by selecting groups of atoms. Once this group of atoms is selected, all subsequent Chime commands are only applied to the selected atoms. This approach can be used to highlight selected groups (i.e. active site residues, bound cofactors, DNA, etc.) within the protein structure by rendering and/or coloring them in a manner that is different from the rest of the protein.

There are a number of methods of selecting atoms. To access these various modes it is necessary to open the Select menu in the pop-up window. A number of the more important items are briefly described below:

Select All: Selects all of the atoms.
Residue: Selection by residue type.
ATOM: Selection by atom type.
Hetero: Selection of various hetero (i.e. non-protein) atoms.
Protein: Wide selection by protein features.
Nucleic: Selection by nucleic acid features.

Three examples are listed below:

A: Do the following two steps to color all of the Phe residues yellow (expected menus shown on the left):
Select¬ Residue¬ PHE
Select¬ Change Color To¬ Yellow

B: Do the following two steps to draw all hydrophobic residues as spacefill:
Select¬ Protein¬ Hydrophobic
Display¬ Spacefill¬ Van der Waals Radii

C: Selecting a specific residue. This is easy to do in RasMol and difficult to do in Chime. The following 5 steps are required to select a specific residue and draw it spacefilled:
1. Select¬Mouse Click Action¬Toggle Residue's Selected State. This action changes the color of the molecule to reflect those atoms which have been selected. Since all atoms have been selected at this time the entire molecule changes color.
2. Now click the mouse on the residue(s) you want selected. The selected residue(s) should change back to its original color. Complete the following menu selections.
3. Select¬Invert SelectionThis will cause only the residue(s) that you clicked on to be selected.
4. Display¬Ball & Stick.
5. Select¬Highlight Selection. This will return the color of the molecule to the original color.