ResProp

ResProp is a tool for:

coloring the 20 standard amino acids according to category
defining new amino acid categories

There are several predefined sets (a set is also called a schema): hydrophobic, positive, negative, polar, charged, small, tiny, aromatic, and aliphatic. It is possible to change the assignments of residues to these sets, create new sets, and designate colors for members and nonmembers of each set. The sets, whether predefined or custom-made, are listed in the Chimera Select menu (under Select... Residue... amino acid category).

There are several ways to start ResProp, a tool in the Structure Analysis category. Starting ResProp opens the Residue Property Colorer window, which has several sections.

Residue Property Colorer Under Residue Schema is a pulldown menu of schema names. The name of the current schema is shown (Charged in the figure). Checkboxes next to the names of the 20 standard amino acids indicate which residues are included in the current set. Other previously defined sets can be accessed from the pulldown menu and made the current schema. Changes in the residue list and colors are instantly applied to the current schema. Thus it is important to either create a new schema (see below) or change to the schema for which changes are desired before making any changes. However, if a predefined schema is changed accidentally, its default state can be rescued with the Revert to defaults button.

The Schema Colors section contains color wells for:

Chosen side chains - side chain atoms of residues in the set (residues for which the boxes are checked)
Remaining side chains - side chain atoms of residues not in the set
Chosen main chain - main chain atoms (N,CA,C,O) of residues in the set
Remaining main chain - main chain atoms of residues not in the set
Unknown residues - anything other than the 20 standard amino acid residues

If color changes to only the current schema (not every schema) are desired, make sure that the checkbox marked Apply color changes to all schemas is off before any colors are edited. Clicking on a color well activates it (turns the border white) and opens the Color Editor. Changes within the Color Editor are reflected in the active color well. Activating another color well does not open another Color Editor, but switches the connection of the already opened Color Editor to the newly activated well. Clicking the No Color button in the Color Editor makes the associated color well show a gray checkerboard and the word No. This "no color" assignment means that when the schema is applied, the colors of the indicated atoms, ribbon, and/or surface will not be changed; the pre-existing colors will be retained.

Colors will change according to the current schema when Apply is clicked (either at the top or the bottom of the panel). Color changes can be applied to atoms, ribbon, and/or surface. With Color atoms, side chain and main chain atoms can be colored differently from one another. Color ribbon sets per-residue ribbon colors, using the colors specified for side chains. Color surface changes the surface color source to atoms if it is set to model and sets per-atom surface colors. Ribbons can be displayed with the command ribbon or the Actions menu. Surfaces can be displayed with the command surface or the Actions menu.

Under Schema Editing, New schema... allows entry of a new schema name and makes the new schema the current schema. Each new schema is added to the listing under Select... Residue... amino acid category in the Chimera menu, making it easy to select all residues belonging to the set. Any schema may be renamed (Rename...) or deleted entirely (Delete...). Changes and additions are stored in .chimera/ResProp/schemaData.py in the user's home directory and will be carried through to subsequent Chimera sessions. Clicking Revert to defaults will restore the default state of each predefined schema, including colors; any user-defined schema with a name different than those of the predefined sets, however, will be retained.

The Apply buttons at the top and bottom are the same; clicking either will apply the current schema to the display. Help brings up this manual page in a browser window. Close closes the Residue Property Colorer.

UCSF Computer Graphics Laboratory / July 2005