H-ras (121p) rendered by residue percentExposed
(see examples)

Items in Chimera such as atoms, bonds, residues, molecule models, and segmentation regions have attributes: properties with names and values.

Values of many attributes can be viewed and changed in the attribute inspectors.

Attributes of atoms, residues, and molecule models can be created:

• automatically by Chimera [atoms] [residues] [molecule models]
• arbitrarily (or changed) with Define Attribute, defattr, or setattr
• by combining other attributes using the Attribute Calculator
• by various other Chimera tools such as Add Charge, Values at Atom Positions, and Multalign Viewer

• rendered visually with Render by Attribute or rangecolor
• displayed as labels (see command labelopt or custom labeling options under Actions... Label)
• used in selection and command-line atom specification
• saved to an assignment file
• reported with list

There are several ways to start Define Attribute, a tool in the Structure Analysis category. Starting Define Attribute brings up a dialog for opening an input attribute assignment file.

One or more molecule models should be chosen from the Restrict to models list; only these will be considered during attribute assignment. Individual models or blocks of models can be chosen with the left mouse button. Ctrl-click toggles the status of an individual model. To choose a block of models without dragging, click on the first (or last) and then Shift-click on the last (or first) in the desired block.

Additional options:

• Open Render/Select by Attribute - whether to open the Render/Select by Attribute tool after assigning attribute values. Even when this option is off, the attribute(s) will be available within the Render/Select by Attribute tool if it is opened later in the session.
• Send match info to Reply Log - whether to send details about the attribute assignments to the Reply Log

Assignments can only affect structures that are open when the attribute is defined/assigned. For example, atoms in models opened after radii have been changed using Define Attribute will have the Chimera default radii.

ATTRIBUTE ASSIGNMENT FILES

Attribute assignment files are simple user- or program-generated text files that can be read by Define Attribute or the command defattr to create attributes and assign their values. Examples are provided below.

A hash symbol # at the beginning of a line indicates a comment. Basic properties of an attribute are described in control lines of the form:

identifier: value

The attribute assignments are described in assignment lines of the form:

(Tab)atom-spec(Tab)attr-value

Control lines and comments can be interspersed with assignment lines. However, if multiple attributes are defined in the same file, the attribute control line should precede all other lines for the corresponding attribute.

Allowed attr-value types are:

• real number (float)
• integer
• boolean (true or false, case-independent)
• color - an attribute whose name ends with color (case-independent) will be interpreted as a color-valued attribute. A color value can be expressed as:
  • a color name (a built-in name or one defined previously with colordef)
  • RGBA values, four space-separated numbers each ranging from 0 to 1 (inclusive) that represent the red, green, blue, and opacity components of the color; if the last number is omitted, the opacity is set to 1 (completely opaque)
• string - a string of any characters except tabs; values that might be interpreted as one of the other types should be enclosed in double quotes

ATTRIBUTE ASSIGNMENT EXAMPLES

• percentExposed.txt creates a new residue attribute, percentExposed, and assigns values previously calculated by Getarea for the protein structure 121p (see raw results). The figure at the top of the page was generated by opening the structure, defining the attribute, and then using Render by Attribute to color the structure and render it as a worm. Atoms are undisplayed except for the ligand (yellow spheres).
  
  
• areaSESgxg.txt creates a new residue attribute, areaSESgxg, solvent-excluded surface area of each type of amino acid in the context of a Gly-X-Gly tripeptide. The values can be used to normalize residue areaSES (automatically generated when a molecular surface is shown) to give fractional exposures of amino acids in protein structures. Thanks to the Murgita laboratory at McGill University for the data. The literature reference is provided in the file, along with instructions for calculating fractional exposures with Attribute Calculator.
  
  
• midasrad.txt assigns atomic radii, i.e., sets values for the existing atom attribute radius. The first specification in the file is #, which assigns a value to all atoms. Subsequent lines reassign the radii of atoms of particular elements. Remember that atoms in models opened after the assignment will have the default radii instead of those in midasrad.txt.
  
  
• rescol.txt sets values for the existing atom attribute color and the existing residue attribute ribbonColor according to amino acid type. Non-amino-acid residues are colored dark gray. The colors are specified with built-in names. Note that the same results can be achieved with a Chimera command file (rescol.com).
  
  
• Several files with different amino acid hydrophobicity scales are provided as alternatives/additions to the built-in Kyte-Doolittle scale (residue attribute kdHydrophobicity):
  • wwHydrophobicity.txt
  • hhHydrophobicity.txt
  • mfHydrophobicity.txt
  • ttHydrophobicity.txt (contributed by Shyam M. Saladi)