Define Attribute Define Attribute icon

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

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:

and then: Define Attribute reads atom, residue, and molecule model attributes from assignment files. Values of existing attributes can be reassigned, or entirely new attributes created. The resulting attributes are included in saved sessions. Define Attribute is also implemented as the command defattr. See also: the Attributes tutorial, segmentation region attributes

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:

OK performs the assignment and dismisses the dialog, whereas Apply performs the assignment without dismissing the dialog. Close simply dismisses the dialog. Help opens this manual page in a browser window.

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 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
Possible control line contents:
identifier value description
alphanumeric string without spaces; can include underscores; cannot begin with a digit or underscore; atom attributes with names containing area, volume, or charge (after word separation by camel case and/or underscores) will be totaled automatically to give the corresponding residue attributes attribute name, existing or new
match mode
any (default)
expected matches per assignment line (an error message will be sent to the Reply Log when a line's match behavior differs from the match mode)
atoms (default)
level of attribute assignment
none handling
None (default)
treatment of values given as none or None: as the Python value None, as a string, or as removal of any assignment of that attribute from the specified item

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

Any kind of atom specification can be used.

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:

New numerical attributes will appear in the attribute lists of Render/Select by Attribute; boolean and string attributes will be listed only in the Select by Attribute portion; color attributes will not be listed.


UCSF Computer Graphics Laboratory / August 2020