Define Attribute Define Attribute icon

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

Atoms, residues, and molecule models have attributes (properties) that can be:

Attribute values can be rendered visually (Render by Attribute, rangecolor) and used in atom specification and selection (Select by Attribute).

Define Attribute allows assignment of attribute values to atoms, residues, and models. New attributes can be created or values (re)assigned for existing attributes. Define Attribute is also implemented as the command defattr.

There are several ways to start Define Attribute, a tool in the Programming and Utilities categories. 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 molecule models that are open when the attribute is defined/assigned. For example, atoms in models opened after radii have been assigned by element will have the default radii, not the element-based ones.

ATTRIBUTE ASSIGNMENT FILES

Examples are provided below.

Comment lines begin with # and can be placed anywhere in the file. Otherwise, the file starts with one or more control lines of the form:

identifier: value
Possible control line contents are:
identifier value
(defaults in bold)
description
attribute alphanumeric string without spaces attribute name (existing or new)
match mode any
non-zero
1-to-1
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)
recipient atoms
residues
molecules
level of attribute assignment

The control lines can be in any order, and only the attribute line is required.

The attribute assignments are described in assignment lines:
(Tab)atom-spec(Tab)attr-value
Additional control lines and comments can be interspersed with the assignments. Any kind of atom specification can be used. Allowed attr-value types are: New numerical attributes will appear in the attribute lists of Render/Select by Attribute; string attributes will be listed only in the Select by Attribute portion; boolean and color attributes will not be listed.

ATTRIBUTE ASSIGNMENT EXAMPLES


UCSF Computer Graphics Laboratory / November 2004