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Tool: Render by Attribute

Render by Attribute colors atomic models and molecular surfaces to show the values of a numerical attribute such as atomic bfactor or residue area. Render by Attribute is the graphical interface to the command color by attribute. See also: Surface Color, Color Key, the color bfactor icon in the Molecule Display Toolbar

The Render by Attribute dialog can be opened from the Depiction or Structure Analysis section of the Tools menu and manipulated like other panels (more...).

Choosing Model and Attribute

The Models list includes all open atomic models. 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.

The Attribute of menu specifies whether the attribute of interest is at the level of atoms, residues, or structures (atomic models). The Attribute can then be chosen from the list of attributes available within the chosen models. Only numerical attributes can be used for coloring; these may include:

Custom attributes of atoms, residues, and molecule models can be created arbitrarily with defattr and setattr and (if numerical) mapped to colors with this tool.

Histogram and Colors

Choosing an attribute as described above shows a histogram of its values in the chosen models. Each threshold or vertical bar on the histogram has a Value (position on the histogram) and a Color. Together, the thresholds specify how colors map to values. Clicking on a threshold shows its Value in black. Clicking elsewhere within the histogram shows the Value (X-coordinate) of the mouseclick in gray. A threshold can be moved by changing its Value and then pressing Enter (return) or by dragging it horizontally with the left mouse button.

Thresholds can be added by Shift-clicking on the histogram, whereas Shift-clicking an existing threshold deletes it. The Color square (color well) applies to the threshold most recently moved or clicked. Clicking the color well opens the system color editor to allow choosing a color interactively.

Coloring can be applied to atoms, cartoons, and/or molecular surfaces.

The Color missing values with (a color well, default
) option allows coloring atoms, residues, or models that have no value assigned for the chosen attribute. For example, nucleic acid residues do not have peptide backbone phi angles. If the option is turned off (unchecked), any no-value atoms, etc. will retain their current colors.

Restrict to selection limits coloring to the current selection.

Clicking Apply performs the coloring without closing the dialog, whereas Apply performs the coloring and dismisses the dialog. Close simply dismisses the dialog, and Help shows this page in the Help Viewer.


UCSF Resource for Biocomputing, Visualization, and Informatics / October 2022