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
Histogram and Colors

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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:

• atoms
  • bfactor – B-factor (temperature factor; generally read from PDB or mmCIF)
  • occupancy – occupancy (generally read from PDB or mmCIF)
  • radius – VDW radius
  • atom attributes generated by certain actions, such as area from using measure sasa, charge from using addcharge, etc.
• residues
  • chi1, chi2, ... amino acid sidechain angles
  • phi, psi, omega – peptide backbone angles
  • residue attributes generated by certain actions, such as area from using measure sasa, or seq_conservation and seq_rmsd from the Sequence Viewer
• structures (atomic models)
  • model attributes generated by certain actions, such as modeller_GA341 and modeller_zDOPE quality scores from comparative modeling

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.

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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 Value and Color settings apply to the threshold most recently moved or clicked:

• A threshold can also be moved by entering a new Value.
• Clicking the Color square (color well) opens the system color editor for choosing a color interactively.

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

• Color missing values with (a color well, default ) 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.
  
  
• Choosing a Palette changes the colors without changing the number of thresholds or their positions. The desired number of thresholds should be present before the palette is chosen; individual colors can be changed afterwards with the system color editor, as described above. Many built-in palettes are available. Only the ones with the same number of colors as the current number of thresholds will be listed; for example, the rainbow palette will not be listed unless there are exactly 5 thresholds in the histogram. If any colors are set interactively, the palette name will be shown as custom.
  
  
• Clicking Reverse threshold colors reverses the current colors without changing the number of thresholds or their positions.
  
  
• Clicking Create corresponding color key opens the Color Key tool and populates it with the current colors and values; a color key can then be drawn interactively in the graphics window using the settings in that tool.
  
  
• Restrict to selection limits coloring to the current selection.

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