1pho coloring and worms by B-factor (more...)

Tool: Render/Select by Attribute

Render/Select by Attribute performs functions according to the values of attributes (built-in or user-defined):

• visual rendering of numerical attributes with colors, atomic radii, or worms, where a worm is a specialized cartoon of variable radius per residue
• selection by numerical, boolean, or string attribute value

Render/Select by Attribute is the graphical interface to the commands color byattribute, size byattribute, cartoon byattribute, and select (with command-line specification by attribute). See also: Surface Color, Color Key, the color bfactor icon in the Molecule Display Toolbar, the Select menu, measurements

Render/Select by Attribute set to its Render tab can be opened from the Depiction or Structure Analysis section of the Tools menu and manipulated like other panels (more...). Choosing Select... By Attribute Value... from the main ChimeraX menu opens the tool set to its Select tab.

Choosing Model and Attribute
Histogram or List of Attribute Values
Buttons and Context Menu
Colors
Radii
Worms

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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, chains, or structures (atomic models). The Attribute can then be chosen from the list of attributes available within the chosen models.

In the Render tab, only numerical attributes are available, whereas the Select tab also allows using boolean and string-valued attributes. 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
• chains
  • chain attributes (presumably user-defined, as the built-in ones may not be interesting for visualization)
• 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 or List of Attribute Values

In the Render section:

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). It also has an associated Color (if the Colors tab is chosen), Atom radius (if the Radii tab is chosen), or Worm radius (if the Worms tab is chosen). Together, the thresholds specify how the colors or radii should 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.

Restrict to selection limits rendering by attribute to the current selection.

The Select tab of Render/Select by Attribute performs selection of atoms, residues, and structures (atomic models) based on their attribute values. In this section:

If the chosen attribute is numerical, the dialog shows a histogram of its values in the chosen models. The two thresholds or vertical bars on the histogram define a value range for selection, either between (inclusive) or outside their positions. Each threshold can be moved by dragging or directly entering a new value. The Value field applies to the threshold most recently moved or clicked. The no value option allows selecting items with no value assigned for the chosen attribute. For example, nucleic acid residues do not have peptide backbone phi angles.

If the chosen attribute is boolean, checkboxes allow specifying whether to select items for which the attribute is true or false.

If the chosen attribute is string-valued, a list of the values is shown. Individual rows or blocks of values can be chosen/unchosen by mouseclick or drag. Note that for the alt_loc attribute, only the values of currently used locations are listed, not all those present in the input file. Which alternate locations to use can be set with the AltLoc Explorer or the altlocs command.

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Buttons and Context Menu

Clicking Apply performs the action (rendering or selection) without closing the dialog, whereas OK performs the action and dismisses the dialog. Clicking Save File... opens a dialog to save attribute values to an attribute assignment file. Close simply dismisses the dialog, and Help shows this page in the Help Viewer.

Render/Select by Attribute has a context menu with choices including:

• Histogram Scaling – histogram bar heights indicate the prevalence of different values of the attribute, with scaling as follows:
  • Linear
  • Logarithmic (default)

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Colors

The Value and Color settings apply to the threshold most recently moved or clicked. Clicking a 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. 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.

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Radii

The Value and Atom radius settings apply to the threshold most recently moved or clicked. Rendering will change the VDW radii of the atoms. If needed, default VDW radii can be restored with the size command.

• Atom style
  • sphere (default) – display radius same as VDW radius, directly reflecting the user-specified sizes
  • ball – VDW radius multiplied by the ball scale factor (usually 0.3)
  • unchanged – retain the pre-existing style of each atom (stick, ball, or sphere); note stick size is unaffected by VDW radii
  
  
• Affect no-value atoms – whether to use the No-value radius (below) for atoms, residues, or atomic 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 VDW radii.
  
  
• No-value radius – VDW radius to assign to no-value atoms when the Affect no-value atoms option (above) is used

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Worms

The Value and Worm radius settings apply to the threshold most recently moved or clicked. Attribute values are mapped to worm radius on a per-residue basis, and only biopolymer chains can be shown as worms. If an atom attribute is given, the average value over all atoms in a residue is used for that residue.

• No-value radius – worm radius to use for biopolymer residues that have no value assigned for the chosen attribute

Once generated, the worm radii are remembered separately from the other cartoon parameters as a residue attribute named worm_radius. Clicking Deworm returns to the previous non-worm cartoon. The command cartoon byattribute (worm) can also be used to toggle back and forth between the previous non-worm cartoon and a previously defined worm display.