ChimeraX docs icon

Command: size

size  spec  [ atomRadius  [+|-]ra | default ] [ ballScale  [+|-]b ] [ stickRadius  [+|-]rb ] [ pseudobondRadius  [+|-]rpb ]

The size command sets radius parameters. Each parameter can be set to a specific value or adjusted relative to the current value(s) by adding or subtracting a constant amount. Relative changes are indicated with a plus or minus sign, for example:

size ligand atomRadius +.5


Style is controlled with the style command and/or Molecule Display icons.

Bonds and pseudobonds can be specified by their endpoint atoms or directly by selection and using the word sel. Pseudobonds can also be specified by pseudobond model number or built-in classifications: pbonds, hbonds.

Marker and link radii can also be adjusted in the Marker Placement tool, with the mouse , or with marker change. See also: cartoon style, set subdivision, hbonds, crosslinks, setattr, Selection Inspector

Atomic Radius by Attribute

Usage: size byattribute  attribute-name   atom-spec  [ values-and-radii ] [ noValueRadius  radius ] [ style  sphere | ball | unchanged ] [ average  residues ]

Atomic VDW radii can be adjusted to show the values of a numerical attribute. Several attributes are present automatically, but others can be defined by the user arbitrarily or created by various ChimeraX tools and commands (details...). The graphical interface to size byattribute is Render by Attribute. See also: color byattribute, cartoon byattribute (worm)

The values and radii specification can be given as two or more space-separated pairs of the form:


...where value can be min or max as well as a numerical value of the attribute. The default mapping is:

min:1 max:4

Atoms without an assignment (or within residues or atomic structures without an assignment) for the specified attribute will be left unchanged unless a radius is specified with the noValueRadius option.

The style option indicates what style the atoms should be assigned:

  • sphere (default) – display radius same as VDW radius, directly reflecting the user-specified sizes
  • ballVDW 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

    Using average residues means to use the average attribute value over a whole residue for each atom within that residue.

    UCSF Resource for Biocomputing, Visualization, and Informatics / March 2024