Command: size

Usage:
size  spec  [ atomRadius  [+|-]r_a | default ] [ ballScale  [+|-]b ] [ stickRadius  [+|-]r_b ] [ pseudobondRadius  [+|-]r_pb ]

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

Parameters:

• atomRadius r_a – atomic VDW radius as shown in sphere style. The default VDW radii assigned by atom type can be restored by giving default as the value. Since VDW radii are also used to find interatomic clashes and contacts, generate molecular surfaces, measure surface areas, and identify chain-chain interfaces based on buried surface areas, it may be appropriate to restore default values before such calculations.
  
  
• ballScale factor (initial default 0.3) – scale factor to multiply by VDW radius for ball style. The ballScale parameter applies to an entire atomic model even if only part of the model is specified.
  
  
• stickRadius r_b (initial default 0.2 Å) – bond stick radius and display radius of singleton (zero-bond) atoms in stick style. Within a single atomic model, different bonds can have different stick radii, but a single “stick” radius is used for all singletons and will be adjusted if any singleton in that model is specified.
  
  
• pseudobondRadius r_pb – pseudobond stick radius

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

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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:

value:radius

...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: