[ atomRadius ra | default ]
[ ballScale b ]
[ stickRadius rb ]
[ pseudobondRadius rpb ]
The size command sets the following:
– atomic VDW radius as shown in
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 the 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.
(initial default 0.2 Å)
– bond stick radius and display radius of singleton (zero-bond) atoms in
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.
– 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.
UCSF Resource for Biocomputing, Visualization, and Informatics /