Since essentially all calculations can be said to involve measurement, this list is not exhaustive.

Distances between atoms (or markers):

**distance**command,**Distances**tool – between a specified or selected pair of atoms- selection context menu when two atoms are selected
**clashes/contacts**– all-by-all distances within a cutoff for two sets of atoms, optionally shown as labels**hbonds**– H-bond distances, optionally shown as labels**label**– label bonds or pseudobonds by length**measure length**– sum the lengths of all bonds between specified atoms**crosslinks histogram**– plot pseudobond length distribution

Angles:

**torsion**– torsion angle defined by four atoms

Center coordinates:

Surface areas, atomic:

**measure sasa**– area of solvent-accessible surface enclosing a set of atoms**measure buriedArea**– area of solvent-accessible surface buried between two sets of atoms**interfaces**– all-by-all pairwise buried areas for chains in an atomic model, with corresponding network diagram

Fit measures:

**align**– root-mean-square distance (RMSD) between two sets of atoms**matchmaker**– pairwise RMSD between biopolymers using one point per residue**fitmap**– average map value at atom positions, or map-map overlap or correlation

Other map (volume data) measurements:

**measure mapstats**– min, max, standard deviation, root-mean-square deviation from zero**measure volume**– isosurface-enclosed volume**measure area**– isosurface area (sum of triangle areas)**bumps**– isosurface protrusions

Coloring or other display of spatially varying quantities:

**color byattribute**– coloring by atomic B-factor or other numerical attributes of atomic structures**mlp**– molecular surface coloring by lipophilicity potential**color sample**,**color electrostatic**– surface coloring by map value**color gradient**– surface coloring by map gradient norm**measure convexity**– surface coloring by convexity at each vertex**measure motion**– “prickles” showing the offset between a surface and a map isosurface (to compare time steps in a volume series)

UCSF Resource for Biocomputing, Visualization, and Informatics / January 2019