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

Distances between atoms or markers:

- selection context menu when two atoms are selected
**Distances**tool,**distance**command,**distance**mouse mode – create a distance monitor (which updates automatically as needed) between a specified or selected pair of atoms-
**Clashes/Contacts**tools,**clashes/contacts**commands – all-by-all distances within a cutoff for two sets of atoms, optionally shown as labels **H-Bonds**tool,**hbonds**command – H-bond distances, optionally shown as labels**pbond**command – pseudobond length, optionally shown as a label**label**– label bonds or pseudobonds by length**measure length**– sum the lengths of all bonds between specified atoms**crosslinks histogram**– plot pseudobond length distribution**tape measure**mouse mode – drag to measure distance; also works with volume data, cartoon, and molecular surface displays (details...)**Axes/Planes/Centroids**– distances between axis, plane, and/or centroid objects; min/max/mean distances between such objects and selected atoms

Angles:

**angle**– angle defined by three atoms, four atoms, or two objects (axes and/or planes)**torsion**– torsion angle defined by four atoms**Angles/Torsions**– both kinds of angle measurements**Axes/Planes/Centroids**– angle defined by two objects (axes and/or planes)

Center coordinates:

Best-fit axes:

**Axes/Planes/Centroids**, command**define axis**

Best-fit planes or inertia ellipsoids, respectively:

Surface areas:

**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**measure contactarea**– area of one surface within a cutoff distance of another surface

Fit measures:

**align**– root-mean-square distance (RMSD) between two sets of atoms after fitting**rmsd**– RMSD between two sets of atoms without fitting**matchmaker**– pairwise RMSD between biopolymers using one point per residue**fitmap**– average map value at atom positions, or map-map overlap or correlation**measure correlation**– map-map correlation in current positions (without fitting)**measure rotation**– not exactly a measure of fit, but of the current transformation of one model coordinate system relative to another

Other map (volume data) measurements:

**Measure Volume and Area**, commands**measure volume**and**measure area**– total enclosed volume and surface area (sum of triangle areas) of a surface model**Measure and Color Blobs**, command**measure blob**– surface area, enclosed volume, and dimensions of individual blobs (disconnected surface parts)**Map Coordinates**– grid position and scaling in x,y,z coordinates (voxel size,*etc.*)**Map Statistics**, command**measure mapstats**– min, max, mean, standard deviation, root-mean-square deviation from zero**measure mapvalues**– assign map values at atom positions as an attribute that can then be used for coloring, command-line specification,*etc.***measure symmetry**– check for certain symmetries in standard orientations**bumps**– isosurface protrusions**vseries measure**– for each member of a volume series: isosurface level, centroid, distance from previous centroid, cumulative path length along centroids, surface-enclosed volume, surface area, lengths of principal axes

Coloring or other display of spatially varying quantities:

**Render by Attribute**tool,**color byattribute**command – coloring by atomic B-factor or other numerical attributes of atomic structures**Render by Attribute**tool,**size byattribute**command – adjusting atomic radii to show numerical attributes**coulombic**– molecular surface coloring by Coulombic electrostatic potential**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 / April 2024