Measurements

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
  • the distance command can also measure distances from an atom to an object (axis or plane) or between two objects, but without adding a distance monitor
• 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:

• measure center
• Axes/Planes/Centroids, command define centroid

Best-fit axes:

• Axes/Planes/Centroids, command define axis

Best-fit planes or inertia ellipsoids, respectively:

• Axes/Planes/Centroids, command define plane
• measure inertia

Sum of atomic weights:

• measure weight

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
• Find Cavities, kvfinder – surface areas (as well as volumes) for the identified cavities and pockets

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)