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:
Center coordinates:
Best-fit axes:
Best-fit planes or inertia ellipsoids, respectively:
Surface areas:
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:
UCSF Resource for Biocomputing, Visualization, and Informatics /
April 2024