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Command: measure

measure  property  arguments

The measure command performs various calculations and sends results to the Log. Possible values of property:

See also: interfaces, surface, surface zone, VDW radii

measure buriedArea  atom-spec1  withAtoms2  atom-spec2  [ probeRadius  rad ] [ listResidues  true | false ] [ cutoffArea  area ] [ select  true | false ] [ color  color-spec ]
Calculate the solvent-accessible surface (SAS) area buried between two sets of atoms, defined as:
½ (sasa1 + sasa2 – sasa12)
where  sasa1 is the area of the SAS enclosing the atoms in  atom-spec1,  sasa2 is the area of the SAS enclosing the atoms in  atom-spec2, and  sasa12 is the area of the SAS enclosing both sets of atoms together. The sets of atoms should be specified with care; they should not overlap, and solvent, ions, and ligand residues are not excluded automatically. Unspecified atoms are ignored. The default probeRadius rad for calculating each SAS is 1.4 Å, often used to approximate a water molecule. Residues with at least cutoffArea area buried (default 1.0 Å2) can be:

The buried area of a residue is its SAS area in the individual set minus that in the combined set. Examples:

measure buriedarea (/c & protein) with (/d & protein)
– calculate buried surface area between the protein parts only of chains C and D

measure buried ligand with protein list T sel T
– select and list residues with ≥ 1.0 Å2 area buried between ligand and protein
measure convexity  surf-model  [ smoothingIterations  N ] [ writeSurfaceData  filename ] [ patches  convexity-threshold ]  palette-options 
Color a surface based on the convexity at each vertex, calculated as 2π minus the cone-angle spanned by the triangles incident at the vertex. Convexity values are smoothed by averaging with neighboring (edge-connected) vertices for a specified number of iterations (default 5). Smoothing is generally recommended, given that this definition of convexity is nonstandard and the unsmoothed values depend strongly on the triangulation: vertices surrounded by large triangles on a smooth surface will have sharper cone angles than vertices surrounded by small triangles. (Normalizing by triangle areas does not help because the patch around a vertex is often irregular in shape.) The surface vertex positions, normals, convexity values, and triangles can be saved to a text file with writeSurfaceData, where filename can be a pathname including the directory location.

The remaining options specify coloring. The patches option randomly assigns colors to contiguous patches of vertices with convexity values above the convexity-threshold. Otherwise (patches not used), the surface will be colored by the convexity value per vertex, with palette-options as described for color, except with defaults

palette cyan-gray-maroon  range -1,1
Unsmoothed values typically give mottled coloring. See also: mlp, color, bumps
measure length  atom-spec 
Sum the lengths of all bonds between specified atoms (markers); primarily used to measure the length of traced paths of markers.
measure motion  surf-model  toMap  map-model  [ color  color-spec ] [ steps  M ] [ scale  f ] [ pricklesModel  N ]
Draw “prickles” to show the change in position of a surface relative to a volume (map) isosurface, for example, between time steps of a volume series. Prickles are line segments drawn perpendicular to the surface. They are extended from the vertices of surf-model in increments of map grid units (using the smallest spacing along the three axes, if they differ) until they intersect with the map isosurface or reach steps M grid units in length (default 10). Prickles are shown in the specified color (default lime) and can be amplified or shrunken in length by a scale factor f. If a model number is specified with pricklesModel N, the prickles will be added as a submodel of N. If a model number is not specified, the new model will be a submodel of surf-model.
measure sasa  atom-spec1  [ probeRadius  rad ] [ setAttribute  true | false ] [ sum  atom-spec2 ]
Calculate the area of a solvent-accessible surface (SAS) enclosing the atoms in  atom-spec1 and report the total value in the Log. The setAttribute option specifies whether to assign the values per atom and residue as attributes named area (default true). The sum option can be used to report the area contribution from some subset of the atoms (given as  atom-spec2). The calculated SAS is not displayed. The atoms should be specified with care; solvent, ions, and ligand residues are not excluded automatically. Unspecified atoms are ignored, as are atoms in  atom-spec2 that are not also in  atom-spec1. The default probeRadius rad for calculating the SAS is 1.4 Å, often used to approximate a water molecule. Example:
measure sasa #1/a & protein sum :phe,tyr,trp
– calculate the SAS of the protein in model #1 chain A and report both the total area and the collective contribution from phenylalanine, tyrosine, and tryptophan residues

UCSF Resource for Biocomputing, Visualization, and Informatics / May 2018