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Command: measure

Usage:
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 ]  palette-options 
Color a surface by the convexity at each vertex, calculated as 2π minus the cone-angle spanned by the triangles incident at the vertex, optionally 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.) Unsmoothed values typically give mottled coloring. The palette-options for coloring are the same as described for color, except with defaults:
palette cyan-gray-maroon  range -1,1
See also: mlp, color
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 sasa  atom-spec1  [ probeRadius  rad ] [ sum  atom-spec2 ]
Calculate a solvent-accessible surface (SAS) enclosing the atoms in  atom-spec1 and report the total surface area in the Log. In addition, the area contribution from some subset of the atoms (given as  atom-spec2) can be obtained with the sum option. The surface 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 contribution from phenylalanine, tyrosine, and tryptophan residues

UCSF Resource for Biocomputing, Visualization, and Informatics / December 2017