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

**area**- report the area of an existing surface (sum of surface triangles)**buriedArea**- calculate solvent-accessible surface area buried between two sets of atoms**convexity**- calculate convexity at each surface vertex, color the surface accordingly**length**- sum bond lengths**mapstats**- report volume data min, max, mean, SD, and RMSD values**motion**- show changes in surface position by drawing lines**sasa**- calculate solvent-accessible surface area**volume**- report the volume enclosed by an existing surface

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

Report the total surface area of an existing surface model, computed as the sum of the areas of its triangles. The•includeMaskedoption controls whether to include parts of the surface that have been hidden, such as withsurface dustorsurface zone(clipping does not affect the measurement, however). See also:measure sasa

Calculate the solvent-accessible surface (SAS) area buried between two sets of atoms, defined as:•½ (wheresasa1+sasa2–sasa12)sasa1is the area of the SAS enclosing the atoms inatom-spec1,sasa2is the area of the SAS enclosing the atoms inatom-spec2, andsasa12is 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 defaultprobeRadiusradfor calculating each SAS is1.4Å, often used to approximate a water molecule. Residues with at leastcutoffAreaareaburied (default1.0Å^{2}) can be:

- listed along with their buried areas in the
Logusing thelistResiduesoption- selected with the
selectoption- colored using
colorcolor-specThe 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 theproteinparts only of chains C and D

measure buried ligand with protein list T sel T

– select and list residues with ≥ 1.0 Å^{2}area buried betweenligandandprotein

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 withwriteSurfaceData, wherefilenamecan be a pathname including the directory location.The remaining options specify coloring. The

patchesoption randomly assigns colors to contiguous patches of vertices with convexity values above theconvexity-threshold. Otherwise (patchesnot used), the surface will be colored by the convexity value per vertex, withpalette-optionsas described forcolor, except with defaults:

Unsmoothed values typically give mottled coloring. See also:palette cyan-gray-maroon range -1,1mlp,color,bumps

Sum the lengths of all bonds between specified atoms (markers); primarily used to measure the length of traced paths of markers.•

Report the minimum value, maximum value, mean, standard deviation (SD) from the mean, and the root-mean-square (RMS) deviation from zero for the specified volume data models, if any, otherwise all such models. The•stepandsubregionoptions can be used to limit the calculation to a subsample or spatial subregion of the data. The step size must be an integer; 1 indicates all data points (default), 2 indicates every other data point, 3 every third point,etc.If a single number is supplied, it is used along all three axes; if three numbers are supplied (separated by commas but not spaces), they are used along the X, Y, and Z axes, respectively. A subregion can be specified by:See also: measurements

namepreviously assigned with thenameRegionoption ofvolume- grid indices
i1–i2along the X axis,j1–j2along the Y axis, andk1–k2along the Z axis. Grid indices must be integers separated by commas but not spaces.- the word
all, indicating the full extent of the data (default) rather than a subregion

Draw “prickles” to show the change in position between a surface and 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-modelin increments of map grid units (using the smallest spacing along the three axes, if they differ) until they intersect with the map isosurface or reachstepsMgrid units in length (default10). Prickles are shown in the specifiedcolor(defaultlime) and can be amplified or shrunken in length by ascalefactorf. If a model number is specified withpricklesModelN, the prickles will be added as a submodel ofN. If a model number is not specified, the new model will be a submodel ofsurf-model.

Calculate the area of a solvent-accessible surface (SAS) enclosing the atoms in•atom-spec1and report the total value in theLog. ThesetAttributeoption specifies whether to assign the values per atom and residue as attributes namedarea(defaulttrue). Thesumoption can be used to report the area contribution from some subset of the atoms (given asatom-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 inatom-spec2that are not also inatom-spec1. The defaultprobeRadiusradfor calculating the SAS is1.4Å, often used to approximate a water molecule. Example:See also:measure sasa #1/a & protein sum :phe,tyr,trp

– calculate the SAS of theproteinin model #1 chain A and report both the total area and the collective contribution from phenylalanine, tyrosine, and tryptophan residuesmeasure area

Report the volume enclosed by an existing surface model. TheincludeMaskedoption controls whether to include parts of the surface that have been hidden, such as withsurface dustorsurface zone(clipping does not affect the measurement, however).

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