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)**blob**– measure surface area, enclosed volume, and dimensions of a disconnected surface blob**buriedarea**– calculate solvent-accessible surface area buried between two sets of atoms**center**– calculate center of mass of map, atoms, and/or surface**contactarea**– report the area of one surface within a cutoff distance of another**convexity**– calculate convexity at each surface vertex, color the surface accordingly**correlation**– report map-map correlation**inertia**– calculate inertia ellipsoid**length**– sum bond lengths**mapstats**– report volume data min, max, mean, SD, and RMSD values**mapvalues**– calculate volume data values at atom positions and assign them as an atom attribute**motion**– show changes in surface position by drawing lines**rotation**– report transformation of one model relative to another**sasa**– calculate solvent-accessible surface area**symmetry**– check map for certain symmetries in standard orientations**volume**– report the volume enclosed by an existing surface**weight**– report the sum of atomic weights in daltons

See also:
**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. Parts hidden by clipping are always included, however (details...). See also:measure sasa,surface splitbycolor,Measure Volume and Area

Report measurements for the blob (disconnected surface part) in the specified surface model containing•triangleNumberN. The surface-model specification cannot be blank. Although not generally known in advance, the triangle number is included in the command echoed to theLogwhen thepick blobmouse mode is used, so that the action could be replicated in a script. Measurements include:Blob color is left unchanged unless a

volumeenclosed in the blobareaof its triangulated surface- if
reportSizeistrue(default), thesizein dimensions from longest to shortest of the bounding box aligned with principal axes (details...)coloris given. Theoutlineoption shows the bounding box as an outline in the specifiedoutlineColor(defaultlime). See also:

marker connected,Measure and Color Blobs

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 betweenligandandproteinFor surfaces without associated atomic coordinates, see

measure contactarea. See also:interfaces

Calculate the center of mass of each density map, surface (other than a map surface), and/or set of atoms in•spec. The centers of mass are reported in scene coordinates, and map centers also in grid indices. The approach for surfaces is analogous to that for atoms, except that the points in space are the vertices of the triangulated surface. Each vertex is weighted by ⅓ of the sum of the areas of all attached triangles. This treats the surface as a thin shell. Theleveloption indicates using only map regions abovecontour-level. Ifmarkistrue, a marker will be placed at at each computed center, with radiusmarker-radius(default based on the contents ofspec) and color (default#b4b4b4). The marker model is opened as number

model-number(default next unused number) with namemodel-name(default based on the contents ofspec). Atomic mass-weighting is always used, but the related commanddefine centroidallows calculating the non-mass-weighted center of a set of atoms. See also:cofr

Report the surface area of one surface model (•surf-model1) that lies withindistanced(default3.0Å) of another surface model (surf-model2). Unlessshow falseoroffset 0is specified, a new surface model is created to show the corresponding patch ofsurf-model1. The default color for the patch isred. The new surface can beoffsetfrom the originalsurf-model1by a distanced2(default1.0Å). An offset of zero indicates recoloringsurf-model1to show the patch instead of creating a new surface model. Theslaboption overrides anyoffsetand generates a slab of finite thickness instead of a single layer of surface. If a single value is supplied for the slabwidth, its inner and outer layers will be offset fromsurf-model1by ±½(width). Alternatively, two values separated by a comma but no spaces can be used to specify the offsets of the two slab layers independently. Patch or slab offsets can be positive (outward) or negative (inward)., which is taken at theOffsets affect only the display, not the area measurementsurf-model1surface. Thesmoothoption smooths the new surface but is generally not recommended. Theoptimizesetting speeds up the calculation by disregarding far-apart portions of the surfaces.For atomic structures,

measure buriedareamay be more appropriate.

Color a surface based on the convexity at each vertex, calculated as 2π minus the cone-angle (in steradians) 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 relate to 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. Whenpalette cyan-gray-maroon range -1,1measure convexityis run interactively (in gui mode and not via a script), thekey trueoption can be used to startColor Keyand draw a color key with the corresponding colors and values.

Calculate the correlation between two volume data sets (maps) in two ways:•

< u,v>correlation=| u||v|where vector

< u–u_{ave},v–v_{ave}>correlation about mean=| u–u_{ave}||v–v_{ave}|ucontains the values of the first map (volume-spec1) andu_{ave}is a vector with all components equal to the average of the components ofu. Vectorsvandv_{ave}are defined analogously for the second map (volume-spec2), except that the values are sampled at the grid point locations of the first map using trilinear interpolation. Ifenvelopeistrue(default), the calculation will include only the grid points in the first map with values above its lowest contour level inVolume Viewer. Otherwise, all nonzero-valued grid points will be included.See also:

volume,molmap,fitmap,Fit to Segments

Calculate the inertia ellipsoid for•atom-spec, which could include atoms and/or surfaces. Atoms are mass-weighted; surfaces are treated as thin shells with mass proportional to surface area (details...). If both atoms and surfaces are specified, separate ellipsoids are calculated (a combined calculation cannot be performed). Principal axes, lengths, moments, and center are reported for each ellipsoid, using the model coordinate system of the first atom or surface specified to define it. The vectors v1, v2, and v3 are the principal axes (longest to shortest). The lengths a, b, c are half-diameters along axes v1, v2, and v3, respectively. The moments r1, r2, and r3 are calculated as (inertia/mass)^{½}about axes v1, v2, and v3, respectively. They can be considered effective radii; placing all of the mass at that distance from the center would reproduce the moment of inertia calculated for the structure around that axis.The

perChainoption indicates whether to calculate a separate ellipsoid for each chain inatom-spec. IfshowEllipsoidistrue(default), the ellipsoid(s) will be opened as a surface model withmodelIdmodel-number(default the next unused number), containing multiple submodels if there are multiple ellipsoids. Thereplace trueoption allows replacing an existing model when the specifiedmodel-numberis already in use. If ellipsoidcoloris not specified, each ellipsoid will be colored to match the first atom or surface in its calculation.Another way to generate a low-resolution representation of an atomic structure is with

molmap. See also:define,shape ellipsoid, 3D object formats, convex hull recipe

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:The default is to use the current subregion (if cropped) and current step size of each specified map. This command is also implemented as

- 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 rather than a subregionMap Statisticsin theVolume Datasection of theToolsmenu.

Calculate volume data (map) values at atom positions and assign them as an atom attribute. The•attribute-nameshould be enclosed in quotation marks if it contains spaces; if no name is supplied,mapvaluewill be used. Atoms that fall outside the map bounds are not assigned values. Assigning an attribute allows coloring the atoms by value withcolor byattribute, specifying them by value in the command line,etc.The new attribute is saved in session files.

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 a

scalefactorf. 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.

Report the transformation of•model1relative tomodel2as:

- a matrix in which the first three columns describe a rotation and the fourth describes a translation (performed after the rotation)
- an axis of rotation (a unit vector), point on the axis, rotation angle, and shift parallel to the axis
It reports the current rotation and translation between the coordinate systems of the two models, which would be zero unless one model was moved relative to the other, either with the mouse (using one of the rotate/translate selected modes) or with some other tool or command such asThis command does not evaluate how to best fit or match the two models.Fit in Map,align, ormatchmaker. (Moving everything collectively, such as rotating or zooming to get a better view, does not change the positions of models relative to each other.)To get the transformation between atomic structures that are similar but displaced from one another (without actually superimposing them), using the

aligncommand withmove falseandreportMatrix trueis recommended instead.The transformation is expressed in the coordinate system of

model2unless specified otherwise with thecoordinateSystemoption. IfshowAxisistrue(default), a model showing the axis as a rod will be created, with the specifiedlength(default the largest dimension of the bounding box of the displayed part ofmodel2),radius(default 2.5% of the length), andcolor(default#d2d264). The

axisTypeoption specifies whether the axis should be created as a marker model (default) or as an axis object (such as could be used to reorient the view or in various measurements). IfshowSlabsistrue(defaultfalse), two rectangular slabs showing the rotation axis and angle and the shift will be created as surface models, with the specifiedlength(default described above),width, andthickness(defaults 50% and 2.5% of the length, respectively) and colored according tocolorandcolor2(defaults#d2d264and

cornflower blue, respectively).

See also:

fitmap,view matrix, ChimeraX positions files

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

Check each specified volume data model (map) for cyclic, dihedral, tetrahedral, octahedral, and icosahedral symmetries in standard coordinate systems. Helical symmetry can be considered if approximate parameters are supplied. The symmetry assignment can be used by other commands such as•sym,molmap, andfitmap, and is included in Chimera map format. For direct assignment of a specified symmetry, seevolume symmetry.If the correlation of the map with itself after symmetry transformation is at least

mincorr(default0.99), the detected type of symmetry will be reported, and ifsetis true (default), assigned to the map in ChimeraX. The correlation calculation uses only map points with values above the displayed contour level; if the number of such points exceedsmaxpts(default10,000), a random sample ofmaxptsis chosen from them and used. Values in the first copy of the map are compared with the superimposed (interpolated) values in the rotated copy of the map.Center of point symmetry is considered only at the following:

For cyclic and dihedral symmetry, rotation is considered only about the Z axis, and for dihedral symmetry, flipping symmetry only about the X or Y axes. Cyclic (C

- the grid point nearest the average indices of grid points with values above the displayed contour level. The map's lowest contour level in
Volume Vieweris used.- one or two grid points based on the overall map dimensions: only the midpoint along axes with odd numbers of points, and along axes with even numbers of points, those on either side of the midpoint. Rather than all possible combinations for axes with even numbers of points, only the two points with all indices lower or all higher are evaluated.
n) symmetry is checked for ordernup tonMax, default8. If more than one Cnsymmetry meets the criterion, those for which a higher multiple is also found are discarded, and of the remaining, the one with the highest correlation is assigned. For example, ifn= 2, 3, 6, and 7 were to meet the criterion, 6-fold would override 2- and 3-fold, and 6-fold or 7-fold symmetry, whichever gave the highest correlation, would be assigned. Tetrahedral symmetry is considered in two orientations:

- 2-folds along X, Y, and Z, with a 3-fold along axis (1,1,1)
- 3-fold along Z, with a second 3-fold in the YZ plane such that rotation about the X axis by ~110° is a symmetry operation (EMAN convention)
Icosahedral symmetries are only considered in eight orientations:

- 222 – with two-fold symmetry axes along the X, Y, and Z axes
- 2n5 – with two-fold symmetry along X and 5-fold along Z
- n25 – with two-fold symmetry along Y and 5-fold along Z
- 2n3 – with two-fold symmetry along X and 3-fold along Z
- 222r – same as 222 except rotated 90° about Z
- 2n5r – same as 2n5 except rotated 180° about Y
- n25r – same as n25 except rotated 180° about X
- 2n3r – same as 2n3 except rotated 180° about Y
The

helixoption specifies looking for helical symmetry with approximaterise(in physical units of distance, typically Å) andangle(degrees) per asymmetric unit. If this option is used, the other types of symmetry are not considered except for combined helical and cyclic symmetry (for example, EMD-1757, approximately 42 Å rise and 21° twist per subunit). Helical symmetry is infinite, but the number of copies to place when considering that symmetry,n, is necessarily finite. If not given,nwill be determined by dividing the apparent length of the helix in the map by the rise and rounding to the nearest positive integer. Theoptkeyword indicates optimizing the fit of the map copies to itself to identify more accurate helical parameters.

Report the volume enclosed by an existing surface model. The•includeMaskedoption controls whether to include parts of the surface that have been hidden, such as withsurface dustorsurface zone. Parts hidden by clipping are always included, however (details...). See also:Measure Volume and Area

Report the total mass in daltons of the specified atoms. Atoms missing from the structure (e.g.hydrogens, truncated sidechains, missing segments) will not be included.

**Inertia calculation**.

The command **measure inertia**
computes the moments of inertia of a set of atoms as in classical mechanics:

II is a 3x3 matrix with indices j and k (j=1,2,3 and k=1,2,3). Each matrix element is a sum over atoms, where m_{jk}= Σ_{i}(m_{i}(δ_{jk}|x_{i}|^{2}– x_{i,j}x_{i,k}))

- For atoms, we show the surface of a uniform-density solid ellipsoid that has the same principal axes and moments as the atoms.
- For surfaces, we show an ellipsoidal surface that as a thin shell has the same axes and moments as the measured surface.

UCSF Resource for Biocomputing, Visualization, and Informatics / October 2024