measure or measures or monitor or monitors 

Turns on and off the distance, angle, dihedral measurement labels and measurement lines. (To turn off just the labels, use set measurement OFF

Changes all previously defined measurement labels of a given type (n = 2, 3, or 4) to the indicated format. The default label is "%VALUE %UNITS" for all types. Specifically for distances, the suffix //A will use angstroms for the default label for distance measurements. Other suffixes include //nm, //pm, and //vdw. Also available is %#(percent number-sign), which gives the 1-based number of the measurement. Atom information can be included as for labels, adding 1 or 2 to the format code to indicate which atom. So, for example, measure "2:%a1 -- %a2 distance = %0.0VALUE" delivers the two atom names along with the value of the measurement rounded to the nearest integer with no units indicated. Specific units for the measurements can be given after two slashes: measure "2:%a1 -- %a2 distance = %0.1VALUE //A" would display the distance rounded to the nearest 0.1 Angstrom.

Show the distance, angle, or dihedral angle formed by the FIRST atom in each atom expression. The format is optional.

Two atoms specify a distance measurement with an optionally given format. This syntax selects the first atom in the current frame set.

Three atoms specify an angle measurement. The format is optional. This syntax selects the first atom in the current frame set.

Four atoms specify a dihedral angle measurement. The format is optional. This syntax selects the first atom in the current frame set.

Show the distance, angle, or dihedral angle formed by ALL atoms in the first expression with ALL atoms of each additional atom expression. The format is optional.

Show the distance, angle, or dihedral angle formed by ALL atoms in the first expression with ALL atoms of each additional atom expression, provided they form a connected set. The format is optional.

Deletes all measurements.

Deletes a specific measurement, in order of their creation, starting with 1.

Deletes all matching distance, angle, or dihedral angle measurements that are currently defined based on the atom expressions.

Lists all measurements. (Same as show measurements.)

Adding RANGE and two decimal numbers modifies the above commands to limit the measurements created or deleted to only those within this specific range of values in Angstroms (distance) or degrees (angles). The word "RANGE" itself is optional but recommended.

The SEARCH (or SMARTS) option for MEASURE allows powerful atom selection using Jmol SMARTS, particularly involving braces { } to designate the desired two, three, or four atoms. For example, set measurementUnits HZ; measure SEARCH "{[H]}CC{[H]}" will display all three-bond coupling constants calculated for a compound, because { } indicates that we want to do the full match but then only return these specific atoms from that search.

Selects the specified measures for actions without creating or removing it; if the described measure does not exist, the command is ignored; for example:

load $caffeine
measure {_N} {_O} all

measure SELECT 4.5 {_N} {_O}
color measures yellow
measure SELECT 3.5 4.5 {_N} {_O} color green


Selects all measures

List the currently selected measures

Carry out the change only on the currently selected measures; "default" (quoted) parameter sets the format string and units to default values; for example:

load $caffeine
measure {_N} {_O} all
measure SELECT 4.5 {_N} {_O} color orange
measure SELECT 4.5 {_N} {_O} "pm"
measure SELECT 4.5 {_N} {_O} color orange "pm"
measure SELECT 4.5 {_N} {_O}
measure SELECTED color orange
measure SELECTED delete


For a given set of selected measurements, resets units and label format to null (indicating default units and format)

Creates a measure line with ticks along it. There are three levels of ticks - major, minor, and "subminor." Only the major ticks have labels. Which of these tick levels are displayed and the distance between ticks depends upon the parameter that takes the form of a point. The optional keyword FORMAT allows formating of the labels for the major ticks. These are based on an array of strings given after the FORMAT keyword. If the array is shorter than the number of ticks, the formats in the array are repeated. Following that, the optional keyword SCALE allows setting the scale either for each axis direction independently {scaleX, scaleY, scaleZ} or overall (as a decimal number). An optional keyword FIRST allows setting of the initial value of the measure. Finally, two points must be indicated.

See also:

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