The Structure Measurements panel has four sections:

• Distances - monitor distances
• Angles/Torsions - monitor angles and torsions
• Adjust Torsions (now located in Build Structure) - rotate bonds
• Axes/Planes/Centroids - show axes, planes, and centroids based on sets of atoms, perform related measurements

Atomspec display style in the General preferences controls how atoms are listed in the Structure Measurements dialog. The Distances figure shows the simple style (residue name, residue specifier, and atom name). For an example of command-line specifiers, see the Adjust Torsions figure.

Save saves measurements to a file. Close closes the measurements panel, and Help opens this manual page in a browser window.

Distances

The Distances section of Structure Measurements is a table of distance monitors (measurements that update if there are changes). Distance monitors are saved in sessions. See also: distance

There are several ways to start Distances, a tool in the Structure Analysis category. Distance monitors can be created in several ways:

• Selecting exactly two atoms, then clicking the Create button on the dialog. With default mouse settings, two atoms can be picked (selected from the graphics window) by Ctrl-clicking the first and Shift-Ctrl-clicking the second.
• Doubleclick-picking an atom when one other atom is already selected, then choosing Show Distance from the resulting context menu.
• Doubleclick-picking an atom when 0 or >3 other atoms are already selected, then choosing Show Distances to Nearby Residues from the resulting context menu.
• Using the distance command.

Distances - simple atom listings

A distance monitor can be chosen by clicking on its line, and more than one can be chosen at a time. Chosen lines are highlighted in the dialog. Ctrl-click toggles the status of a line, while clicking on the first (or last) line of a contiguous block and then Shift-clicking on the last (or first) chooses all of the lines in the block.

Choosing a distance listing selects the corresponding distance pseudobond. The Choosing in table... option allows additionally selecting the corresponding atoms. Remove deletes the chosen distance monitors. If there is only one, it is not necessary to choose it before using Remove.

The Labels setting applies to all distance monitors and can be switched among:

• None - no label
• ID - distance monitor ID number (the first column in the listing)
• Distance - the distance in angstroms

The lines drawn to represent distance monitors are pseudobonds in a group named distance monitor. Clicking Display options... brings up a list of pseudobond attributes for this group, allowing changes in properties such as color, linewidth, and whether the lines are dashed. When an individual pseudobond is selected, its attributes can be altered with the Selection Inspector.

Angles/Torsions

The Angles/Torsions section of Structure Measurements is a table of angle monitors (measurements that update if there are changes). A “bond angle” is measured for three atoms and a “torsion angle” for four atoms; however, it is not necessary for the atoms to be contiguous or even bonded to one another. Angle monitors are saved in sessions.

Angles/Torsions reports changes but cannot be used to change the angles. Angles can be changed using Adjust Bond Angles and Adjust Torsions.

There are several ways to start Angles/Torsions, a tool in the Structure Analysis category. Angle monitors can be created in various ways:

• Selecting exactly three atoms for a bond angle or four atoms for a torsion angle, then clicking the Create button on the dialog. With default mouse settings, atoms can be picked (selected from the graphics window) by Ctrl-clicking the first and Shift-Ctrl-clicking additional atoms.
• Doubleclick-picking an atom when two other atoms are already selected, then choosing Measure Angle from the resulting context menu.
• Doubleclick-picking an atom when three other atoms are already selected, then choosing Measure Torsion from the resulting context menu.

A measurement in the list can be chosen by clicking on its line, and more than one can be chosen at a time. Chosen lines are highlighted in the dialog. Ctrl-click toggles the status of a line, while clicking on the first (or last) line of a contiguous block and then Shift-clicking on the last (or first) chooses all of the lines in the block.

Choosing an angle monitor also selects the corresponding atoms and bonds when the Choosing in table... option is on. Remove deletes the chosen measurement(s). If there is only one measurement, it is not necessary to choose it before clicking Remove.

The Decimal places setting controls how angles are reported in the table; the number of digits shown after the decimal can be changed by clicking or holding down one of the arrows on either side of the value.

The command angle can also be used to measure bond angles and torsions; however, it yields a static measurement rather than a continuously updating monitor.

dopamine D3 receptor helix axes, membrane planes (see Image Gallery entry)

Axes/Planes/Centroids

The Axes/Planes/Centroids section of Structure Measurements allows defining geometric objects (axes, planes, centroids) based on sets of atoms and performing measurements involving the objects. Axes are displayed as rods, planes as disks, and centroids as spheres. Objects to be listed in the Axes/Planes/Centroids table can also be created with the command define. Each object is created in the coordinate system of the lowest-numbered model involved in its calculation. Axes/Planes/Centroids objects and information are saved in sessions. See also: distance, angle, shape, measure inertia, PipesAndPlanks, BILD format

There are several ways to start Axes/Planes/Centroids, a tool in the Structure Analysis category.

Clicking Define axes... opens a dialog for specifying atom sets and other axis parameters. Eigenvectors/values are calculated from the coordinates of each set of atoms after subtracting the position of their centroid. Each axis is anchored at the corresponding centroid and aligned with the first eigenvector of the corresponding coordinates (prior to any helical correction).

• Each helix in [models] - define an axis for each peptide/protein helix in the molecule model(s) chosen in the list. Peptide/protein helix assignments are taken from the input structure file or generated with ksdssp. Only the backbone atoms N, CA, C are used to define the axes. Sometimes two helices are adjacent in sequence (not separated by any other residues), and the integer-valued residue attribute ssId is used to distinguish them. Although such cases are detected automatically, ssId can also be set manually with setattr.
  
  
• Selected atoms (axis name [name]) - define a single axis named name using all selected atoms
  
  
• Axis Parameters:
  • Mass weighting (only available for the Selected atoms option) - calculate major inertial axis by mass-weighting the atoms; cannot be combined with helical correction
  • Use helical correction - adjust axis orientation to reduce the spread of atom-axis distances; cannot be combined with mass weighting. While usually small, helical correction improves results for short helices.
  • Replace existing axes - whether to remove any/all pre-existing axis objects
  • Color (a color well, default No Color, meaning to match the structure as much as possible)
  • Radius
    • average axis-atom distance (default) - if this setting is chosen but an axis is based on only two atoms, the last used constant value (below) will be applied instead
    • angstroms (a constant value)

Clicking Define plane... opens a dialog for defining a plane based on the selected atoms. Eigenvectors/values are calculated from the atomic coordinates after subtracting the position of their non-mass-weighted centroid. The plane is anchored at the centroid and aligned with the first two eigenvectors (the third eigenvector is normal to the plane).

• Plane name
• Replace existing planes (true/false) - whether to remove any/all pre-existing plane objects
• Color (a color well, default No Color, meaning to match the source atoms as much as possible)
• Set disk size to enclose atom projections (true/false) - whether the disk radius should be set to span the projections of the defining atoms back onto the plane. If true, an Extra radius (padding) can be specified (default 0.0 Å). If false, a Fixed radius can be specified (default 10.0 Å). The disk center is the non-mass-weighted centroid of the atoms.
• Disk thickness (Å)

Clicking Define centroid... opens a dialog for defining a centroid based on the selected atoms:

• Centroid name
• Mass weighting (true/false) - whether to mass-weight atoms when calculating the centroid
• Replace existing centroids (true/false) - whether to remove any/all pre-existing centroid objects
• Color (a color well, default No Color, meaning to match the source atoms as much as possible)
• Radius (Å)

Columns in the Axes/Planes/Centroids table of objects:

• Name
• color - an object can be recolored by clicking its color well and using the Color Editor, or by selecting the object and using the Actions... Color menu
• ID - object identifier, aN for axes, pN for planes, cN for centroids
• Shown - whether the object is displayed
• Length - axis length, end-to-end distance needed to span the projections of the defining atoms back onto the axis
• Radius - object radius

An object can be chosen by clicking on its line, and more than one can be chosen at a time. Chosen lines are highlighted in the dialog. Ctrl-click toggles the status of a line, while clicking on the first (or last) line of a contiguous block and then Shift-clicking on the last (or first) chooses all of the lines in the block.

Choosing any two objects reports their applicable geometric relationships below the table and in the Reply Log. For angle measurements, axes and planes are treated as infinite. For distance measurements, axes are treated as finite line segments, while planes are treated as infinite. Optionally, choosing objects also:

• selects object - selects each object (currently nothing can be done to such a selection, but the objects are highlighted in the graphics window)
• selects atoms - selects the atoms used to define each object

Clicking Delete removes the chosen objects. In addition, closing a molecule model or deleting atoms removes any objects defined using those atoms. Rename allows changing the names of the chosen objects; this will change their order in the table if sorting is currently by name. Report distance measures distances between the chosen objects and selected atoms; results are sent to the Reply Log. If a single atom is selected, the distance to each chosen object is reported; if multiple atoms are selected, the minimum, maximum, and mean distances are reported.

Axis/plane/centroid information written out with Save includes name and untransformed center coordinates (x_c,y_c,z_c). Axis information also includes length and orientation expressed as a unit vector (x_u,y_u,z_u). Axis endpoint coordinates (x₁,y₁,z₁) (x₂,y₂,z₂) can be generated as follows:

Plane information also includes radius and orientation expressed as a normal unit vector.