The Structure Measurements panel has four sections:

• Distances - monitor distances
• Angles/Torsions - monitor angles and torsions
• Adjust Torsions - 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), while the Adjust Torsions figure shows command-line specifiers.

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 three ways:

• The Create button creates a distance monitor between two atoms that have been selected (exactly two atoms must be selected).
• Picking one atom and Shift-double-picking the second atom (that is, doubleclicking it with the button assigned to picking) elicits a button marked Show Distance. Clicking it creates the distance monitor and leaves the atoms in a selected state. Clicking elsewhere removes the button without creating a distance monitor but leaves the atoms in a selected state.
• The command distance can also be used.

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. To modify torsions, use Adjust Torsions instead.

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

• The Create button creates an angle monitor for atoms that have been selected (exactly three or four atoms must be selected; a bond angle is measured when three atoms are selected, a torsion angle when four atoms are selected).
• Picking two atoms and then Shift-double-picking the third (that is, doubleclicking it with the button assigned to picking) elicits a button marked Measure Angle. Clicking it creates a bond angle monitor and leaves the atoms in a selected state. Clicking elsewhere removes the button without creating a monitor but leaves the atoms in a selected state.
• Picking three atoms and then Shift-double-picking the fourth (that is, doubleclicking it with the button assigned to picking) elicits a button marked Measure Torsion. Clicking it creates a torsion angle monitor and leaves the atoms in a selected state. Clicking elsewhere removes the button without creating a monitor but leaves the atoms in a selected state.

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.

Adjust Torsions

The Adjust Torsions section of Structure Measurements is a table of active (rotatable) torsions. Active torsions are saved in sessions. See also: Rotamers, rotation, swapaa

There are several ways to start Adjust Torsions, a tool in the Structure Editing category. Torsions can be activated in several different ways:

• The Activate button activates a rotation around a bond that has been picked in the graphics window.
• Double-picking a bond (that is, doubleclicking it with the button assigned to picking) elicits a menu with the option Rotate Bond. Choosing this option activates the torsion, opens Adjust Torsions (if it is not already open), and leaves the bond in a selected state. Clicking elsewhere removes the menu without activating a torsion but leaves the bond in a selected state.
• The command rotation can also be used.

Adjust Torsions - command-line specifiers

If the four atoms defining a torsion are called 1-2-3-4, 1 is the Near atom and 4 is the Far atom, which will move when the bond is rotated. The angle in degrees as defined by the current Near and Far atoms is shown in the Torsion column. Torsion can be toggled to Delta; the reported value is then the angle in degrees relative to the starting angle, and there are no Near and Far columns. For a terminal bond (lacking additional atoms on one end), the value shown is always a delta, even if the column header is toggled to Torsion.

A bond can be rotated by entering a new angle value (and pressing return), clicking the arrows flanking the angle value, or manipulating the dial. The Dial size can be set to small, medium, or large. Further, torsions can be manipulated in the graphics window with the mouse. This can be done by checking Rotate [torsion] using [button] and choosing the desired torsion and mouse button from the pulldown menus.

The Bond column contains a pulldown menu for each active rotation, labeled with identifiers for atoms 2->3 (those flanking the rotatable bond):

• Revert - restore the original torsion angle
• Reverse - change which side of the torsion moves when the bond is rotated (change the torsion definition from A-B-C-D to D-C-B-A)
• Deactivate - deactivate the bond rotation and remove it from the table. Note that the torsion will not automatically revert to its original value when deactivated; Revert should be used before Deactivate to retain the original torsional angle. Even if the same rotation is reactivated later, Revert will not work to restore the angle, since the original value has not been saved.
• Select - select the rotatable bond and deselect any others; when in the Torsion mode, also select the two flanking bonds if the rotatable bond is nonterminal

When atom 2 is bonded to more than two atoms, there is more than one possible Near atom, and alternatives (if any) are available in a pulldown menu from the current Near atom name. Likewise, when atom 3 is bonded to more than two atoms, there is more than one possible Far atom, and alternatives (if any) are available in a pulldown menu from the current Far atom name. For the first torsion in the example (figures above), there are two choices for the Near atom, C8 and C4, and two choices for the Far atom, O4' and C2'. For the second torsion, there are two choices for the Near atom, O4' and C3', and only one possible Far atom, O5'. Of course, if Reverse is used, the Near and Far choices are interchanged, and in the Delta mode, there are no Near and Far columns.

The Labels setting applies to all active torsions and can be switched among:

• None - no label
• ID - torsion ID number (the first column in the listing)
• Name - identifiers for atoms 2->3 (as shown in the Bond column)
• Angle - the angle in degrees

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. Each axis is anchored at the the centroid of the defining atomic coordinates and aligned with the principal component of the 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:

• 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 (a color well)
• 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.