The Structure Measurements panel has three sections shown as index cards:

• Distances - monitor distances
• Angles/Torsions - monitor angles and torsions
• Adjust Torsions - rotate bonds
• Axes - show axes for helices and other sets of atoms, perform related measurements

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). 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

Atoms can be listed in a simple style consisting of residue name, residue specifier (number.chain), and atom name, as shown in the figure, or with command-line specifiers (see the Adjust Torsions figure). Atomspec display style in the General preferences controls which style is used.

The distance list can be sorted by the values in any column by clicking the header. Clicking the header once sorts the entries in order of increasing value and places an up arrowhead (triangle) in the header. Clicking again sorts the entries in decreasing order and places a down arrowhead (inverted triangle) in the header.

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. 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. 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.

Clicking on a listing allows it to be deleted with the Remove button. If there is only one angle monitor, it is not necessary to click on its listing before using 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. See also: Rotamers, 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 or brotation can also be used.

Adjust Torsions - command-line specifiers

Atoms can be described with command-line specifiers, as shown in the figure, or in a simple style consisting of residue name, residue specifier (number.chain), and atom name (see the Distances figure). Atomspec display style in the General preferences controls which style is used.

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.

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 (to show all four atoms defining the torsion).

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 (not yet implemented)
• Name - identifiers for atoms 2->3 (as shown in the Bond column)
• Angle - the angle in degrees

Axes

The Axes section of Structure Measurements is a table of axes defined for protein helices and/or other sets of atoms. Axes are displayed in the graphics window as rods. See also: PipesAndPlanks

There are several ways to start Axes, a tool in the Structure Analysis category. Clicking Define axes... opens a dialog for specifying atom sets and other axis parameters:

• 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.
  
  
• Selected atoms (axis name [aname]) - define a single axis named aname using all selected atoms
  
  
  • Mass weighting - calculate inertial axis by mass-weighting the atoms. Only available for selected-atoms axis definition, overrides mutually exclusive option to use helical correction.
    
    
  • Use helical correction - adjust initial axis orientation to reduce the spread of atom-axis distances. An axis is anchored at the the geometric center (centroid) of the defining atomic coordinates and is initially aligned with the principal component of the coordinates. While usually small, helical correction improves results for short helices.
    
    
  • Replace existing axes - remove any/all pre-existing axis displays when creating new ones
    
    
  • color (a color well, default No Color, meaning to match the structure as much as possible)
  • radius (default 1.0 Å)

The table of axes lists Name and Length, and entries can be sorted by either column by clicking the header. The length of an axis is that needed to span the projections of the defining atoms back onto the axis. Individual axes can be hidden and shown using the Shown checkboxes.

An axis 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 two axes reports their crossing angle and closest distance (treating the axes as infinitely long) below the table and in the Reply Log. Optionally, choosing axes also:

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

Delete removes the chosen axes. In addition, closing a molecule model or deleting atoms removes any axes defined using those atoms.

Axis information written out with Save includes name, length, and untransformed position in terms of center coordinates (x_c,y_c,z_c), 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:

x1 = xc − 0.5(length)(xu) y1 = yc − 0.5(length)(yu) z1 = zc − 0.5(length)(zu)

x2 = xc + 0.5(length)(xu) y2 = yc + 0.5(length)(yu) z2 = zc + 0.5(length)(zu)