Structure Measurements

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

Only one card is shown at a time, and clicking the tab for another brings it to the front. Each section is listed as a tool in the Structure Analysis category. Tools can be started in several ways.

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

Distances icon

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:

Distances - simple atom listings
Distances

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.

Clicking on a distance listing allows it to be deleted with the Remove button. If there is only one distance monitor, it is not necessary to click on its listing before using Remove. Clicking on a distance listing selects the corresponding distance monitor pseudobond and deselects any others; if the distance monitor is already selected, it is deselected.

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

The Decimal places and Show Angstrom symbol settings control how distances are reported in the table and (when Labels is set to Distance) in labels. The Decimal places can be changed by clicking or holding down one of the arrows on either side of the value. Of course, decimal places beyond those present in the input coordinates are not very meaningful.

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 icon

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:

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

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 icon

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:

Adjust Torsions - command-line specifiers
Adjust Torsions
An error message will appear if an attempt is made to activate a bond that is terminal (no additional atoms attached to one or both ends), within a ring, or already rotatable.

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.

bond rotation example 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):

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:

The Decimal places and Show degree symbol settings control how angle values are displayed when Labels is set to Angle. The Decimal places can be changed by clicking or holding down one of the arrows on either side of the value.

Axes icon

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:

Clicking Apply (or OK, which also closes the dialog) calculates the axes, adds them to the table, and generates the corresponding displays. Axes are defined in a two-step process:
  1. the axis is anchored at the geometric center (centroid) of the atomic coordinates and aligned with the principal component of the coordinates
  2. the orientation is adjusted to reduce the spread of atom-axis distances
The table lists axis Name and Length, and entries can be sorted by either by clicking the column header. Axes can be chosen with the left mouse button. Ctrl-click toggles the status of an individual axis. A block can be chosen by dragging, or by clicking its first (or last) line and then Shift-clicking its last (or first) line.

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:

Clicking Distance measures distances between the chosen axes and selected atoms; results are sent to the Reply Log. If a single atom is selected, the distance to each chosen axis is reported; if multiple atoms are selected, the minimum, maximum, and mean distances are reported.

Deleting any of the atoms used to define an axis or closing their models deletes the axis.


UCSF Computer Graphics Laboratory / March 2008