Structure Measurements enables measurements of molecular geometry (distances, bond angles, and torsion angles) and adjustments of torsion angles. It 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. Structure Measurements can be opened by starting any of its sections; there are several ways to start each of the three sections, classified as tools in the Inspectors category.Save saves measurements to a file. Close closes the measurements panel, and Help opens this manual page in a browser window.
The Distances section of the Structure Measurements panel is a table of distance monitors. There are several ways to start Distances, a tool in the Inspectors category. Distance monitors can be created in three ways:
| Distances Panel - simple atom listings |
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The simple atom listing consists of residue name, residue number, and atom name; the alternative is an atom specification string (see the Adjust Torsions figure). The style is controlled in the General preferences.
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:
Distance monitors are pseudobonds in a group named distance monitor. Thus, they can be controlled collectively with the PseudoBond Panel. When selected, an individual distance monitor pseudobond can be altered with the Selection Inspector.
There are several ways to start Angles/Torsions, a tool in the Inspectors category. (This section is under construction; for now, use the command angle.)
The Adjust Torsions section of the Structure Measurements panel is a table of active (rotatable) torsions. There are several ways to start Adjust Torsions, a tool in the Inspectors category. Torsions can be activated in several different ways:
| Adjust Torsions Panel - atom specification listings |
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Once a bond is rotatable, the two atoms in the bond are listed in the leftmost
column of the table. If the 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.
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.
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. The leftmost column of the table (listing atoms 2->3) contains a pulldown menu for each active rotation:
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.