The Measurements panel (see Figure 9.1 on page 140) provides tools to determine the geometric relationships between atoms in the Workspace, and other geometry-dependent prop- erties. These tools are contained in six tabs—Distances,Angles,Dihedrals,H-Bonds,Contacts, and1H NMR Coupling.
To open theMeasurements panel, chooseMeasurements from theTools menu.
9.2.1
Measuring Distances, Angles, and Dihedrals
The controls forDistances,Angles, andDihedralsare very similar, as are the actual measure- ment procedures for these quantities. To measure a distance, you need to specify only two atoms or one bond, for an angle you must specify three atoms or two bonds, and for dihedrals you must specify four atoms or three bonds.
Figure 9.1. The Distances tab of the Measurements panel.
To select atoms for measurement, select theAddmode, then chooseAtomsorBondsfrom the
Pickoption menu in theDefine atoms for measurementsection, and select the atoms or bonds in the Workspace. When you have selected the requisite number of atoms, the measurement is made and entered into the measurement list. IfShow markersis selected, a dashed line indi- cating the atom locations and the numerical value obtained from the measurement is displayed in the Workspace. Distances are marked in purple, angles in green, and dihedrals in red. Once you have defined atoms for a measurement, those atoms remain defined until you delete the atom set or remove the structure from the Workspace. If you only temporarily want to undisplay the results of your measurements, deselectShow markers. However, if you no longer need the measurement value itself, you can remove it by selecting the corresponding list item and clickingDelete. To delete all of the atom sets currently defined for a particular type of measurement, clickDelete All. You can also select theDeleteoption underModeand click the defined atoms in the Workspace to delete a measurement.
You can make measurements with theMeasure distances, angles or dihedrals toolbar button.
To make a measurement, chooseDistance,Angle, orDihedralfrom the button menu, then click the atoms in the Workspace. The measurement is made, and any options that are set in the
Measurements panel are applied: for example, if Create property for selected entries is selected, the property is created.
9.2.2
Displaying Hydrogen Bonds and Contacts
The procedures for displayingH-BondsandContactsare similar. Unlike distance, angle, and dihedral measurements, you can display hydrogen bonds and contacts for an unlimited number of atoms, and you define the desired atoms by placing them in sets. Two sets can be defined at any given time, and you can choose to display the hydrogen bonds or contacts between the atoms of a set or between the two separate sets.
To see hydrogen bonds or contacts marked in the Workspace, selectDisplay H-bondsorDisplay Contacts. For contacts, you must also select the type of contact—Good,Bad, orUgly—that you want to measure.
Default criteria for defining hydrogen bonds or contacts are given in the text boxes at the top of the tab. To change these criteria, enter a new value in the relevant text box. For hydrogen bonds you can set theMaximum distance,Minimum donor angleandMinimum acceptor angle. For contacts, you can alter the contact cutoff ratios in theGood contacts,Bad contacts, orUgly contacts text boxes, and you can exclude bad or ugly contacts that meet the criteria for H-bonds by selectingExclude H-bonds from contacts.
To define an atom set, use the picking tools, clickSelectto open theAtom Selectiondialog box, or enter an ASL expression in theASLtext box. If you define onlyAtom set 1, the H-bonds or contacts are displayed within that set. If you define bothAtom set 1 andAtom set 2, the H- bonds or contacts are displayed between the two sets.
You can also display hydrogen bonds from the toolbar. First, chooseInter H-bondsorIntra H- bonds from theDisplay H-bonds button menu:
Then select a molecule in the Workspace. If you choose Inter H-bonds, hydrogen bonds between the selected molecule and the rest of the atoms in the Workspace are displayed. If you chooseIntra H-bonds, hydrogen bonds within the selected molecule are displayed.
9.2.3
Displaying H-H NMR Coupling Constants
NMR spin-spin coupling constants can be estimated for vicinial hydrogen atoms using a modi- fied Karplus-type calculation. To display the estimated coupling constants, you must select two hydrogen atoms that are bonded to two carbon atoms, and these carbon atoms must be bonded to each other. The controls are the same as for distance measurements. You can also display coupling constants from the toolbar, using theMeasurements button.
9.2.4
Storing the Results of Measurements
You can include measurements as properties in the Project Table, and you can export measure- ments to a tab-delimited or comma-delimited file.
To create properties for measurements, selectCreate property for selected entriesbefore you define the measurements. The measured properties are added to the selected entries in the Project Table. Each distance, angle, or dihedral becomes a separate property, and is labeled with the nameDistance,Angle, orDihedral and the atom numbers that define the geometric quantity. For hydrogen bonds and contacts, the property is the number of H-bonds or contacts of each type.
Each tab in the Measurements panel has a Write button, which allows you to write a file containing the measurements. The Write button opens a panel in which you can specify a delimiter for the file, the numbering of the atoms, and a file name. If you specify a name or a relative path in theFiletext box, the file is written relative to the Maestro working directory. If you clickWrite To, a dialog box is displayed in which you can navigate to the desired directory and select a file or enter a file name.
9.2.5
Defining Dummy Atoms for Measurements
Dummy atoms can be useful for making measurements. For example, you can measure the distance between the centroids of two ring systems by placing dummy atoms at the centroids. You can place dummy atoms in two ways:
1. Use theCentroid panel to define a centroid atom.
A dummy atom is placed at the mean position of the picked atoms.
2. Use Draw mode in theBuildpanel to place an atom in the Workspace, then retype it with the appropriate MacroModel atom type.
Several kinds of dummy atoms are defined in the Atom Type (Macromodel)list in the
Atom Propertiestab of theBuildpanel. If you attach the dummy atom to your structure, you can adjust its position using theAdjust panel.