The Model module is used for visualization of interaction between displays containing molecular coordinates, experimental NMR data (usually NOESY spectrum), and back-calculated NMR data. This chapter provides an introduction to the basic capabilities of this module and describes the menu interface.
To access the Model module, select the Model pulldown from the menu bar. Before you can start working you must select the Model/Setup/Connect command to set up the environment.
Currently, Model supports XPlor .pdb format and Insight II .car format for coordinate file input. Before you can start working with Model you must read in a molecule using the File/Open menu item. The default directory for these files is defined by the xyzpfx symbol.
In addition to setting up your system and reading a file of molecular coordinates, you must also load an experimental NOESY spectrum and a current list of cross-peak positions and volumes.
Before you begin, a matrix must be open and the cross-peak information must be present in the database. A common error here is to use a cross-peak volume entity that is not current with the cross-peak position entity. If you encounter this error, you must remeasure your cross-peak volumes before entering this option.
Your spectrum should already be at least partially assigned, since most of the interaction between the NMR spectrum and the molecule coordinates relates to atom names. Thus, it is extremely important that the names entered in your NMR database in the peaks entity be identical to those used in your coordinate file. For example, if you used Insight II to calculate your molecule structures, then the cross-peak names in the peaks entity must use the same naming convention. For XPlor coordinate files, FELIX creates Insight II-type names.
A crucial part of the Model module is its ability to calculate the theoretical proton NOEs for a model structure. The basic physical principles underlying these calculations are described in Calculation of theoretical nuclear Overhauser effects (NOEs).
The Model/Setup/Connect (<Alt>-mc) menu item sets Model up to deal with experimental data, back-calculated data, and molecule view. FELIX can display molecules in its own viewer or you can establish a hotlink connection between FELIX Model and Insight II NMR-Refine. Setting Connect Insight to Yes and specifying the active molecule name in the Molecule Name option, then setting Show Atoms in Insight to Yes allows you to use the Model/Show Atoms command to highlight atoms in Insight II while interacting with assigned peaks in Model.
If you set Measure Distance in Insight to Yes, a distance monitor appears between the two atoms to which the current peak was assigned. The Show Atoms function also draws the assigned atoms in CPK mode, and, in stick mode, the residue(s) to which the assignment was made. A zone is defined, starting from both atoms to which the peak was assigned, and only the atoms within that zone are displayed. Within this menu item you can set the Stick Thickness, the CPK Radius, and the Zone Radius.
The Model/Matrix Doubling menu item (<Alt>-mx) is used to set the parameters for and execute the back-calculation in the matrix doubling method. Here you need to indicate which peak and volume entity to store the back-calculated peaks and intensities in, as well as the mixing time in seconds and the rotational correlation time of the molecule in nanoseconds. The Z-leakage parameter represents magnetization that disappeared from the diagonal peak but has not appeared as NOESY cross peaks. The cutoff radius is used to define a containment shell around each proton for the NOESY calculation. The minimum-intensity parameter sets a value for the smallest back-calculated intensity that is then saved. By default, a value of 0.005 (which represents 0.5% NOE) is used. NOEs that are smaller than this value are not included in the resulting list of database footprints. Finally, you must enter the spectrometer frequency in MHz for which the simulation should be executed.
The Model/Set Scale menu item (<Alt>-ms) contains two methods used to set the scale factors for the back-calculated spectra. You select a peak in the experimental data whose intensity is used to scale the data in the theoretical data.
If the Method is set to Via Cursor, you use a crosshair cursor to select, from the experimental spectra, the cross peak whose intensity is to be used for generating a scaling factor to scale all the points in the theoretical data.
If the Method is set to Enter, enter the specifications in a control panel for the atom that corresponds to the cross peak whose scale factor is to be used for the theoretical spectra.
This menu item refreshes the spectrum in the experimental frame (<Alt>-me>).
The Model/Draw Theoretical menu item (<Alt>-mt) is used to model the data using the current peak entity. You may change the peak entity and volume entity or the slot number in the control panel.
This menu item redraws the molecule without the interactive interface (<Alt>-md>).
The next section of menu items contains functionality that mainly deals with the molecule display.
The Model/Interactive Draw menu item (<Alt>-mi) is used for rotating, viewing, and changing the orientations of the displayed atoms, labels, and highlights of a molecule.
When you select this menu item, the 3D rotation interface that lets you rotate objects becomes active. This interface is identical to that used for 3D NMR data display. When this interface is active, the standard menus are no longer accessible. To access standard menu items, you must first select the Exit button found at the bottom of the 3D rotation interface.
Within the 3D rotation interface are buttons that switch the mode of action of the mouse - Rotation, Translation, and Zoom. When Rotation is active, pressing the left mouse button and moving the cursor causes rotation around the x or y axis. Pressing the <Shift> key together with the left mouse button causes z-axis rotation. For Translation and Zoom, your actions are similar (that is, pressing the left mouse button and moving the cursor horizontally or vertically (x or y translation). The Options button activates a control panel whereby symbols can be set that affect the current graphical display. Included in this control panel are items that turn objects on or off within the molecule (atoms, bonds, labels, lines, or monitors), set stereo views and stereo separations, or set auto-rotation parameters. The Reset button resets the display to its initial state. The Exit button closes the 3D rotation interface and places the program back in its last mode.
The Model/Blank menu items are useful for blanking out or redisplaying atoms and/or residues of the displayed molecule.
If the Type is set to Atoms you can blank out a specified atom from the molecule or display a specified atom from an invisible molecule. Enter the name of the atom to be blanked out in the control panel, set the Blank Mode to ON and select OK. This blanks out the specified atom. To make the atom reappear, set Blank Mode to OFF and press <Enter>.
If you set the Atom Name to wildcard (*) you can blank out the entire molecule. If the Blank Mode toggle is set to ON, the whole molecule is blanked out; if Blank Mode toggle is OFF, the whole molecule is visible.
If the Type is set to Single Residue you can blank out a single residue at a time, and if Type is set to Multiple Residues you can define the start and end residue to blank out. If the Blank Mode toggle is set to ON, the designated residues are blanked out; if Blank Mode is set to OFF, the residues are visible.
The Model/Label menu item (<Alt>-ml) is used to show an atom on the molecule by entering the atom name in the control panel. This menu item displays the atom name on the molecule if it is found or shows an error message in the text window saying that the atom was not found. If Label in is set to Off, you can clear labels; if the Atom name is set to wildcard (*), then all labels are cleared.
With the Model/Color (<Alt>-mr) menu item you can change the coloring scheme of the molecule. For example, you can change the color of all protons or all amide protons to yellow.
You can draw monitors between any pair of atoms with the Model/Monitor (<Alt>-mm) menu item.
The Model/Show Peaks Via Cursor menu item (<Alt>-mp) brings up a crosshair cursor that you use to select two atoms on the molecule that constitute a cross peak. This cross peak is displayed on the spectra if it was found.
The Model/Show Peaks Manual menu item (<Alt>-mw) opens a control panel in which you enter the names of the atoms that belong to a specific cross peak. After selecting OK, the cross peak that was assigned to these atoms is highlighted on the spectra.
The Model/Zoom Peaks menu item (<Alt>-mz) is used to zoom in on the molecule around the atom pair selected with the previous two menu items.
You can highlight assigned atoms from a peak using the FELIX viewer or the Insight II molecule viewer.
When you select the Model/Show Atoms menu item (<Alt>-ma>), a crosshair cursor appears. You then select a cross-peak footprint in the displayed experimental NMR spectra. Remember that you are selecting cross peak footprints for comparison with molecular models, not the actual spectrum data. This means you may first need to redraw your footprints by selecting the View/Draw Peaks menu item. After you select a cross peak, the molecule frame is activated and the atom pair that makes up the cross peak is searched for. If the atom pair is found then the atoms on the molecule are labelled. The display shows only those atoms that are within 6 Å of the two selected protons. The atom pair names and the distance are also printed in the text window.
To properly use this menu item you must have the Insight II program running on your computer and the Model/Setup/Connect menu item must have been already successfully executed.
You must at least have frequency assignments for peaks. When you select the Model/Show Atoms (<Alt>-ma) menu item, a crosshair cursor appears. Clicking peaks of atoms to which the peak was assigned (in FELIX) produces a display in CPK mode in Insight II. The atom that belongs to the D1 assignment of the peak will be purple, and the atom that belongs to the D2 assignment is turquoise. Then the residue to which these atoms belong is shown in stick style. Those atoms belonging to possible frequency assignments, if any, are also displayed as CPK with higher transparency than the peak assignments, but with the same colors. Finally a zone is defined such that only those atoms that are within a previously defined distance from the atoms belonging to the peak assignments are displayed. If the Measure Distance in Insight was set during setup, then a distance monitor is drawn between the atoms belonging to the peak assignment.
The Model/Show Volumes menu item (<Alt>-mv) is used to display the assignments together with the volumes for peaks in both the experimental and the theoretical spectra. You can select the peaks in either of the two spectra and obtain the assignments of the cross peak if they exist in the spectra. The volumes are also displayed.
The Model/Color Peaks menu item (<Alt>-mk) colors peaks based on several criteria: separate colors can be assigned to experimental peaks that have matching theoretical peaks, to experimental peaks that have their matching theoretical peak overlapped (but the major contributor is that assignment), to experimental peaks that have multiply assigned matching theoretical peaks, and to experimental peaks that have no matching theoretical peak. Different colors can also be assigned to theoretical peaks that have no experimental counterpart. The major contribution can be defined in volume (Volume Threshold).
Generally accessible menu items can have special effects if the molecule window is the active frame.
If the molecule window is the active frame, then selecting the Preference/Plot Parameters menu item (<Alt>-pp) opens a control panel where you can set plotting parameters pertaining to the molecule viewer: you can set the van der Waals value to use in drawing the atoms on the molecule (the default is 0.0), the bond thickness (default is 1), the display type to be all atom or Ca trace, and the default coloring to match either Insight II's defaults or WebLab Viewer's defaults.
Selecting the Measure/Cursor Position menu item while the molecule viewer is the active frame causes it to stop tracking cursor movement. Instead, if you click an atom, the name of that atom, its position, and a label are displayed in the text window.