Graphics Window

The Graphical Representations or ``Graphics'' window controls how molecules are drawn. Molecules are represented by reps, which are defined by four main parameters: the selection, the drawing method, the coloring method, and the material. The selection determines which part of the molecule is drawn, the drawing method defines which graphical representation is used, the coloring method gives the the color of each part of the representation, and the material determines the effects of lighting, shading, and transparency on the representation.

Draw Style Tab

Figure 5.6: The Graphics window (in Draw Style mode)

Select a molecule for editing using the `Selected Molecule' chooser at the top of the window. The browser below this chooser lists the reps available for the molecule. Each line of the browser summarizes information about the drawing method, the coloring method, and the selection. Below this browser, choosers and a text input filed reflect the current state of the rep, and provide controls for changing the properties of the rep. Each drawing method has specific controls which will appear when it is selected. When the `ColorID' coloring method is selected, a text entry box is shown allowing you to specify the index of a color to use for the selection, which may be a number from 0 to 16.

Changing a rep.

To change a representation, select it in the representation browser. The atom selection for that rep will appear in the Selected Atoms text area and the controls will update to reflect the current settings. Changing the settings will immediately affect the displayed representation if the Apply Changes Automatically check box is selected. When it is disabled updates will only occur when the Apply button is pressed. Changing the drawing method brings up method-specific controls and defaults. If you go back to the previous draw style, VMD restores any changes that you may have made to the settings. Pressing the Default button will restore the default settings. The display will be updated after every change.

Adding a rep.

To add a new representation of the molecule, enter the selection into the Atom Selection text area (or keep what is there) and press Create Rep. This adds the representation to the currently selected molecule.

Deleting a rep.

To delete a representation, select the representation in the browser and press the Delete button. Bear in mind that this does not delete the molecule, it only deletes one of its graphical representations.

Hiding a rep.

To hide a rep, double-click its entry in the browser. The text will turn pink to indicate that the rep is hidden. Turn the rep back on by double-clicking again on the same line. Hidden reps will not recalculate their geometry if the animation frame changes until the rep is turned back on.

Selections Tab

Figure 5.7: The Graphics window (in Selections mode)

The Selections tab provides access to browsers which display the lists of atom names, residue names, and so forth for the selected molecule. When the Selections tab is pressed, several browsers appear in place of the drawing and coloring method controls. These are used to list the available keywords, macros, and values for use in selecting atoms for the associated representation. The top browser lists singlewords and macros such as all, water, and hydrophobic. The botton left browser contains a list of the keywords and functions understood by the selection command. If a keyword is selected which can take on a value (for instance, name and index), then the possible names will be displayed in the bottom-rightmost browser. The functions can be identified by the ( to the right of the name. After selecting a keyword, the right browser will display all the names associated with the keyword. For example, selecting resname in the left browser will show all the three-letter residue names known for the selected molecule.

Clicking on a field in the value browser will add it to the selection text field. Double clicking a keyword field adds the keyword to the text field. Press Apply to actually change the atom selection for the current rep. Press Reset to restore the atom selection to its original value.

The Selections tab also shows the atom selection macros that have been defined. These macros let you define a commonly used atom selection as a single word so that it can be inserted into a rep more conveniently. Atom selection macros can currently be defined only through the Tcl or Python text interfaces; see these sections for details.

Trajectory Tab

Selection and Color auto-update.

When an atom selection such as water within 3 of protein is made, the atoms in the selection are computed for the current animation frame. When the animation frame changes, the selection is not normally recalculated; thus the displayed atoms may not correspond to those that would be selected if the atom selection were performed for the new animation frame. If the Update Selection Every Frame checkbox is highlighted by clicking on the checkbox, then the atom selection for the current rep will be recalculated every time the animation frame changes. Similarly, if the Update Color Every Frame checkbox is activated, the color will be recalculated for every frame.

Color Scale Data Range.

Several of the coloring methods available in Draw Style tab operate over data fields that have no specifically implied range of values. It is often useful to highlight a very specific range of data values, in order to accomplish this the color scale range can be manually set to a specific starting and ending values, overriding the default behavior which is to autoscale from the minimum value to the maximum value. This feature is particularly useful when displaying trajectories, since the range of values of interest may be quite different from the autoscaled range for a single frame or all frames.

Draw Multiple Frames.

Draw multiple trajectory frames or coordinate sets simultaneously. This setting allows the user to select one or more ranges of frames to display simultaneously. The frame specification takes one of the following forms now, frame_number, start:end, or start:step:end.

Trajectory Smoothing.

The Trajectory Smoothing Window Size is used to control the application of a per-representation windowed-averaging smoothing function. This simple smoothing feature can be used to eliminate much of the thermal noise inherent in a molecular dynamics trajectory so that one can more easily see structural changes occuring over a wider time scale. The window size parameter controls how many frames are averaged together to produce the coordinates which are actually displayed. One important consideration when using the trajectory smoothing feature is that VMD does not take periodic boundary conditions into consideration when smoothing trajectory coordinates, so any atoms which wrap around within the span of the window will cause erratic motions in the displayed representation. This can be avoided by unwrapping trajectory coordinates prior to loading into VMD or by using atom selections to eliminate atoms which wrap around.

Periodic Tab

The Periodic tab controls the display of periodic images of a molecule. In order to display periodic images, a molecule must have unit cell information set for a, b, c, alpha, beta, and gamma, which are discussed in section 9.3.22. When the proper unit cell information is present, the periodic display feature can show periodic images of the unit cell by transforming and rendering additional copies of the structure. The current implementation of this feature doesn't provide for complex crystallographic symmetry operations. Unit cells that can be replicated by translation along the three unit cell axes are the only ones supported presently. The periodic images to be drawn are selected by enabling images in one or more of the six faces of the unit cell. The Self image selects the untranslated unit cell itself, so that one my render a representation consisting of only replica images. This feature allows the unit cell and its periodic images to be displayed using different materials, for cases where it is desirable to draw more attention to the original unit cell or to one ore more of the replicas. The Number of Images counter controls how many replicas are made in each of the six directions. Some file formats read by VMD may not include unit cell information, in such cases you can use the scripting interface to set the unit cell information manually. PDB files containing CRYST1 records are an example of a file format that provides unit cell information.