GUI

Menu bar
The organization of the menu bar and the function of its components are shown below.


 * 1) File menu


 * 2) Display menu


 * 3) Colors menu


 * 4) Options menu


 * 5) Help menu

Open-Local dialog
Selecting each menu item in the [File] – [Open – Local] menu opens the open-local dialog. For example, Figure 5 shows a dialog opened by the [File] – [Open – Local] – [mmCIF] menu item.



Users can enter a local file path at the ‘Enter file’ text filed, or select a file by using a file chooser dialog that your operating system provides by clicking the ‘Browse…’ button. If a file ID that is already opened in the application is specified at the ‘fit’ text field, the transform of the newly opened file is set identical to that of the specified file. A biomolecule structure can be specified by entering assembly ID at the 'biomolecule' text field. For a biomolecule structure, a distinct model ID is assigned to each transform operation, which is listed by 'show information' command. Note that the biomolecule parameter is not available for flat PDB files. When a filter expression is entered at the ‘filter’ text field, only atoms that matches a given filter are loaded. The filter takes any atom expressions except some keywords (bonded, helix, sheet, turn, within and pdbj:). The atom expression should be double-quoted or enclosed in a parenthesis when it contains spaces.

Open-Remode dialog
Selecting [mmCIF], [PDBML], [PDB], [Polygon], [Script] or [Animation] menu item in the [File] – [Open – Remote] menu opens the open-remote dialog that can handle a URL with parameters. For example, Figure 6 shows a dialog opened by the [File] – [Open – Remote] – [mmCIF] menu item.
 * 1) URL with parameters



When ‘Add’ button is clicked, a new parameter line is appended in the table at the center of the dialog. Figure 6 shows an example of a URL with one parameter. By clicking the ‘Add’ button the necessary number of times, you can attach multiple parameters. When ‘Remove’ button is clicked, a highlighted line in the parameter table is removed. When ‘Clear’ button is clicked, all parameters are removed.



The ‘type’ column in the parameter table is selected from the follows.
 * 2)'type' column and mouse pick

For the case of a type to which mouse pick works, selecting an atom in the screen by mouse pick sets the corresponding value to the ‘value’ column in a highlighted line in the parameter table. The value of the ‘delimiter’ field is used to delimit atom’s x, y, and z coordinate.

By clicking the ‘save’ button, a file chooser dialog appears and the current configuration can be saved to a file. In the same way, a configuration can be loaded by clicking the ‘load’ button. The contents of a configuration file are in XML format as follows.
 * 3) Saving and loading the configuration

    

Three text fields entitled fit, biomolecule and filter work the same way as opening a local file. How to use them is described at the previous ‘Open-Local dialog’ section.
 * 4) fit, biomolecule and filter

When the ‘OK’ button is clicked, a new file is loaded and the dialog is closed. When you use ‘Submit’ button, on the other hand, the dialog remains visible even after a new file is loaded.
 * 5) Execution

Animation control dialog
The animation control dialog is visible only if [Options] - [Animation] menu is checked. When there is no animation file loaded, the animation control dialog is as Figure 7. If some animation files are opened, the animation control dialog is altered according to the number of the files. Figure 8 indicates the dialog in the presence of two files.





Users can select which files are controlled by their checkbox. The frame position and playback and stop of the animation can be controlled individually to each file. The playback-speed and the selection of ‘loop’ and ‘swing’ modes are common for all files.