The organization of the menu bar and the function of its components are shown below.
- 1) File menu
|Open - Local||mmCIF||A local mmCIF file is opened.|
|PDBML||A local PDBML file is opened.|
|PDB||A local PDB file is opened.|
|Polygon||A local polygon file is opened.|
|Polygon CGO||A local polygon CGO file is opened.|
|Script||A local script file is opened.|
|Animation||A local animation file is opened.|
|Open-Remote||PDB ID||A PDBML file at the PDBML FTP site is opened.|
|eF-site ID||A set of molecular and polygon files stored in eF-site database are opened.|
|mmCIF||A remote mmCIF file is opened.|
|PDBML||A remote PDBML file is opened.|
|PDB||A remote PDB file is opened.|
|Polygon||A remote polygon file is opened.|
|Polygon CGO||A remote polygon CGO file is opened.|
|Script||A remote script file is opened.|
|Animation||A remote animation file is opened.|
|Information||Information about the selected files are shown.|
|Close||The specified file is closed.|
|Save||mmCIF||A mmCIF format file that contains the current atom coordinates is created.|
|PDB||A PDB format file that contains the current atom coordinates is created.|
|Script||A script by which the present condition is reproduced is created.|
|PNG||The current image is saved as PNG.|
|JPEG||The current image is saved as JPEG.|
|Exit||The application is terminated.|
- 2) Display menu
|Wireframe||The selected atoms are displayed in a wire frame model.|
|Backbone||The selected atoms are displayed in a backbone model.|
|Sticks||The selected atoms are displayed in a stick model.|
|Spacefill||The selected atoms are displayed in a space-fill model.|
|Ball&Stick||The selected atoms are displayed in a ball & stick model.|
|Ribbons||The selected atoms are displayed in a ribbon model.|
|Cartoon||The selected atoms are displayed in a cartoon model.|
- 3) Colors menu
|Monochrome||The selected atoms are colored in white.|
|CPK||The selected atoms are colored by CPK color scheme.|
|Shapely||The selected atoms are colored by the color scheme in which each amino acid and nucleic acid is assigned a unique color according to the amino acid and nucleic acid properties.|
|Group||The atoms of every chain are drawn as a smooth spectrum from red (N-terminal of the molecule) to blue (C-terminal).|
|Chain||The selected atoms are colored by the color scheme in which each chain is assigned a unique color.|
|Temperature||The selected atoms are drawn as a smooth spectrum from red (high value) to blue (low value) according to the value of the temperature factor.|
|Structure||The secondary structures are colored by the color scheme in which each secondary structure is assigned a unique color.|
|Charge||The selected atoms are drawn as a smooth spectrum from blue (positive) to red (negative) according to the charge.|
|Amino||The selected atoms are colored by the color scheme in which each amino acid is assigned a unique color.|
- 4) Options menu
|Hetero Atoms||Users can choose whether the heterogeneous atoms described by ‘HETATM’ in PDB files are selected or not.|
|Hydrogens||Users can choose whether the hydrogen atoms are selected or not.|
|Slab||Users can choose whether the z-clipping plane is located on the default position or is shifted.|
|Stereo||Off||Disables stereo display.|
|Wall-Eyed||Enables side-by-side wall-eyed stereo viewing.|
|Cross-Eyed||Enables side-by-side cross-eyed stereo viewing.|
|Red-Blue||Enables red-blue anaglyph 3D rendering.|
|Red-Cyan||Enables red-cyan anaglyph 3D rendering.|
|Red-Green||Enables red-green anaglyph 3D rendering.|
|Load To Center||Users can choose whether a new image is added to the center of screen or not when a new file is opened.|
|Pick||Off||The mouse-pick is disabled.|
|Ident||The atom and residue names, their serial numbers, chain identifier and file ID of the object picked by mouse-click are represented.|
|Coordinates||The atom and residue names, their serial numbers, chain identifier, file ID and coordinate of the object picked by mouse-click are represented.|
|Distance||The distance between the first and second clicked atoms is calculated and shown.|
|Center||The center of rotation and window are transferred to the clicked position.|
|Select||Only clicked files are operated.|
|Animation||The animation control dialog is opened.|
- 5) Help menu
|About jV||Information about this application is shown.|
|Open Manual||A manual page is opened with a web browser.|
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.
- 1) URL with parameters
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.
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.
- 2)'type' column and mouse pick
The ‘type’ column in the parameter table is selected from the follows.
|text||arbitrary value||does not work|
|atom ID||atom ID||work|
|atom||set of chain ID, residue ID and atom ID||work|
|residue||set of chain ID and residue ID||work|
|orig_coords||atom coordinates written in the molecule file||work|
|curr_coords||atom coordinates currently displayed||work|
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.
- 3) Saving and loading the configuration
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.
<?xml version="1.0"?> <remote_file url="http://example.com"> <params attach="true" coordinates_delimiter=","> <param name="param1" value="value1" type="text"/> </params> </remote_file>
- 4) fit, biomolecule and filter
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.
- 5) Execution
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.
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.