GUI

From jV

Contents 1 Menu bar 2 Open-Remode dialog 3 Animation control dialog

Menu bar

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

1) File menu

Component		Function
Open - Local	PDBML	A local PDBML file is opened.
	PDB	A local PDB file is opened.
	Polygon	A local polygon 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.
	PDBML	A remote PDBML file is opened.
	PDB	A remote PDB file is opened.
	Polygon	A remote polygon 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	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

Component	Function
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

Component	Function
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

Component	Function
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	Users can choose whether the stereo display is enabled or not.
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.
Pick Ident	The atom and residue names, their serial numbers, chain identifier and file ID of the object picked by mouse-click are represented.
Pick Coordinates	The atom and residue names, their serial numbers, chain identifier, file ID and coordinate of the object picked by mouse-click are represented.
Pick Distance	The distance between the first and second clicked atoms is calculated and shown.
Pick Center	The center of rotation and window are transferred to the clicked position.
Pick Select	Only clicked files are operated.
Animation	The animation control dialog is opened.

5) Help menu

Component	Function
About jV	Information about this application is shown.
Open Manual	A manual page is opened with a web browser.

Open-Remode dialog

1) URL with parameters

Selecting [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 5 shows a dialog opened by the [File] – [Open – Remote] – [PDBML] 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.

type	values	mouse pick
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) Copy of the transform

When a file ID that currently exists is entered to the ‘fit to’ field, the transform of the newly opened file is set identical to that of the specified file.

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.