The Japanese version help is here.
The Protein Globe is a graphical interface to the PDBj and other services.
What it is
The Protein Globe provides a global view and representation of the protein universe. Each protein fold is represented as a point on a globe (sphere), and structurally similar folds (as judged by the ASH program) are placed closer together on the globe than structurally dissimilar folds. We can observe that there are many clusters or islands of folds on the globe. Cartoon representations of folds are provided for some large clusters.
You can interact with the Globe by using your mouse: Rotating the Globe, picking a point, etc. The Globe is an application based on jV (PDBjViewer, version 3).
In order to use the Globe, you need to have the following softwares installed on your computer:
How to use
The Globe is only semi-quantitative.
The shapes of the continents and islands may changes their shapes, time to time.
Making links to the Protein Globe
When you know all PDB ID, chain ID, and domain ID
You can make a direct link to the protein domain on the Globe. For example, if you know that there exists on the Globe a domain with PDB ID '1ash' with chain 'A' and domain ID '1' , then you can make a link to the point by writing:
By clicking this link, you will have the Globe with the corresponding domain focused.
When you know only PDB ID
While PDB ID and chain ID are standard PDB items, domain ID is not. Nobody can blame you if you don't know the domain ID of a particular protein fold. Thus, you can make a link to the Globe by specifying only the PDB ID like:
In this example, we are fortunate enough to have only one domain with the PDB ID '1ash' on the Globe so that the domain is automatically focused. Although the Globe page says error, this can be safely ignored in this case.
However, what if there are multiple domains with the same PDB ID on the Globe? Try the following:
This time, the Globe is not focused. But there should be three buttons on the right-center of the page, each corresponding to a domain with the PDB ID '2awa'. If you find the one you want among the buttons, click it, and you have that one focused on the Globe.
Changing the colors of sea and lands
People have likes and dislikes. Or maybe you want the Globe to be of different colors time to time for a change. By specifying "s" parameter in the Globe URL, you can have the colors shown in the following figure:
You can specify the colors like:
where xy should be 0 to 59 (inclusive). the first digit (x) of xy specifies the land color, and the second digit(y) the sea. If there is no x, then only specify y (0-9). For example, by specifying 's=55', you have the dark green sea with cyan lands ( http://www.pdbj.org/globe/globe.cgi?s=55 ); and with 's=39', you have the grey sea and the light green lands ( http://www.pdbj.org/globe/globe.cgi?s=39 ), etc.
Alternatively, xy can be random (literally). In this case, the colors will be chosen randomly among the 60 choices every time the Globe is (re)loaded.