The PDB Viewer button makes use of a "proposed" MIME types chemical/x-pdb to deliver a native PDB file. Once launched the client-side "viewer" allows the interactive visualization and manipulation of the selected structure. The suggested PDB viewer, RasMol is available for Mac, PC-Windows and Unix.
The Mage Viewer button makes use of the suggested MIME type chemical/x-kinemage
to deliver the PDB file in a form to be handled by a client-side "viewer"
which is capable of reading and displaying a Kinemage
data file. This option is currently limited in that it only
generates a structure for the alpha carbon backbone of proteins.
Additionally, it is capable of generating the backbone structures
for multimeric proteins, up to a maximum of 20 chains.
[This latter feature is particularly useful for looking at NMR derived
structures.]
The suggested viewer, Mage, is available for Mac, PC-Windows and Unix.
The motif Viewer button makes use of a MIME type
chemical/x-rasscript to deliver a Rasmol script file and native PDB file
combined into one. This experimental system allows for the delivery of
a PDB file and an associated collection of RasMol commands. In this
implementation the resultant molecule is delivered with the ligand (if
any) rendered in ball and stick format (yellow) and any protein motifs
which matches an entry in the prosite database color coded.
As mentioned above this feature is only available on systems
which have RasMol 2.6 installed. The following MIME type
chemical/x-rasscript; rasmol -script %s definition must be
placed in either the global mailcap file or
the .mailcap file in the users home directory.
To view the structure in VRML one requires either a stand alone VRML viewer or a VRML netscape-plugin. This format is specified by the mime type x-world/x-vrml. If the appropriate plugin is present no further action is necessary. However, if you are using a standalone viewer it should be keyed to this mime type. (i.e. make the appropriate entry in the browsers "helper application" setup, or in the .mailcap file.)
These features combined with the full-text search of the PDB data provide a very powerful and user friendly interface for browsing through the PDB structure data.