Molecules To Go Request FORM - Interactive Viewer

Through the Molecules To Go Request FORM one may request a PDB data file to be returned as a raw data file to be handled by a client-side external viewer.
Molecules To Go is designed to interact with client-side viewers via three different MIME-types:
  1. chemical/x-pdb (for a PDB file viewer, e.g. Rasmol)
  2. chemical/x-kinemage (for a Kinemage file viewer, e.g. Mage)
  3. chemical/x-rasscript (RasMol 2.6)
  4. x-world/x-vrml (for VRML viewer of plug-in)
In order to make use of these features the following steps must be performed:
  1. Install and configure the appropriate "viewer application" on your local computer.
  2. Configure your Web browser to recognize one or all of the above MIME types and to launch the appropriate application (identified by program name and directory path).
  3. (Optional) Associate a given file extension with the recently defined MIME types.
  4. Frequently it will be necessary to restart a Web browser before these changes will become effective.
The specific methods one used to achieve these ends will depend on the computer architecture and Web browser you are using. Detailed instruction on configuring the "chemical/x-kinemage for the Mage program are provided by Protein Science and should be used as a prototype for configuring all these mime types.

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.

Last Updated: 3/4/99
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Molecules To Go - Peter_FitzGerald@nih.gov
National Institutes of Health (NIH), Bethesda, Maryland 20892