What do I need to see the pages properly?

Browser Spec: It is recommended that you use a modern browser for these pages, since they use a lot of the most recent features of HTML.

3D Image Formats: Some of these pages contain 'hyperactive' 3D images in formats such as pdb (protein database) or MDL molfiles (.mol). You can rotate and manipulate these files in real time if you have the correct set-up, and this depends upon the format of the page. There are 5 page formats currently used, H, C, J, JM and V (see below).

HTML-only pages (H): These pages are written in basic HTML, and no add-ons or plug-ins are required to view the page. Any 3D structures will be available as hyperlinks to the appropriate files (e.g. a pdb or mol file). To view these files you will need a 3D viewer program such as Rasmol. You then have two options:

• You can shift-click or right-click on the image, and download the pdb or mol file to your hard disk. You can then use a 3D molecular viewer program, such as Rasmol, on your computer to view it locally.
• Alternatively, you can set the 'Helper Programs' in your Browser configuration to recognise the following MIME type:

  chemical/x-pdb

  and filename suffix

  .pdb

  and associate this with Rasmol. If you have configured correctly, then clicking on the pdb links on the page should activate your viewer with the molecule in its window. Similar statements would be needed for other MIME types, such as x-mol, etc.

As well as Rasmol, other helper files that can be used are MacMolecule2/PCMolecule2 and WebLab Viewer.

Chemscape Chime (C): This was a system which worked using a browser plug-in called CHIME. It allowed 3D molecular structures to be represented on the page without the user having to have an external helper program. CHIME was developed by MDLI in the States, but they stopped supporting it in the mid 2000's and CHIME became unavailable. There are still some legacy pages that use it, but most recent MOTM pages have used JMol instead.

VRML (V): Virtual Reality Markup Language allows the user to 'fly' around and through the object they are viewing, e.g. a building or, in this case, a molecule. To view these files you'll need a VRML browser, or a browser plug-in, such as Cortona.

Note for authors: VRML files can be created very simply using Frank Oellien's web page at the University of Erlangen. This web page allows you to specify a molecular structure either by SMILES string, or by simply using the existing 3D files (.xyz, .pdb, .mol, etc), and it will return the VRML (.wrl) file to you.

JMol (JM): JMol is another Java applet that doesn't require any plug-ins, although it does need Java to be enabled. It is relatively new (late 2003) but most of the newer MOTM pages use it. JSmol (JS) is a more recent (2015) upgrade which uses javascript, and removes the need for Java to be enabled on your browser.

Other helper files - a list of other useful Chemistry plug-ins is held at Liverpool University.

RSS - the latest MOTMs are broadcast via an RSS newsfeed. If you have an RSS viewer (such as My Yahoo, or Bottomfeeder, then you can simply point them to this URL (http://www.chm.bris.ac.uk/motm/rss.xml) to get each month's MOTM's updated in your viewer automatically.

[Version of this page in Ukrananian]

Back to Molecule of the Month Page