# CMLRSS Distribution

## http://www.ch.ic.ac.uk/rzepa/cmlrss_distrib/

RSS is a protocol for creating "News Feeds" and CMLRSS is a chemically-aware extension. More information can be found in the reprint here or the earlier article.

## Downloading the CMLRSS Distribution

For convenience a single ZIP archive is available for download here (

## Creating a CMLRSS Feed

This can be accomplished in either a static or a dynamic manner.

1. Static feeds take the form of creating an XML document (example here with source) describing a feed channel and a list of items within that channel. To include molecular coordinates, you can use openBabel to convert from legacy formats.

   To invoke Babel, use the command line (Windows users, Run cmd, and CD to the directory which contains BOTH babel.exe and cygwin1.dll)

       ./babel -imdl  moleculefilename.mol -ocml moleculefilename.xml -x2an

   (if the legacy format is Molfile. Modify as needed for other formats). The resulting CML file can then be text edited into the overall item container of the RSS file.
2. Dynamic feeds can be created by querying a suitable database. Thus

       http://www.ch.ic.ac.uk/csdemo/feed.php

   will query a MySQL database (using default values for the search variables, in this case returning the last ten items entered into the database).

## Viewing a CMLRSS Feed

1. If the feed contains the following stylesheet declaration

       <?xml version="1.0" encoding="iso-8859-1"?>
       <?xml-stylesheet href="http://www.w3.org/2000/08/w3c-synd/style.css" type="text/css"?>

   then the RSS will be formatted to more or less display sensibly in a Web browser.
2. Generic RSS viewers can be used. A wide variety are available (an overview is available here). These viewers will honour the default RSS elements, and will gracefully ignore the chemistry specific components.
3. Chemically aware RSS viewers include Jmol (3D coordinates) and JChemPaint (2D coordinates). We anticipate that extension to Crystallographic coordinates and unit cells will be shortly available via JMol.
   - To install Jmol, place the enclosed Jmol.jar file in your $HOME directory and invoke it from a command line by:

         java -jar Jmol.jar

     This will (probably) create a new folder in your $HOME directory called .jmol (note the dot before the jmol!). Inside this folder (you may have to take some actions to make it visible, its most easily accessed from the command line. Hint: Programs such as Cocktail for OS X can make such folders visible) you will place the attached rssviewer.props file (which is used to add further channels if you wish) and the plugins folder, containing rssviewer.jar. New versions of all these files are available at http://jmol.sf.net/. The version in this distribution dates from February 24th.
   - Run Jmol as above (you might also be able to simply doubly click it). The effect should be thus:
     You can view single channels or aggregated channels. In the aggregated view, the entries can be sorted by various fields. Shortly, a Unique ID field will be added, which will enable duplicates (identical molecules) to be detected. Simple (elemental) filters can also be applied to the aggregated displays.
4. JChemPaint can be installed in a manner similar to Jmol. This allows display and editing of 2D structures (and allows 2D coordinates to be created from structures which only have 3D coordinates).

## FAQs

Queries etc will be recorded here.

March 1st, 2004.