{"id":22910,"date":"2020-11-05T08:11:31","date_gmt":"2020-11-05T08:11:31","guid":{"rendered":"https:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=22910"},"modified":"2020-11-06T12:36:38","modified_gmt":"2020-11-06T12:36:38","slug":"internet-archeology-an-example-of-a-revitalised-molecular-resource-with-a-new-activity-now-built-in","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=22910","title":{"rendered":"Internet Archeology: an example of a revitalised molecular resource with a new activity now built in."},"content":{"rendered":"
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In Internet terms, 23 years ago is verging on pre-history. Much of what was happening around 1997 on the Web was still highly experimental and so its worth taking a look at some of this to see how it has survived or whether it can be “curated” into a form that would still be useful. I had noted in my earlier comment<\/a> a site which early on had become non-functional and then speculated whether any volunteers might have suggestions for how to best rescue it.<\/p>\n

There are two ways of approaching any such rescue operation; a manual editing of the code behind the site (the HTML) or a more automated approach to doing so. The site in question in fact probably has more than 200 HTML documents that would need such an edit, which is impractical (or costly) for human curation. But the underlying well-formed structure of HTML lends itself to automation and now a saviour in the form of \u00c1ngel<\/a> has indeed come forward with the solution!<\/p>\n

One of the least stable aspects of Web pages written in the period 1993-1998 or so was the manner in which extensions to perform specialised tasks were handled. The first solution in chemistry[1]<\/a><\/span> was to use the Web page itself to launch an external molecular viewer such as Rasmol via<\/em> a protocol known as MIME,[2]<\/a><\/span> but that depended very much on the viewer already being pre-installed on the device being used. This was a shop-stopper if you did not have the administrative rights to do so. Netscape was a company set up in 1994 whose main product was an innovative browser which could be extended by “embedding” a window directly into the display page using a plug-in rather than the earlier solution of having a separate window. \u00a0In 1995, one such plugin appeared for the Netscape browser called “Chime”, which allowed 3D coordinates representing a molecule to be displayed as an interactive model within the page. The plugin still had to be pre-installed by the user and this is how in 1997\u00a0https:\/\/www.ch.ic.ac.uk\/vchemlib<\/a> was set up to function.<\/p>\n

The limitations of plugin pre-installation soon became apparent. A partial solution was to download the plugin as part of invoking the web page itself. For this to work across a range of different devices running different operating systems, the plugin had to work on all of them. The solution was based on Java applets, which in turn would still rely on an initial underlying installation (with admin rights) of the JRE (Java Run-time Environment) on the device. This would now support a wide variety of different Java applets, rather than requiring each of them to be pre-installed by the viewer of the page. Between the period 1998 or so up to around 2015, the functionality of the Chime plugin was implemented and indeed greatly extended into the Java-based Jmol applet<\/strong>.[3]<\/a><\/span> Unfortunately, using this did now require rewriting the underlying HTML code for each individual Jmol invocation.<\/p>\n

The next step brings us up to the present method, which was to replace the Java applet by a Javascript-based module which would NOT require a JRE to be pre-installed. All the required installation would be handled by the browser itself; the runtime environment in effect was now built into browser itself. This again required a change to the HTML code for the invoking this tool. So the nature of the curation required to revitalise https:\/\/www.ch.ic.ac.uk\/vchemlib\/<\/a> can now be defined: replace the HTML code used to invoke Chime by new code which invokes its current replacement, JSmol<\/strong> (which stands for JavaScript Jmol\u2021<\/sup>). The good news is that this is a simple programmatic procedure, which itself can be implemented using Javascript. Here is where Angel comes in. He has freshly written\u00a0convert.js<\/tt><\/strong>\u00a0as a script which performs this task. It is now invoked by simply adding a header to every HTML document as <script src=\"convert.js\" type=\"text\/javascript\"><\/script><\/tt> and all the necessary conversion from the old Chime syntax is then done on the fly when the page is loaded.<\/p>\n

The big win is that as a toolkit, JSmol is very much more capable than Chime ever was! One of the many interesting things it can do that was not previously possible is “computation”. I thought I would illustrate how this veritable resource has not only been curated back into (mostly) working order, but also how its functionality as a molecular toolkit has been greatly enhanced.\u00a0<\/p>\n

\"\"<\/a><\/p>\n

We are going to illustrate this using the tool\u00a0optimize structure<\/strong>, the menu for which can be invoked by a right-mouse click anywhere in the molecule window. What does this mean? Well, I need to start by covering the basic sources for 3D molecular coordinates, which can be generated using a wide variety of methods, some of which are listed below.<\/p>\n

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  1. They may be derived from simple 2D flat diagrams such as produced by e.g.<\/em> Chemdraw, with some indication of 3D using chemical hashes and wedges. The “z” coordinate can be zero for all atoms. Clearly not optimal.<\/li>\n
  2. A 3D structure can be generated from a 2D one using very simple rules about the 3D environment about each atom, such as tetrahedral carbons and simple standard bond lengths and angles. Programs such as Avogadro<\/strong>[4]<\/a><\/span> can do this as part of loading a molecule with only\u00a02D coordinates present.<\/li>\n
  3. This simple rule can be extended to using a full force field<\/strong>, which includes much more information about bond distances, bond angles, torsions, inclusion of van der Waals attractions and repulsions and electrostatic effects (but significantly not any effects based on electronic structure).<\/li>\n
  4. Full-blown quantum mechanical computation of the geometry, including electronic effects.<\/li>\n
  5. Experimental coordinates such as obtained using crystallography.\u00a0<\/li>\n<\/ol>\n

    In general, information on which of the above categories were used to obtain the 3D coordinates are infrequently, if ever, actually declared on the web page. Indeed, this information for the site https:\/\/www.ch.ic.ac.uk\/vchemlib\/<\/a> is missing, only the original author might know! Of these types, #3 is computationally fast enough to be implemented into a Javascript such as JSmol, so we can now test how “optimised” any set of 3D coordinates actually is (#4 is not yet possible). Here are some instructions on how to proceed. For illustration I will use this molecule from the site, accessed as https:\/\/www.ch.ic.ac.uk\/vchemlib\/mol\/direct_pdb.html?senses\/vision\/colour\/pdbs\/carotene.pdb<\/tt><\/small><\/a> The coordinates are expressed in the so-called PDB format, which was originally developed with proteins in mind and\u00a0not small molecules.<\/p>\n

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    1. Load the link above and right-click to bring up the toolbar menu shown below:
      \n      \"\"<\/a><\/li>\n
    2. When doing any computation (especially one that might turn out to be slow!), it is useful to get feedback and this is done by opening the Console<\/tt>. With the molecule now available to inspect, you might notice some anomalies\u2660<\/sup> indicated with red arrows.
      \n      \"\"<\/a><\/li>\n
    3. The top panel of the Console shows JSmol responses and the bottom panel is where you can type commands for JSmol<\/a>. Type the following commands one at a time into this bottom panel, each ending with pressing the return key:\n