On 11 Jun 2014, at 00:53, Jim Hu <[email protected]> wrote: > I just pushed a new version of the wordpress plugin for JSmol to GitHub. > Changes: > - added support for some other file types. So far it only accepts these if > the path is specified via a fileurl= parameter. The plugin modifies the > wordpress whitelist to allow upload of additional mime types, but advice on > what to use is needed. > - added support to specify the URL of the data file (useful when wordpress > isn't delivering the path you expect, or for loading the demos in the data > directory) > - more debug info > - fixed (I hope) the bug that prevented loading when permalinks were set to > the default. > - fixed menu popup menu problems on some templates. The problem was an > outdated version of jquery and that I hadn't set the dependency for jquery-ui > properly. On some newer templates, these had already been loaded. > > Thanks to Henry for patience and finding bugs!! > > demo is still at http://biochemistryweb.tamu.edu/biobiodev/testing-jsmol-post/ > > A couple of questions: > - are there equivalents of pdb for remote loading of other file types?
That last is an interesting question. I have long argued that CCDC (Cambridge crystal database) should do the same for CIF files as PDB do for biomolecules. CCDC recently did start to assign a datacite DOI to each crystal structure, starting down the path to doing so. Currently however this doi takes you to a landing page, which requires a human to progress further (after asking questions such as who they are). So I am copying Ian into this in the hope that perhaps CCDC can more helpfully answer Jim’s perceptive question. I would add that we have done what Jim asks for chemical files held on a (Dspace) digital data repository. The Javascript for doing so is at http://www.ch.ic.ac.uk/rzepa/talks/paris14/resolve-api.js and an example showing this can be found at http://doi.org/10.6084/m9.figshare.840483 If you click on the link “log” it will do what Jim asks, and load (in fact a Gaussian log file) from such a repository. To do this, it has to “action the landing page”, which can be done using digital repository (proposed) standards, ones that we have implemented. So to summarise; if a file has a direct URL, it is trivially possible to remote load other file types, but the trick is figuring out what that URL is in the first place. The http://doi.org/10320/loc repository standard is what facilitates this, and http://www.ch.ic.ac.uk/rzepa/talks/paris14/resolve-api.js implements. There are few repositories of chemical data that support this at the moment, but with tools such as Jim’s coming on, I hope this practise spreads.
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