Monthly Archives: February 2015

iOS 8 iBooks annoyances

I generally like the UI of iBooks better than the Kindle app, and I like being able to buy books inside the app. But there are some things about iBooks in iOS that really annoy me… some of these are new or worse in the version in iOS 8, where iBooks comes preinstalled.

  • Updates: a red circle pops up when a book has an update. I’m not sure why iBooks titles have updates in the first place, or why I should update a book I’ve already read and don’t plan to revisit, but the red dot demands attention. So you I go to my purchased list and find:
    • The update all option is gone
    • The number of books with update buttons does not match the number in the dot
    • Several of the books with update buttons don’t update: they bring up a dialog that says “The item you tried to buy is no longer available”. The update count appears to be the number of actually updatable items + 1 if you have any number that can’t be updated because they are no longer available.  Things no longer available include a lot of Project Gutenberg titles.
    • The annoying red circle used to be in a less prominent place in the UI, IIRC.
  • The all books view: At first this seemed great. iBooks collects books in a series into a stack, kind of like a folder, to make navigation easier. It even figures out if there are unpurchased items in a series you might want to buy. But there are problems:
    • the metadata being used to do these arrangements seems to have the quality control that gave us version 1 of Apple Maps.
    • a blue “new” triangle that appears on the upper right corner. This is for flagging a new purchase, which would be fine. But I have several stacks where none of the individual books are new, and I know I’ve read them, and there doesn’t seem to be any way of clearing the stupid New Triangle manually.
  • The iBooks store: Probably related to the poor metadata…
    • OK, I would be a better person if I knew more languages. But even PubMed can limit my search results to English
    • If the app knows that books are part of a series, why is it so hard to find the books in the series in the iBooks store?

Fortunately, once I’m inside a book these mostly don’t matter. But they’re the kinds of annoyances that make me slower to update whenever new versions of iOS and OSX come out.

JSmol2wp plugin released at

A while ago I wrote a WordPress shortcode plugin to embed Bob Hanson’s JSmol molecular structure viewer into WordPress posts and pages. Last weekend I finally got it into the plugin repository.

The basic usage for proteins is via a shortcode like this:

[jsmol pdb='1LMB']

The plugin fetches the appropriate record from the PDB and generates an applet like this:


If you use acc key and prefix a chemical name with a $, JSmol looks looks for the structure at NCI.

[jsmol acc=$tryptophan]


You can rotate and zoom the structure with your mouse. These default buttons in the applet are created automatically by the plugin, or you can add custom buttons that run Jmol scripts. Using the outstanding flexibility built into Bob’s code (I just wrapped it for WordPress), you can fetch small molecules from remote repositories, or load files uploaded to your WordPress installation. The plugin whitelists pdb, cif, cml, jvxl, mol, mol2, xyz, and ccp4 filetypes for upload (this might be problematic for some hosting providers).Click the About/Help link to see more examples and documentation.