Macs in Chemistry

Insanely Great Science

Reenabling Extensions after Safari 12 update


The latest update to Safari (Version 12) brings a range of features intended to improve online security and privacy. Unfortunately one of the consequences is that only Safari Extensions available from the App Store are enabled and you will get a message that Safari no longer supports unsafe extensions and you are directed to the App Store.


Whilst I'm sure that extensions from major developers will migrate to the App Store I suspect that those Extensions provided by scientists may well not make the transition. This is a shame because some are very useful. However you can build the extension yourself to get around the problem.

This tutorial shows how to extract the code from an existing extension and then build it using Extension Builder.


Web browser usage


Occasionally developers contact to ask about platforms/operating systems/versions/web browsers that are used by readers.

Recently I was asked about web browsers and so I contacted a number of scientific databases, scientific app developers, web sites. They were kind enough to provide information but asked that the details were not made public. The 12 sites range from 10's of thousands of hits per month to many millions hits of hits per month. The data shown below is from Jan 1st this year. It appears that Internet Explorer has almost disappeared as a mainstream browser.


Some people reported that they felt the drop in IE use was due to poor javascript performance.


I've just been sent this image which also serves to underline the dramatic fall in the use of Internet Explorer (at least among chemists).

Screen Shot 2016-03-15 at 12.12.05 AM


ChemSpider Safari Extension updated


The ChemSpider Safari extension has been updated. It sports a cleaner interface and provides fixes a bug introduced by an update to ChemSpider.



Indexing the internet in a chemically intelligent manner

Some time ago I described a Safari extension that uses the to index a web page for chemical content.

For an example of a “chemicalized” page have a look at this

As you can see below all molecules mentioned in the page become links that on a mouse over reveal the structure, they also provide a handy ribbon of structures across the top of the page that is useful for quickly scanning and navigation.


A recent publication by Southan and Stracz, Extracting and connecting chemical structures from text sources using Journal of Cheminformatics 2013, 5:20 describes how this information is being used to provide better indexing of the internet in a chemically intelligent manner. They include a demonstration of a number of web pages and document sources that were indexed in this manner including PDF’s from the patent office. now has 15000 unique visitors a month – which is a huge growth compared to spring 2012. These users contribute to the database every day, making sure it’s up-to-date and contains new interests as well. The database today contains 327000 structures that were converted from 545000 names and identifiers coming from 367000 webpages.

These structures and links have now been uploaded to PubChem and if you are interested in what sort of molecules have been registered via you can browse them on the PubChem website here


Cheminformatics on a Mac

I gave a talk at the Cambridge Cheminformatics meeting last week, I’ve put the slides here. It was more of a demonstration than a talk but the slides give an overview and links to the various tools.



A couple of people have asked for a pdf version of the slides for download.


Chemistry Reference Resolver Safari Extension

I’ve added Chemistry Reference Resolver to the page of Safari Extensions. This adds a toolbar to your browser as well as adds a right-click menu option for reference resolving


Applescript to report installed and enabled extensions

When Apple released Safari version 5 one of the most important new features was the support for extensions. Extensions are a great way to add features to Safari to personalise web browsing, they enable the addition of features that you find useful. There is a listing of Extensions that might be useful for chemists and judging by the weblogs these are of significant interest. If you are working with them however it is a bit of a pain to check which are installed and which are enabled. This applescript is a very neat way of getting a report, it also serves as a demonstration of how to link to shell scripts, in particular using the unix command cat, a standard Unix utility that concatenates and lists files, to generate the report.


Safari Extensions

Just updated the chemistry Safari extensions so they are compatible with the upcoming Safari 5.2.


ChEMBL Safari extension

ChEMBL Safari extension

Building Safari Extension

A tutorial showing how to write Safari Extensions

Safari extension for Opsin

The Unilever Centre for Molecular Science Informatics have been at the forfront at developing tools for the creation and curation of molecular data. OSCAR (Open Source Chemistry Analysis Routines) is software for the semantic annotation of chemistry papers a key part of this is Opsin a name to chemical structure converter. There is now a web interface to the program available and the web services can be accessed by anyone. Whilst this is very useful in its own right the beauty of such services is that other can build tools that access them.
There are a number
Safari Extensions described on this site that access similar services and with the help of Matt I'm happy to anounce a new addition.
The Safari Extension for Opsin (
download) allows the user to highlight a chemical name in a web page and then control click affords a dropdown menu, click on "Display ... using Opsin" and a small window will open displaying the chemical structure. What is particularly nice is that in addition to providing the structure in png format the same web service also provides the chemical structure in SMILES, InChi and CML format. If you click one of the buttons and the bottom of the structure window the structure will be downloaded in the appropriate format. You can read more about this extension here.

There is a full listing of the Safari Extensions here.

ChemSpider Safari Extension Updated

If you go to the Safari Preferences and select the extensions tab you will see there is an update to the ChemSpider extension. This fixes a broken URL when linking to the ChemSpider website. Read More...

Safari Updated

Apple have released a new version of Safari, possibly the most important feature is that Extensions are now enabled by default.

There is also a new
Extensions website.

There are a collection of extensions that might be of use to
Chemists here.


ChemSpider Extension Update

The ChemSpider Extension has now been updated thanks to magnificent work by Matt at Mac OSX Tips, the small window that pops up containing the structure now has a number of additional options highlighted below, if you click on the “3D” button the display changes to a 3D rendering using the Java applet JMOL. If you now click on the “Zoom” button

The structure is displayed in a larger window as shown below. Clicking the “Save” button downloads the structure in .mol format.

Back to list of extensions

Safari Extensions

A selection of extensions that should be useful for chemists.

Chemspider :- Displays structure of highlighted chemical/drug and links to ChemSpider page.
PubChem :- Search PubChem for the highlighted compound
eMolecules :- Search eMolecules for the highlighted compound
Chemicalize :- Submit the current URL to
DrugBank :- Search DrugBank for the highlighted compound


Search ChemSpider Safari Extension

Chemistry Safari Extension