Macs in Chemistry

Insanely Great Science

Scientific Applications under Yosemite


I just thought I'd like to thank all those who contributed to the Scientific Applications under Yosemite web page, many users and developers contacted me either via email or in the comments section and they certainly added information about applications that I don't have access to.

To date the page has been viewed well over 10,000 times with readers from 188 different countries. Viewers spent an average of just under two minutes on the page and it still attracts 800 pages views a month.

Given that 75% of the visitors to the site are now using Yosemite I suspect most scientists have now made the transition and I won't be updating the page any more. Once again thanks for the contributions.


A review of Wizard Pro


When I first started the list of data analysis packages for Mac OS X it was a fairly short list, over the years the list has grown and the diversity of packages increased. From free packages like R to enterprise applications like IBM SPSS costing thousands. Some packages are enormously powerful but have a ferocious learning curve, whilst others are very easy to use but have only very limited capabilities. Wizard is an intuitive data analysis tool, designed from the ground up to be readily accessible but still retain the power of the sophisticated command line driven applications that only seem suitable for programmers. Wizard Pro allows the user to explore the data interactively without the need to learn a programming language. Read more here.


I should have added Wizard Pro runs under Yosemite and is on the list of Yosemite compatible applications, and has just been updated to version 1.6.7 (Feb 27th).


Chenomx NMR Suite


The latest update to the Chenomx NMR Suite has just been released, this includes a new batch processing wizard and several improvements. I checked with the developers and this update was built on a machine under Mac OS X 10.10 although the website had not yet been updated to include Yosemite compatibility.

There is a listing of spectroscopy applications here, and a comprehensive summary of compatibility of Scientific Applications under Yosemite here.




Differ is an ultra-fast yet easy-to-use tool to browse, search, split and combine VCFs

Opening a 1.5 GB VCF file in a text editor can take a while, even on modern computers. Differ opens these VCFs in a second or two on any modern Mac (best with SSD).

Differ requires Mac OS X 10.10


Science Apps under Yosemite


I've just updated the page detailing compatibility of science applications under Yosemite of particular note is the update of Spartan’14 version 1.1.9 that includes the new Yosemite supported driver from SafeNet.

Full details are here


Scientific Applications under Yosemite


I've continued to update the Scientific Applications under Yosemite we are now up to the 18th update. Many thanks for the people who have contributed.

With over 5,000 people viewing the page it is clearly pretty useful.


UCSF Chimera (version 1.10) is available


A new production release of UCSF Chimera (version 1.10) is available.

Platforms: Windows, Mac OS X (including Yosemite), Linux. This will be the last release to support OS X 10.6 and 10.7.

New since version 1.9: Protein contact maps color-coded by distance, PDB biounit and CATH domain web fetch, plotting all-atom and backbone RMSDs along sequence alignments (previously only alpha-carbon RMSDs), update to AmberTools 14, "vop scale" density map normalization, Modeller dialog allows specifying distance restraints, further implementation of the MultiDomain Assembler homology-modeling pipeline.

More details are given below; see release notes for the full list:

UCSF Chimera is a highly extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. High-quality images and animations can be generated.


Scientific Applications under Yosemite (Update 12)


Whilst there are many sites that track the compatibility on common desktop applications, it is often difficult to find out information about scientific applications. Given that this seems to be such a major upgrade I thought I’d set up a spare machine to test applications before I update my main machine. I’ll update the list regularly and feel free to send in information.

I have a number of applications/libraries/toolkits installed using Homebrew and installed in usr/local, this is known to cause extended installation times for Yosemite. So don’t worry if it appears the install is stuck at 1 min remaining.

If you do use Homebrew then it is worth updating

brew update
brew upgrade

Aabel 3 appears to be working fine

BBEdit version 10.5.13 and newer are compatible with Yosemite

Beaker all seems OK

ChemBioDraw versions 12, 13 and 14 all function as before.

ChemDoodle all seems to work fine

Chimera aka UCSF Chimera versions 1.10 and higher are working on Yosemite.

Conquest and  Mercury from CCDC works fine but you may need to reinstall Quartz (see below)

Cresset report that after testing that Torch, Spark, Forge and Blaze appear to be compatible with Yosemite, the only cosmetic issues are due to a couple of as yet unresolved bugs in QT here.

Cytoscape 3.1.1 seems to be working fine

DataWarrior no issues

EndNote X7.2 works well with Yosemite.

Findings Electronic Notebook no issues, only small issue is that the ‘+’ button of the window does not trigger full-screen, though it can still be done via the Window menu.

IDL 8.2 and earlier gags on a missing reference in libPng.dyld, but IDL 8.3 and later is OK

Igor Pro version works fine

iNMR no problems reported

MacVector 13.0.6 No significant issues reported

Marvin Marvin, Instant JChem, and JChem suite all work but require Java 7 (available here

Mathematica no issues reported

Matlab 2014b works fine, 2012a thru 2014a need patching (directions available from Mathworks support site. Older versions will not run at all..

MOE works fine but you may need to reinstall Quartz (see below)

OpenBabel no issues so far

Opsin all works fine

OSRA no issues

Papers Current version is compatible but not optimised, they hope to have a beta out of a substantially redesigned version next week.

Pro Fit 6.2 appears to work fine.

Pybel no issues reported

PyCharm works fine

Pymol All these are confirmed to work:

  • MacPyMOL
  • MacPyMOLX11Hybrid after XQuartz reinstall (see below)
  • Open-Source PyMOL with homebrew

Known issues with MacPyMOL: - Movie export broken. Edu-only-PyMOL (free Student version) Does not work.(Now updated to work with Yosemite)
No reports so far about about - Other legacy versions (0.99 etc.) Apparently progam will not open - Open-Source PyMOL with fink or macports

PyRx 0.8 for docking works fine

RDkit no issues reported

SeeSAR all seems to be working fine

Sente 6.7.8 seems to run fine, except that it cannot open a reference library from the File > Open... dialog box. Workaround is to open from Finder.

Spartan 14 does not work because the Sentinel drivers are broken in Yosemite. The problem is NOT with Spartan, it is with the SafeNet developed Sentinel Run-Time Environment driver (the license manager). SafeNet has not given a definitive date when they will release an updated driver with Yosemite compatibility, but they are working on this. Best advice is to not upgrade but if you have to then contact for a temporary alternative license procedure.

Torch no issues

VarSeq no issues

Vortex Upgraded when the developer preview came out.  All works fine

The VVI products work well enough on Yosemite, but I'd like to achieve a higher level of quality for Yosemite (and iOS/iPad). There is an ongoing beta program for this product: which is Graph Builder reincarnated on the iPad. There is also a beta program ramping for Graph Builder on Yosemite: but a last minute interaction bug with Yosemite has delayed that for perhaps a few days. Please feel free to broadcast this information as you see fit. Beta program participation should be directed to

VMD no issues reported

Wizard Pro is fully Yosemite compatible

XQuartz it seems the Yosemite installer deleted the symlink between /opt/X11 and /usr/X11; you can either reinstall Quartz or try "ln -s /opt/X11 /usr/X11"

Updated 30 October 2014


ASObjC Explorer 4


New version for Yosemite and Mavericks users

ASObjC Explorer 4 is a script editor built to take full advantage of AppleScript’s ability to call Cocoa methods. With AppleScriptObjC-based libraries available in Mavericks and Yosemite, and now direct access to AppleScriptObjC code in Yosemite, ASObjC Explorer 4 can help you write and debug your code more quickly, more effortlessly, and more efficiently. It also makes a great external editor for those developing in Xcode.

ASObjC Explorer lets you write your code, write separate testing code, step through your code, log what happened, and even add scripting terminology — all in one document window. When you have finished, you can use your document as a script or library, or export to your favorite format, including Mavericks-compatible applets with embedded script libraries.

Full details are here.


Everyday AppleScriptObjC


Yosemite catches up to 'Everyday AppleScriptObjC'

Myriad Communications pleased to announce the availability of the second edition of 'Everyday AppleScriptObjC', updated for both Yosemite and Mavericks.

Yosemite confirms AppleScriptObjC's position as an important component of AppleScript, giving access to the Cocoa frameworks and their functionality wherever scripts are run. It is now truly an "everyday" option.

'Everyday AppleScriptObjC', Second Edition, provides an introduction to using the Cocoa frameworks from a scripter's point of view. It covers writing the code, in both Mavericks and Yosemite, as well as deployment issues.

The book has been updated to cover Yosemite, as well as to expand coverage in other areas. It is full of usable code snippets, which are also provided in file form in both Mavericks and Yosemite formats.

'Everyday AppleScriptObjC', Second Edition, is by Shane Stanley, author of 'AppleScript Explored', the guide to using AppleScriptObjC in Xcode. You can find out more here:<>. It is available now for $US14.95.


Papers updated


The popular reference management application Papers has been updated.

Freehand annotations that were added using Papers 3 for iOS are now synched and displayed on Papers 3 for Mac! (Freehand annotation editing on Papers 3 for Mac will be added in a future update). Dragging one or more papers from your library into a note annotation will now add the citekey references to that note. Scripting API: It's now possible to set a publication's authors or editors via a string of person names:

tell application "Papers"
    set selectedPapers to selected publications of front library window
    set author names of first item of selectedPapers to "Griekspoor, A.C.; Neefjes, J.J.; Groothuis, T.A.M."
end tell

I’m delighted to see that they are already addressing bugs that have arisen in OS X 10.10 (Yosemite).


Applescript in the future


Applescript has had to take a bit of a back seat in recent years but there have been a couple of posts recently that will be of significant interest to all scripters.

Papers is a multi-award winning reference management application that hugely popular with scientists. I saw a very interesting entry on their blog.

The latest beta version of Papers for Mac adds support for scripting. This allows you to automate tasks or fetch and manipulate data in your Papers library by using AppleScript, or JavaScipt in Yosemite. Papers 3 features extensive AppleScript support that allows data to be fetched from a Papers library. You can also execute commands, like import and export. You can even create new data and set its most important properties. Some parts of the UI can be automated as well: the current selection can be changed, as well as the current view mode.

The importance of adding Applescript support to applications is nicely illustrated in an article by Brent Simmons, Making Your Mac App’s Data Scriptable.

Scripting isn’t a matter of automating button clicks; it’s about exposing the model layer to people who could use your app in their workflows.

There have been many concerns that the introduction of “sandboxing” will compromise the ability of applescripts to automate complex multi application workflows. There has been a recent article that shows the current best practices for controlling another app using AppleScript, Scripting from a Sandbox.

This comment sums things up nicely

While that’s usually a small minority of users (who use applescript), they’re power users — the kind of people who recommend apps to friends and family. They blog and tweet about apps, and people listen to them. They can be your app’s biggest evangelists.

And of course it is easy to share applescripts. I’ve added the links to the Applescript Resources page.