Macs in Chemistry

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Version 3.2 of ASObjC Explorer for Mavericks


Version 3.2 of ASObjC Explorer for Mavericks, the script editor built to take full advantage of AppleScriptObjC, is now available.

The two main new features are Apple event logging, similar to tradition AppleScript editor logging, in addition to Explorer's own logging; and the ability to specify which thread scripts are run on, to facilitate debugging of scripts that use callbacks and times.

There are also a raft of scripting changes, several extra sample scripts, and improvements in several other areas.

You can read more here:


Still waiting for an update?


At the WWDC on June 10 2013 Apple announced the latest version of the Mac OSX operating system and on the following October 22 they announced it was available as a free instal from the Mac App Store. Since then there have been two updates leading to the current 10.9.2.

As soon as the update was announced at the WWDC many software companies started checking and updating their software so that when Mac OSX 10.9 was released they had compatible updates available immediately or shortly after. I kept a list of scientific applications under Mavericks and have updated the list periodically. Most software is now compatible, or there are workarounds. However recently I was made aware of the situation with ChemBioDraw from Perkin-Elmer (formally Cambridgesoft). ChemBioDraw has been a major chemical drawing package on the Mac for as long as I care to remember however the current version is not compatible with Mavericks. Indeed when you look at the support forum there are reported issues with retina display dating back to 2012! A support topic that has been viewed nearly 6000 times but not yet fixed apparently. There are many comments of the support forum but perhaps this gives you a flavour.

I confirm, the copy/paste issue in Mac version of ChemDraw 13 makes it totally unusable!!!! I suggest this is not only a problem with the compatibility with Mavericks. It never worked in Mountain Lion too! This issue is at least one year old and the developers just continue to ignore this issue. ChemDraw 13.0 crashes >90% of the time when you copy/paste a structure.

As of writing there is no indication when there will be a fix or whether earlier versions of ChemBioDraw will also be updated. This software is very expensive $1140 for a one year license! So my question is what is a reasonable length of time to expect to wait for an update?


OEChem Updates


On the 10th anniversary the OEChem toolkit from OpenEye has been updated,

  • Added support for OSX 10.9 Mavericks.
  • The next toolkit release, 2014.Jun, will be the last release to support OSX 10.7.
  • This release will be the last release to support OSX 10.6.
  • The next toolkit release, 2014.Jun, will be the last release to support 64-bit Ubuntu 10.04.
  • GCC 4.8.2 support added for RHEL6. GCC 4.8.1 had a bug that made it impossible to compile OpenEye header files. Please use 4.8.2+.
  • Experimental support for Python 3.3 added.

Scientific Applications under Mavericks (Update 11)


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.

The update went smoothly albeit with an overnight download of the 5.5 GB file.

The update removes both X11 and java so both of these need to be reinstalled, if you forget you will be prompted to download the first time you try to use them.

No issues with cursory testing, users or vendors provided feedback

Cresset software (forge, torch, spark) (no reported issues)
iNMR (No reported issues)
OpenEye (Command line tools OK, OMEGA 2.5.1 (OSX 10.8 version), FILTER 2.5.1 (10.8), ROCS 3.2.0 (10.8), SZMAP 1.2.0 (10.8), EON 2.2.0 (10.8), QUACPAC 1.6.3 (10.8), SZYBKI 1.8.0 (10.8), FLYNN 2.3.0 (10.8), The Python and Java toolkits work fine. The C++ toolkit can be made to work if some of the compiler flags are changed. Please email for more details. For the OpenEye GUI applications, vROCS 3.2.0 (OSX 10.8 version) works fine, for other apps see below
R latest version R 3.0.2 ("Frisbee Sailing")
Reference Tracker

Some issues :-(

MOE install
I downloaded the latest update as a zip file and unarchived it. When I double click on the installer I got a message that it was broken or corrupted. This seems be an issue with the Mac OSX Gatekeeper,

  1. Open Apple menu, then go to System Preferences -> Security & Privacy -> General tab.

  2. In the option list of "Allow Applications downloaded from", select "Anywhere".

Then installs OK. Once installed MOE seems to run fine.

CCDC Software
Mac OSX 10.9 causes most CCDC software to fail - there are now have patches available that address this issue. For enCIFer 1.4: For the 2013 CSD System go to:  For standalone Mercury 3.1 or 3.1.1 go to:
These updates should only be applied on Mac OSX 10.9. NB One reader reported issues with the update.

Chemdraw 13 files pasted into Keynote 6 cannot be copied and pasted back into ChemDraw. In addition, if you open old Keynote files in Keynote 6 all the ChemDraw cannot be copied and pasted. It pastes into Chemdraw as a picture with an all black background. In Mac OS 10.9 with Keynote 5 - round trip editing still continues to work. According to the PerkinElmer Support Forum there are issues with copy/paste in CD 13 to Office 2011 for Mac. Any CD structures that are pasted into PPT or Word cannot be opened or edited with CD.

EndNote X7
We have tested EndNote X7 with Mac OS X 10.9 Mavericks to determine compatibility. We have found some minor issues and are working on a free update patch to be released in the next few weeks.

EndNote X6
EndNote X6 is not officially compatible with Mac OS X 10.9 Mavericks. We are testing EndNote X6 with Mac OS X 10.9 Mavericks to determine informal compatibility and will report any exceptions found on this page.
EndNote X5 and earlier
Due to major compatibility issues, it is not recommend to attempt to use EndNote X5 or earlier on OS X 10.9. When attempting to launch EndNote X5 or earlier, a warning message comes up that will include "unable to load ....ENCore.Bundle". EndNote X5 and earlier will fail to launch after receiving this message. There are no known workarounds for this issue besides moving to a more recent version of EndNote or restoring your computer  (using a Time Machine Backup for example) to a previous version of Mac OS X.

OpenEye Command line tools that require setting the OE_ARCH environment variable (FRED 3.0.1 (OSX 10.7 version), HYBRID 3.0.1 (10.7), POSIT 1.0.3 (10.7), LEXICHEM 2.1.0 (10.6), BROOD 2.0.0 (10.5)

export OE_ARCH=osx-10.9-x64:osx-10.8-x64:osx-10.7-x64:osx-10.6-x64:osx-10.5-x86

For the OpenEye GUI applications, vROCS 3.2.0 (OSX 10.8 version) works without any issues. VIDA requires the OE_ARCH modification shown above but also needs the following additional fixes:

sudo mkdir -p /Applications/OpenEye/arch/osx-10.6-x64/vida/4.2.1/bin/QtCore.framework/Versions/4
sudo ln -s /Applications/OpenEye/arch/osx-10.6-x64/vida/4.2.1/bin/QtCore /Applications/OpenEye/arch/osx-10.6-x64/vida/4.2.1/bin/QtCore.framework/Versions/4/QtCore

Unfortunately, the current vBROOD, AFITT, and MAKE_RECEPTOR GUIs do not work on Mavericks. We are actively investigating these issues. More details

Using Aabel v3 on Mavericks is not recommended due to cosmetic glitches such as misalignment of graphic viewer icons on the Mavericks buttons. Mavericks will be supported in the next major version of Aabel

Papers2 update about to be released

If I hear of anything, I’ll update this page.


ASObjC Explorer updated


I just saw this message from Shane Stanley

As some of you have probably found already, Xcode does not recognize AppleScript's new interleaved syntax when used for action handlers -- you cannot make connections to them from controls. The workaround is to keep using the underscore syntax for action handlers until the problem is resolved. That's not ideal if you use an external editor, though. FYI, I've just released a new version (3.0.7) of ASObjC Explorer for Mavericks to deal with this issue. There is a new preference setting in Preferences -> Other. When checked, every time you save a .applescript file, any single-argument handlers will be changed to use old-style underscore syntax. (The new syntax will appear in Xcode and in the saved file, while the new syntax will still appear in Explorer.)


XQuartz Updated


XQuartz has been updated this contains X11 2.7.5 the first release supported on Mavericks. Full details are available here

The XQuartz project is an open-source effort to develop a version of the X.Org X Window System that runs on OS X. Together with supporting libraries and applications, it forms the that Apple has shipped with OS X since version 10.5.


Applescript and GUI in Mavericks

One of the big changes with Mavericks is the enhanced security and this has an impact on all developers even those who write a “simple” applescript to avoid a tedious or repetitive series of actions.

Developers have often relied upon AppleScript’s ability to control the user-interface, to provide an automation solution when no direct scripting support of an application or process was available. While this valued ability continues to be fully supported in Mavericks, the enhanced security focus of the new OS requires a few changes in how scripters access and apply the Accessibility frameworks.

There is a really comprehensive discussion of Accessibility Preferences and GUI Scripting over on Mac OS X Automation. Well worth a read.




I’ve just updated the listing of Scientific Applications under Mavericks and I thought I’d highlight one application. The page I have on Tools for Fortran Programmers is consistently one of the top accessed Blog entries. I’m sure one of the reasons for this popularity is FTranProjectBuilder the only Mac-native Fortran development environment (IDE) it works with the gfortran, g95, ifort, Absoft Pro Fortran, NAG nagfor and PGI pgfortran compilers. Since I mentioned it last FTranProjectbuilder has been updated six more times, in April, May, July, August and October with new features like the ability to build static libraries, trackpad interaction and compiler errors now being marked in the source code. Full details are in the project notes on the Nocturnal Aviation Software website , and yes, all of the tools, including FTranProjectbuilder are compatible with 10.6.8+, and run fine on 10.9 Mavericks. 

Fortran still has a significant user base in the scientific community where the speed, portability, array handling and access to shared memory make it a very powerful option.

There is a nice comparison of programming languages from the viewpoint of scientists here


Mavericks adoption rate


I’ve been looking at the rate of Mavericks adoption here currently it stands at 13-15% which is quite impressive. Interestingly most of the early adopters seems to be those running Mountain Lion, the numbers using Lion and Snow Leopard seem to be pretty much unchanged.

I’ve also updated the post regarding Scientific Applications under Mavericks, if anyone has any more comments I’ll continue to update the page.


ASObjC Explorer for Mavericks Released


Myriad Communications has released its successor to AppleScriptObjC Explorer, available immediately. The new editor takes advantage of the improvements to AppleScript in the latest release of OS X, which make access to Objective-C frameworks from AppleScript easier than ever.

"The changes to AppleScript in Mavericks have largely flown under everyone's radar, but script libraries open lots of doors for scripters," says the application's developer, Shane Stanley. "Bridging between AppleScript and Objective-C code has become much easier. This sets a new direction for expanding AppleScript's abilities."

ASObjC Explorer for Mavericks is designed to make developing AppleScriptObjC-based script libraries simple, with everything you need in one window. It features customised syntax formatting to take advantage of the new interleaved syntax; intelligent code-completion and shortcuts to take the tedium out of entering code; logging, stepping and breakpoints to aid in debugging; and a built-in simplified scripting-definition editor for adding English-like terminology.

It also makes an ideal external editor for AppleScriptObjC-based Xcode projects in Mavericks

ASObjC Explorer for Mavericks can be downloaded from <>, and can be used free for 30 days. The purchase price is $US49.95.

For further inquiries, contact Shane Stanley at <>.