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.
Aabel 3 appears to be working fine
BBEdit version 10.5.13 and newer are compatible with Yosemite
ChemBioDraw versions 12, 13 and 14 all function as before.
ChemDoodle all seems to work fine
Conquest and Mercury from CCDC works fine but you may need to reinstall Quartz (see below)
DataWarrior no issues
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.
Igor Pro version 184.108.40.206 works fine
iNMR no problems reported
MacVector 13.0.6 No significant issues reported
Mathematica no issues reported
Matlab 2014b works fine, 2013b and 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
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.
Pymol All these are confirmed to work:
- MacPyMOL 220.127.116.11
- MacPyMOLX11Hybrid 18.104.22.168 after XQuartz reinstall (see below)
- Open-Source PyMOL with homebrew
Known issues with MacPyMOL:
- Movie export broken.
Edu-only-PyMOL 1.3r1 (free Student version) Does not work.
No reports so far about about - Other legacy versions (0.99 etc.) Apparently progam will not open - Open-Source PyMOL with fink or macports
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
Torch no issues
Vortex Upgraded when the developer preview came out. All works fine
VMD no issues reported
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 21 October 2014
There have a few new additions to the Mobile Science site taking the total number of apps up to 350.
These include the Chemical Engineering App Suite for iPad and iPhone, and a series of apps from Wavefunction, Inc that cover molecular structure and bonding called the ODYSSEY applications.
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:<http://www.macosxautomation.com/applescript/apps/everyday_book.html>. It is available now for $US14.95.
OpenEye have announced the release of VIDA v4.3. This is a major update with many new features and enhancements, including improvements to depiction, 2D alignment, list manager manipulation, surface selection and display, default colouring schemes, both visual and list-driven atom subset selection, cluster viewing, colouring by SD property and extension management.
One feature I’m sure will be very popular is the new advanced depiction options, including atom property maps from the Grapheme TK, substructure highlighting, and 2D structure alignment, are available for depiction in the 2D window and spreadsheet
Support for Mac OS X 10.8 and 10.9 was added
Mac OS X 10.6 is no longer supported