Macs in Chemistry

Insanely Great Science

Scientific Applications under Yosemite (Update 5)

 

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 6.3.5.5 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 http://support.apple.com/kb/DL1572

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 1.7.2.3
  • MacPyMOLX11Hybrid 1.7.2.3 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

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Mobile Science 350th app added.

 

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.




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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:<http://www.macosxautomation.com/applescript/apps/everyday_book.html>. It is available now for $US14.95.



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iOS8 supasses iOS7

 

I was just glancing at the chart on Mixpanel and I see that iOS8 is now the major iOS version. With iOS8 and iOS7 comprising over 96% of the market share it certainly makes it easier for developers to maintain compatibility.

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VIDA v4.3.0 released

 

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

2Ddisplay

Support for Mac OS X 10.8 and 10.9 was added
Mac OS X 10.6 is no longer supported


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