Macs in Chemistry

Insanely Great Science

BBEdit 11 released

 

My favourite text editor has just been updated!

BBEdit 11 has been released, with improved syntax colouring, a sophisticated text clippings manager, updated “Find Differences” and dialog boxes, floating palettes, and many internal subsystems have been rewritten or updated to support new features, improve performance, add refinement, and make future enhancements possible.

In all, BBEdit 11 contains over two hundred additions, changes, and refinements. The detailed change notes contain complete information.

Always worth a read, I particularly liked

Worked around a bunch of antisocial behaviors in the OS that would cause floating windows to end up all over the place after disconnecting and then reconnecting a display (typically an external display connected to the laptop). Now, the OS may still make your palettes dance around like they're on "The Price Is Right", but once you put them where you want them, the application will remember their positions more reliably.

Check the website for upgrade pricing.



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Scientific Applications under Yosemite (Update 6)

 

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, 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

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.

PyCharm works 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

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 support@wavefun.com for a temporary alternative license procedure.

Torch no issues

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

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 22 October 2014

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Findings LabNotebook

 

Findings LabNotebook for iOS has been released. This comes with Dropbox sync.

screenshot-progress-ios

There is a review of the MacOSX version here.

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New Swift website

 

In addition to the Swift Blog there is now a dedicated Swift website

Swift is an innovative new programming language for Cocoa and Cocoa Touch. Writing code is interactive and fun, the syntax is concise yet expressive, and apps run lightning-fast. Swift is ready for your next iOS and OS X project — or for addition into your current app — because Swift code works side-by-side with Objective-C.

The latest entry on the Swift blog deals with “Failable Initialisers” a new feature in Swift 1.1 part of Xcode 6.1.

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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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