Macs in Chemistry

Insanely Great Science

OS X Source code

 

Apple has released the Darwin source code for OS X 10.10 here.

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Peppermint text editor

 

I’ve just added Peppermint to the list of Markdown Editors, Peppermint is a sophisticated text editor that has dozens of plugins/extensions for everything you need: live preview your HTML, convert LESS or Markdown, beautify CSS/JS/HTML, complete FTP/SFTP support, Regex Editor. Well worth a look.

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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 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

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 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 (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 support@wavefun.com 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: https://itunes.apple.com/us/app/graph-ide/id904733611?mt=8 which is Graph Builder reincarnated on the iPad. There is also a beta program ramping for Graph Builder on Yosemite: https://itunes.apple.com/us/app/graph-builder/id470597599?mt=12 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 support@vvi.com

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

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Biology Applications for MacOSX

 

I’ve been asked if I could include some biology/bioinformatics tools in the alphabetical listing, and I’m happy to add any that are sent to me, this week I’ve added.

CellDesigner

Cytoscape 3.1.1

GenomeBrowse

VarSeq

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WolframAlpha updated

 

The hugely popular Wolfram|Alpha has been updated.

With Wolfram|Alpha on your iPhone or iPod touch, you can explore a vast world of knowledge through an app adapted for your ever-changing, on-the-go lifestyle. Use Wolfram|Alpha to discover new information about the world and to deliver expert knowledge into any facet of your mobile life. The Wolfram|Alpha App plugs directly into the Wolfram|Alpha supercomputing cloud, computing answers to your questions quickly, efficiently, and without draining your battery.


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