Macs in Chemistry

Insanely Great Science

MyScript Calculator - Handwriting calculator


MyScript Calculator - A calculator that supports handwritten input has been updated.

New in version 1.3.2: - iOS 9 support - Jot down a quick calculation or check the history while you're using another app. Only available on iPads compatible with iOS 9 multitasking features.


Protein-Ligand Interaction Profiler has been updated


The PLIP Protein-Ligand Interaction Profiler has been updated.

According to the Changelog


  • Support for DNA and RNA as ligands__
  • Detection of metal complexes with proteins/ligands, including prediction of geometry__
  • Extended result files with detailed information on binding site residues and unpaired atoms__
  • Support for zipped and gzipped files__
  • Rich verbose mode in command line with information on detected functional groups and interactions
  • Automatic fixing of common errors in custom PDB files
  • Refined binding site selection
  • Better overall performance
  • Initial test suite for metal coordination
  • Classification of ligands
  • Improves detection of aromatic rings and interactions involving aromatic rings
  • Single nucleotides and ions not excluded anymore as ligands
  • Generation of canonical smiles for complete (composite) ligands
  • Generation of txt files is now optional
  • Basic support for PDBQT files
  • Correct handling of negative chain positions of ligands
  • Improved check for valid PDB IDs
  • Fixes several bug

The web service includes all the updates and integrates BioLip for flagging biologically relevant interactions. Since ligand molecules (e.g., Glycerol, Ethylene glycol) are often used as additives (i.e., false positives) for solving the protein structures, not all ligands present in the PDB database are biologically relevant.


Science Applications under El Capitan (Update 4)


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 an incremental upgrade I'm hoping most things will be unaffected. I’ll update the list regularly and feel free to send in information.

So far the only issues I've hit are those that involve Java, reading around it looks like this is widespread issue.

When I compiled a similar list for Yosemite it proved very popular with 13,000 page views, and I hope this page is similarly useful.

Aabel 3 seems to be working fine

Avogadro all OK

BBEdit all OK

ChemBioDraw I was in touch with their support and was told "No support for ChemBioDraw on El Capitan", however a couple of readers have said that it appears to work. No information yet on round trip editing.

ChemDoodle I had to reinstall latest version of Java

No issues reported for Cresset tools Torch, Spark, Forge

DataWarrior requires Java installation

Findings 1.2.4 is compatible with El Capitan

iPython Notebook all working fine

KNIME all working OK

MarvinSketch I had to reinstall Java for Mac OSX this is the last version of Java Apple created to support legacy applications, however trying to use the command line tool "evaluate" I got this error

line 128: /System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home/bin/java: No such file or directory

I updated ChemAxon Beans to version and this seems to fix the problem.

MOE all working fine, XQuartz did not need reinstalling. There have not been any reports of issues with the license server which has been an issue in the past.

Papers 3 is compatible with El Capitan

PYMOL seems fine after initial testing

R all seems fine

Safari Extensions still seem to be working.

SeeSAR no issues so far

Stardrop not aware of any issues

Spartan 14 seems fine.

Vortex no problems so far

Wizard Pro all seems fine

Updating Homebrew packages

Part of the OS X 10.11/El Capitan changes is something called System Integrity Protection or "SIP". SIP prevents you from writing to many system directories such as /usr, /System & /bin, regardless of whether or not you are root. However /usr/local is open for developers to use, so Homebrew can still be used as expected. To fix your Homebrew installation if you see permission issues type

sudo chown $(whoami):admin /usr/local && sudo chown -R $(whoami):admin /usr/local

There is a more detailed explanation here

You will also need to install the latest version of the command line tools

Then you can type

brew update
brew upgrade

I did the usual simple tests on the following packages and all worked fine after brew upgrade.

OpenBabel RDkit CDK Opsin Osra Inch Chemspot

Updated 5 October 2015


CLC Drug Discovery Workbench updated


CLC Drug Discovery Workbench 2.5 has been released.

  • Protein optimizer: New interactive tool invoked from the side panel in molecule projects. It allows for manual mutation and repair of amino acids, flipping of side chains, manual selection of side chain rotamers, and local adaption of protein structure to point mutations.
  • Ligand optimizer: The ligand optimizer allows now for custom modification and creation of ring structures. 3D molecule viewer:
  • Molecule surfaces can now be transparent, A clipping plane can cut into surfaces and secondary structures, Options for creating atom groups and visualizing hydrogen bonds have been improved

CLC Drug Discovery Workbench is your virtual lab bench. It gives you access to atomic level insights in protein-ligand interaction, and allows new ideas for improved binders to be quickly tested and visualized.


El Capitan Review in Guardian


OS X El Capitan review: bringing even older Macs up to speed

The latest version of Apple’s laptop and desktop operating system OS X 10.11 El Capitan will genuinely speed up your computer, particularly if you’ve got an older Mac