Macs in Chemistry

Insanely Great Science

EL Capitan

UCSF Chimera (version 1.11) is available


An update to UCSF Chimera (version 1.11) is available for download.

General Changes:

  • model-display checkboxes can be shown below the command line, and the model-active checkboxes can be hidden (see Preferences, Command Line)
  • new input format: IMAGIC density map
  • mouse focus (so that Chimera accepts typed input) can be restored by clicking into the Side View as well as the main window
  • command-line “atomspec” expanded to handle surface piece names (such as from Multiscale Models)
  • new flat ribbon publication preset
  • “wall-eye stereo pair” option added to Save Image dialog
  • revamped Getting Started tutorials, new Ribbon Styles image tutorial
  • molecule descriptions (shown in the status line on mouseover) now read from mmCIF, not just PDB
  • PubChem fetch changed to get structures from PubChem3D (NCBI) instead of Pub3D (Indiana University)
  • command history navigation skips completely identical lines, and additionally pressing Shift (along with Ctrl-p, Ctrl-n, ↑, or ↓) goes to the previous/next occurrence of the same command (same initial string) instead of the * immediately adjacent command
  • atom specification tolerates spaces after commas
  • implemented standard keyboard shortcuts Ctrl-o,s,S,q (on Mac, Command instead of Ctrl) for File menu entries Open, Save Session, Save Session As, and Quit, respectively

Full release note are here

This is the last release for 32-bit operating systems, both the 32-bit and 64-bit versions run on Mac OS X 10.8 or later (including OS X 10.11 "El Capitan")

Chimera is developed by the Resource for Biocomputing, Visualization, and Informatics at the University of California, San Francisco (supported by NIGMS P41-GM103311).


BBEdit Updated


BBEdit is my favourite text editor and I’ve been a user since way before Mac OSX. The latest update BBEdit 11.6 brings a number of bug fixes and updates but also introduces a new demo mode. For 30 days the full feature set is available for free after which time BBEdit will remain permanently functional with a revised feature set that includes its powerful text editing capabilities but not its web authoring tools or other exclusive features. These features may be re-enabled at any time with a purchased license.

BBEdit 11.6 requires Mac OS X 10.9.5 or later, and is compatible with OS X 10.11 "El Capitan".

BBEdit can be obtained from the online store.

There is also a listing of markdown editors here


XQuartz update


XQuartz 2.7.9_rc1 is available for download. This update contains a workaround for an issue that users have been reporting on El Capitan. If you're on El Capitan and have been seeing OpenGL surfaces remain onscreen after they should have been dismissed, please give this update a try and report back to the developers.


Science Applications under El Capitan (Update 11)


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. Looking the CambridgeSoft forum ( it is clear that there are major problems with ChemDraw 15 and El Capitan, as ever it seems that a new release of Mac OSX comes as a complete surprise to ChemDraw developers, "Currently our products are not supported with El Capitan. We plan to support El Capitan for the future release/update".

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.

Mnova no reported issues

Papers 3 is compatible with El Capitan

Plane of best fit I got several errors after upgrading, brew update and recompile solved everything.

R all seems fine

Safari Extensions still seem to be working.

Schrödinger report all their software is supported under El Capitan, MacOSX 10.11 is supported for the 2015-4 release. You must upgrade your Schrödinger software installation to the 2015-4 release, as previous releases are not supported on MacOSX 10.11.

SeeSAR no issues so far

Stardrop not aware of any issues

Spartan 14 seems fine.

UCSF Chimera is also working on El Capitan.

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


Whilst users upgrading a machine that already has XQuartz have not see any issues there seems to be some issues with installing XQuartz onto new machines. It seems the symlink from /usr/X11R6 to /opt/X11 is not present and a reference to /usr/X11R6/lib/libX11.6.dylib fails, a post-install script for XQuartz should have setup the symlink.

The suggested solution if for users to type

/usr/libexec/x11-select /opt/X11

This installs both the /usr/X11 and the /usrX11R6 symlinks

More info on the X11-users mail list at Apple

Update. This has been fixed in a third release candidate of XQuartz 2.7.8 so hopefully an update is imminent.

An updated version of XQuartz has now been released full details are available here and the installer is available here

This also seems to fix X forwarding and window positioning issues some people experienced.

There can be an issue with installing Pymol under El Capitan, if you find it crashes on startup then there is a possible solution at the bottom of this page

Updated 12 December 2015


Pymol under El Capitan


When El Capitan first came out I upgraded a machine with an existing installation of a variety of cheminformatics tools installed using Homebrew and PIP as described here. Under this situation Pymol worked without problem. However I have had a few readers email me saying they are having problems so I took a new machine running El Capitan and tried to instal the same cheminformatics tools including Pymol using Homebrew and PIP. All worked fine except Pymol which opened but crashed with the following error.

Username:~ prompt$ pymol
PyMOL(TM) Molecular Graphics System, Version
 Copyright (c) Schrodinger, LLC.
All Rights Reserved.

    Created by Warren L. DeLano, Ph.D. 

    PyMOL is user-supported open-source software.  Although some versions
    are freely available, PyMOL is not in the public domain.

    If PyMOL is helpful in your work or study, then please volunteer 
    support for our ongoing efforts to create open and affordable scientific
    software by purchasing a PyMOL Maintenance and/or Support subscription.

    More information can be found at "".

    Enter "help" for a list of commands.
    Enter "help <command-name>" for information on a specific command.

 Hit ESC anytime to toggle between text and graphics.

 Detected OpenGL version 2.0 or greater. Shaders available.
 Detected GLSL version 1.20.
 OpenGL graphics engine:
  GL_VENDOR:   NVIDIA Corporation
 GL_RENDERER: NVIDIA GeForce 8600M GT OpenGL Engine
  GL_VERSION:  2.1 NVIDIA-10.0.40 310.90.10.05b12
 Detected 2 CPU cores.  Enabled multithreaded rendering.
libpng warning: Application built with libpng-1.6.19 but running with 1.5.23
/usr/local/bin/pymol: line 4:  3628 Segmentation fault: 11  "/usr/local/opt/python/bin/python2.7" "/usr/local/Cellar/pymol/" "$@&ldquo;

The helpful on the Pymol user list pointed me to this message on the Homebrew-Science issues

First uninstall pymol and libpng

brew uninstall pymol
brew uninstall libpng

then install pymol first.

brew install pymol
brew install libpng

Now when you type pymol in a Terminal window you should see.



El Capitan Review in Guardian

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