Macs in Chemistry

Insanely Great Science

SCINDR - The SCience INtroDuction Robot that will Connect Open Scientists

 

The SCINDR project aims to develop a way to connect, in real time, globally disparate researchers who are doing similar science so that they can work better and faster towards the development of new medicines

Once a researcher has their data stored on the ELN, or on any similar open database, for that matter, SCINDR would be able to detect if similar molecules, chemical reactions, biological assays or other features of importance in health research have been entered by someone else. If the robot identifies another scientist looking into similar features, it will suggest introducing the two to each other, so that they could start working together and combine their efforts and knowledge for the good of both science and the public.

SCINDR


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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 (http://forums.cambridgesoft.com/messageview.aspx?catid=12&threadid=3165&enterthread=y) 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 15.9.28.0 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

XQuartz

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 https://lists.apple.com/mailman/listinfo/x11-users

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 http://xquartz.macosforge.org/downloads/SL/XQuartz-2.7.8.dmg.

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

Comments

Scientific Applications under Yosemite

 

I just thought I'd like to thank all those who contributed to the Scientific Applications under Yosemite web page, many users and developers contacted me either via email or in the comments section and they certainly added information about applications that I don't have access to.

To date the page has been viewed well over 10,000 times with readers from 188 different countries. Viewers spent an average of just under two minutes on the page and it still attracts 800 pages views a month.

Given that 75% of the visitors to the site are now using Yosemite I suspect most scientists have now made the transition and I won't be updating the page any more. Once again thanks for the contributions.

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Science Apps under Yosemite

 

I've just updated the page detailing compatibility of science applications under Yosemite of particular note is the update of Spartan’14 version 1.1.9 that includes the new Yosemite supported driver from SafeNet.

Full details are here http://www.wavefun.com/support/spmac/supportmacLV.html

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Added MathMagic

MathMagic is a WYSIWYG math editor with Graphic user interface, with support for MathML, LaTeX, MS Equation Editor, and more.

There is a video showing it in action here

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Which Mac OSX version do scientists use

Comparison of the version of Mac OS X used by scientists with that used globally. Read More...
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iNMR update

The only NMR specifically designed for MacOSX has been updated to iNMR version 3.03 and adds a number of impressive new features. Read More...
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Software Reviews

New page for software reviews Read More...
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Docking.org

John Irwin has updated the docking.org site. Read More...
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2007 Nobel Prizes

Two European scientists France's Albert Fert and Germany's Peter Gruenberg have won the 2007 Nobel Prize in physics Read More...
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