Macs in Chemistry

Insanely Great Science

Scientific Applications under Mojave 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. Based on the number of page views on the lists for High Sierra, Sierra, El Capitan and Yosemite it is apparently a useful resource.

Apple has said that macOS 10.14 (Mojave) will run on every Mac released from 2012 onwards. Always a good idea to have a Time machine backup when undertaking a major update like this.

Much like prior versions of Mac OS, you can easily create a bootable install drive for MacOS Mojave 10.14. The initial installer is small (15 MB) but after the main installer has successfully downloaded (5GB+), when you are prompted to start the installation process, click Cancel, and the installer will be in the /Applications folder (Install macOS Mojave.app). You must make a copy of this to another location; otherwise if you launch the installer and it completes the Mojave update, it'll be deleted. I found installing or updating to macOS Mojave takes about 45 - 60 minutes depending on the age of the machine.

I’ll update the list regularly and please feel free to send in information.

Amsterdam Modeling Suite has Mojave support, more details soon.

Applescript, the security changes in Mojave have some significant impacts that are described in detail here, particularly to scripting additions..

Avogadro version 1.2.0 no issues

BBEdit have a comprehensive list of compatibility notes for each application and versions https://www.barebones.com/support/new-os.html. BBEdit 12.1.6 has just been released which bring full Mojave compatibility.

ChemDoodle all seems fine no issues reported

ChemDoodle3D all seems fine no issues reported

ChemDraw as a policy they do not test until after new operating systems have been released, will check back later. A user replied "I am on ChemDraw Pro 17.1.1.0 and I have found no compatibility issues on Mojave.".

Chimera Chimera buttons not being shown until the windows containing them are resized. "Just an update that we’ve fixed the button issue in Chimera on Mojave" 1.13.1 candidate release (and recent 1.14 daily builds) working on Mojave

ChimeraX No issues reported.

ChirysView "As far as we know, there are no issues with our products and Mojave".

Cresset No issues to date, more detailed testing underway.

CrystalMaker "CrystalMaker X works beautifully with Mojave. We’re a full 64-bit app with sandboxing and code signing. Our forthcoming 10.4 update (next week or so) will include a “Dark Mode” option".

DataWarrior no issues to date

Findings no issues

iBabel no issues to date

iRaspa no issues

MarvinSketch latest version no issues, earlier versions may require the old Apple supplied JDK to be reinstalled

MarvinView no issues

Microsoft have already announced compatibility notes.

Word, Excel, PowerPoint, Outlook, OneDrive, Skype for Business, and OneNote will install and run on macOS 10.14 Mojave. Microsoft fully supports Office 2016, Office 2019 and Office 365 for Mac on 10.14 Mojave when you have the following Office updates installed:

Office 365/2019 - Build 16.17.0 or later

Office 2016 - Build 16.16.2 or later

Skype for Business 16.21.65 or later

Mnova lite no issues reported

Molecular Materials and Informatics have just released an update for the Molecular notebook app

MOE There seem to be no problems running MOE 2018.01 or higher on MacOS 10.14.

MolSoft We have not had any reported issues about running ICM-Pro or ICM-Chemist-Pro on Mac OSX 10.14 Mojave.

O "It runs on my laptop without problem and I’ve not heard any news from users so I don’t think there are any issues at the moment."

Openbabel no reported issues

PyCharm only very minor issues

PyMOL "Although Mojave was just released, all of our automated and QA tests do not show anything out of the ordinary. While it's probably still too early to declare official support, we haven't encountered anything that suggests users should worry about upgrading with regards to the PyMOL application".

RDKit no reported issues

Schrodinger suites are not yet officially supported on Mojave. Tests are ongoing, and we're hoping to officially support that platform in our next release (2018-4).

SeeSAR "0 issues with Mojave at our end".

StarDrop Our initial tests suggest that everything is working as expected.

TextWrangler is not compatible with Mojave. It has been sunsetted, and is now part of BBEdit.

Vortex no issues reported.

xQuartz I've only done limited testing but all OK for me.

Updated 30 October 2018




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Darwin source code released

 

It is sometimes difficult to remember that the heart of Mac OSX is the open-source Darwin source code.

Apple have recently released the latest update OS X 10.12 Source.

In addition Apple have made Swift open-source which supports a wider variety of platforms.


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Xcode 8 released

 

With the release of iOS 10 comes an update to Xcode. Xcode 8.0 is a free download for OS X 10.11 or later. (An Apple ID is required for iOS development, and App Store submissions require registration in the Apple Developer Program.) The latest version brings Swift 3 and SDKs for iOS 10, watchOS 3, tvOS 10, macOS Sierra, Siri extensions, iMessage apps, and sticker packs for Messages, along with many other changes.

Xcode 8 includes everything you need to create amazing apps for iPhone, iPad, Mac, Apple Watch, and Apple TV. This radically faster version of the IDE features new editor extensions that you can use to completely customize your coding experience. New runtime issues alert you to hidden bugs by pointing out memory leaks, and a new Memory Debugger dives deep into your object graph. Swift 3 includes more natural and consistent API naming, which you can experiment with in the new Swift Playgrounds app for iPad.

Swift 3 is the first major release of the innovative programming language built completely in the open with the community of developers at Swift.org. This release unifies core API naming rules under a new public API Naming Guidelines document that makes writing Swift code feel even more natural. Popular system APIs such as Core Graphics and Grand Central Dispatch are more expressive and harmonize well with Swift.


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End to End Swift

 

This looks interesting, Perfect

Perfect is an application server for Linux or OS X which provides a framework for developing web and other REST services in the Swift programming language. Its primary focus is on facilitating mobile apps which require backend server software, enabling you to use one language for both front and back ends.

Perfect relies on Home Brew for installing dependencies on OS X, once done you are up and running and can follow the Perfect tutorials


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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 Mavericks (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 such a major upgrade I thought I’d set up a spare machine to test applications before I update my main machine.

The update went smoothly albeit with an overnight download of the 5.5 GB file.

The update removes both X11 and java so both of these need to be reinstalled, if you forget you will be prompted to download the first time you try to use them.

No issues with cursory testing, users or vendors provided feedback

Avogadro
BBEdit
ChemDoodle
ChemSpotlight
Cresset software (forge, torch, spark) (no reported issues)
Elemental
FTranProjectBuilder
iBabel
ICM-Pro
ICM-Homology
ICM-VLS
ICM-Chemist
iNMR (No reported issues)
Matlab
Marvin
MOE
Openbabel
OpenEye (Command line tools OK, OMEGA 2.5.1 (OSX 10.8 version), FILTER 2.5.1 (10.8), ROCS 3.2.0 (10.8), SZMAP 1.2.0 (10.8), EON 2.2.0 (10.8), QUACPAC 1.6.3 (10.8), SZYBKI 1.8.0 (10.8), FLYNN 2.3.0 (10.8), The Python and Java toolkits work fine. The C++ toolkit can be made to work if some of the compiler flags are changed. Please email support@eyesopen.com for more details. For the OpenEye GUI applications, vROCS 3.2.0 (OSX 10.8 version) works fine, for other apps see below
R latest version R 3.0.2 ("Frisbee Sailing")
Reference Tracker
StarDrop
Vortex
XQuartz

Some issues :-(

MOE install
I downloaded the latest update as a zip file and unarchived it. When I double click on the installer I got a message that it was broken or corrupted. This seems be an issue with the Mac OSX Gatekeeper,

  1. Open Apple menu, then go to System Preferences -> Security & Privacy -> General tab.

  2. In the option list of "Allow Applications downloaded from", select "Anywhere".

Then installs OK. Once installed MOE seems to run fine.

CCDC Software
Mac OSX 10.9 causes most CCDC software to fail - there are now have patches available that address this issue. For enCIFer 1.4: http://www.ccdc.cam.ac.uk/SupportandResources/Downloads/pages/ProtectedDownloadAgreement.aspx?d=15 For the 2013 CSD System go to: http://www.ccdc.cam.ac.uk/SupportandResources/Downloads/pages/ProtectedDownloadAgreement.aspx?d=47  For standalone Mercury 3.1 or 3.1.1 go to:  http://www.ccdc.cam.ac.uk/SupportandResources/Downloads/pages/ProtectedDownloadAgreement.aspx?d=37
These updates should only be applied on Mac OSX 10.9. NB One reader reported issues with the update.

ChemBioDraw
Chemdraw 13 files pasted into Keynote 6 cannot be copied and pasted back into ChemDraw. In addition, if you open old Keynote files in Keynote 6 all the ChemDraw cannot be copied and pasted. It pastes into Chemdraw as a picture with an all black background. In Mac OS 10.9 with Keynote 5 - round trip editing still continues to work. According to the PerkinElmer Support Forum there are issues with copy/paste in CD 13 to Office 2011 for Mac. Any CD structures that are pasted into PPT or Word cannot be opened or edited with CD.

EndNote X7
We have tested EndNote X7 with Mac OS X 10.9 Mavericks to determine compatibility. We have found some minor issues and are working on a free update patch to be released in the next few weeks.

EndNote X6
EndNote X6 is not officially compatible with Mac OS X 10.9 Mavericks. We are testing EndNote X6 with Mac OS X 10.9 Mavericks to determine informal compatibility and will report any exceptions found on this page.
EndNote X5 and earlier
Due to major compatibility issues, it is not recommend to attempt to use EndNote X5 or earlier on OS X 10.9. When attempting to launch EndNote X5 or earlier, a warning message comes up that will include "unable to load ....ENCore.Bundle". EndNote X5 and earlier will fail to launch after receiving this message. There are no known workarounds for this issue besides moving to a more recent version of EndNote or restoring your computer  (using a Time Machine Backup for example) to a previous version of Mac OS X.

OpenEye Command line tools that require setting the OE_ARCH environment variable (FRED 3.0.1 (OSX 10.7 version), HYBRID 3.0.1 (10.7), POSIT 1.0.3 (10.7), LEXICHEM 2.1.0 (10.6), BROOD 2.0.0 (10.5)

export OE_ARCH=osx-10.9-x64:osx-10.8-x64:osx-10.7-x64:osx-10.6-x64:osx-10.5-x86

For the OpenEye GUI applications, vROCS 3.2.0 (OSX 10.8 version) works without any issues. VIDA requires the OE_ARCH modification shown above but also needs the following additional fixes:

sudo mkdir -p /Applications/OpenEye/arch/osx-10.6-x64/vida/4.2.1/bin/QtCore.framework/Versions/4
sudo ln -s /Applications/OpenEye/arch/osx-10.6-x64/vida/4.2.1/bin/QtCore /Applications/OpenEye/arch/osx-10.6-x64/vida/4.2.1/bin/QtCore.framework/Versions/4/QtCore

Unfortunately, the current vBROOD, AFITT, and MAKE_RECEPTOR GUIs do not work on Mavericks. We are actively investigating these issues. More details

Using Aabel v3 on Mavericks is not recommended due to cosmetic glitches such as misalignment of graphic viewer icons on the Mavericks buttons. Mavericks will be supported in the next major version of Aabel

Papers2 update about to be released

If I hear of anything, I’ll update this page.

Comments

Xcode updated

With the release of the iPad mini Xcode has been updated to version 4.5.2 this update includes:-

Support for iPad mini and iPad with Retina display (4th generation).
Additional bug fixes and stability improvements.

Xcode 4.5 includes

  • SDKs for OS X 10.8 Mountain Lion and iOS 6.
  • Auto Layout now supported on both OS X and iOS.
  • New localization workflow can share a single base .xib or .storyboard file for multiple locales.
  • OpenGL debugger for iOS analyzes performance and suggests improvements.
  • Debugger watchpoints can be set when running on a connected iOS device.
  • Objective-C @synthesize command is generated by default when using properties.
  • Objective-C adds literal syntax for numbers, arrays, dictionaries, and expressions.
  • Xcode 4.5 runs on both OS X Lion and OS X Mountain Lion.
  • Enhanced for the MacBook Pro with Retina display.

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Operating systems market share

The latest monthly market share data is available from Net Applications and Mac OS X continues to show a steady rise now up to 7.16% (a rise of 0.3%). Adoption of Mac OS X 10.8 is now over 25% of the Mac OS X version share and steadily increasing.

In the mobile/tablet space iOS continues to dominate (63.48%) this represents just under 10% of the online presence with desktop/laptop still at 90%.

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XQuartz Updated

XQuartz was updated recently to version 2.5.3

Read More...
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Applescript Resources

A few new resources. Read More...
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APBS Update

Adaptive Poisson-Boltzmann Solver (APBS) -- Software for evaluating the electrostatic properties of nanoscale biomolecular systems Read More...
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New Applications Added

ORCA (quantum Chemistry), HADDOCK (Molecular Docking). Read More...
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COSMOtherm now available on Mac

COSMOtherm is a program for the quantitative calculation of solvation mixture thermodynamics based on quantum chemistry. 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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Cambridge Structural Database, Mercury available

Mercury CSD version 2.0 is now available from the Cambridge Structural Database. Read More...
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LabView on the Mac

A summary of the LabView on Mac meeting. Read More...
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