Macs in Chemistry

Insanely Great Science

Scientific Applications under Big Sur: Update 7

 

General Issues with Big Sur

If you want an overview of Big Sur I'd recommend the excellent arstechnica review.

Apple has officially confirmed that the following Macs are compatible with Big Sur.

  • MacBook (2015 or newer)
  • MacBook Air (2013 or newer)
  • MacBook Pro (Late 2013 or newer)
  • Mac mini (2014 or newer)
  • iMac (2014 or newer)
  • iMac Pro (2017)
  • Mac Pro (2013 and later)

In addition there is issue of the new Apple Silicon Macs with the new Apple M1 chip, if there is specific information about the new machines I've included it.

Snazzy Labs has an interesting commentary on the new Apple Silicon machines and promises a in depth technical review of all 3 models they have on order. The first reviews on Apple Silicon are now in

Scientific Applications

I've contacted all developers I know and their responses to date are shown below.

4-Peaks no known issues

Absoft Absoft Pro Fortran 2021 For macOS and OS X Fully compatible with macOS Big Sur (11.0)

alvaDesc We tested all our products and all of them work properly on MacOS Big Sur.

Amsterdam Modeling Suite As we only just finished our 2020 release our developers didn't dare switching to Big Sur yet. I can try on my own macbook shortly.

Anaconda seems to be working fine.

APE make sure you download the 64-bit version

Avogadro Been running Big Sur betas for a while - everything works. The next beta of Avogadro v2 will have some interface tweaks that are more noticeable on Big Sur (e.g., warning dialogs changed to be Mac-native). Don't yet have universal binaries, but working on it for Open Babel and Avogadro v2 betas (e.g. 1.94). Should still work fine on Apple Silicon computers.

BBEdit version 13 is compatible with macOS Big Sur. BBEdit 13.5 adds support for Apple Silicon

Brainsight macOS 11 Big Sur is coming out very soon, but do not upgrade your Mac yet, because Brainsight is not yet compatible with Big Sur

ChemAxon Most of our software in general requires Java, so as long as the appropriate Java version is installed, there should be no problem.

ChemDraw current version products (ChemDraw Professional 20.0.0.48 and ChemDraw Prime 20.0.0.48) supported with Mac OSX Catalina (v20.0 qualified with Mac OS 11.0 Beta)

ChemDoodle “The latest versions of ChemDoodle 2D (v11) and ChemDoodle 3D (v6) are fully supported on macOS Big Sur (macOS 10.16/11.0) and there are no known issues. In addition to supporting the operating system update, ARM based Macs (like those just released with the new Apple Silicon chip) are also fully supported for ChemDoodle 2D and ChemDoodle 3D with no known issues."

Conquest and Mercury from CCDC The full CSD software portfolio, including Mercury, ConQuest, Mogul, GOLD, CSD-CrossMiner, the CSD Python API and other components, has been tested and is not currently compatible with macOS Big Sur. Please note that our upcoming 2020.3 CSD Release will not be compatible with macOS Big Sur at point of release. We are working hard on a series of improvements to make our software portfolio compatible and fully supported, which we will make available to users as an update as soon as possible. In the meantime, a number of enhancements have been made to our products to simplify the configuration of and support specifically on macOS platforms. Examples are the removal of XQuartz as a dependency and removal of the need to run an X windows display for full use of the CSD Python API. These enhancements will be incorporated in future CSD software releases."

Cresset testing underway

CrystalMaker Works swimmingly! We’ve tested all our software on Big Sur - including a machine with Apple Silicon - and are happy to confirm full compatibility for CrystalMaker 10.5.5, SingleCrystal 4.1.0 and CrystalDiffract 6.8.5. Free updates to CrystalMaker 10.5.5 and SingleCrystal 4.1.0 were released yesterday morning and are recommended for anyone using “Big Sur”.

We are also very-pleased to announce the immediate availability of CrystalMaker 10.6 for Mac, SingleCrystal 4.1 and CrystalDiffract 10.9 for Apple Silicon: these are Universal Binaries and provide 100% native performance on the new Apple Silicon Macs, as well as 100% native performance on Intel.

As one of the vanishingly-few Mac science developers left, we’re proud of our reputation of developing genuine, native Mac apps. We’ve been doing this for over 25 years now and this is our fourth Mac hardware platform! (we’ve gone from Motorola 68K to PowerPC to Intel and now to Apple Silicon).

CYLView 1.0 does not work under Catalina.

DataWarrior Seems to be working fine.

Delta We are working on an update for Delta and will post it as soon as it is available.

DEVONagent fine under Big Sur on Intel, not tested on Apple Silicon.

DEVONthink fine under Big Sur on Intel, not tested on Apple Silicon.

Elemental Fine under Big Sur and on Apple Silicon

EndNote We are in the process of testing and we will be updating our Compatibility page once our testing is complete. Users report no issues on Intel.

EnzymeX no issues reported

EverNote is compatible with Big Sur

Findings no issues reported

Fujitsu ScanSnap .

GAMESS

Gaussaian As far as we can tell so far, both of our current releases, Gaussian 16 rev. C.01 and GaussView 6.1.1 for macOS 64-bit Intel CPUs, run normally on macOS Big Sur. We do not have any reports of problems so far. We do not have a native port for Apple Silicon chips for either G16 or GaussView 6. However, for now, both of the Intel binaries that I mentioned above should run on Apple Silicon using Rosetta 2. We have not done full certification on the Apple Silicon at this point but Apple claims that Rosetta 2 should be capable of handling running existing binaries for Intel chips.

Highlights The PDF Reader for Research, updated for Big Sur with version 2020.3. Big Sur also fixes an annoying issue from PDFKit on Catalina where superscript text (e.g. citations) would break text selection.

Homebrew For most seems to work fine, remember to reinstall Xcode command line tools.

All the ICM products are compatible with Big Sur:

Other products that are compatible include:

IDL

Igor Pro Igor Pro 8.04 is the first version of Igor that is notarized and includes notarized WaveMetrics XOPs. We therefore recommend that you run Igor Pro 8.04 if you are using macOS 10.15 or macOS 11.0.

iNMR

JalView Jalview works on macOS 11.0 Big Sur!

KaleidaGraph

KNIME We are testing the upcoming version 4.3 of KNIME Analytics Platform against Big Sur and plan to have it supported by the time we do that release in the first week of December.

Manuscripts no issues reported

Matlab MATLAB is compatible with macOS 11 (Big Sur) from release R2020b onwards, support for Apple Silicon is in development

Mathematica no issues for latest version. system requirements

Mendeley no issues reported

Microsoft Office Microsoft has announced that Office 365 is ready for Big Sur - Apple Silicon M1 Macs will use Rosetta 2 for now

Mnova The current version of Mnova LiteCDE is compatible with MacOS Big Sur

NAG Fortran compiler Fortran compiler for Apple Silicon Macs now available to download

MOE Our initial tests showed no issues with this version.

MOPAC

ODYSSEY Molecular Explorer version 6 looks good.

Papers no issues reported

Parallels Parallels 16 is ready for Big Sur. Older Parallels Desktop versions only partially support working on macOS Big Sur due to technical reasons may experience issues depending on the configuration.

PGOPHER

pro Fit pro Fit 7 is now at version 7.0.18, supporting dark mode, Catalina, and Big Sur.

PYMOL On Intel Macs with macOS 11, PyMOL works fine, no known issues. We have not tested Apple Silicon (M1) yet.

Python Python 2.7 is no longer included - use Python 3 instead Python works fine on Apple Silicon and is "mad fast!".

QMForge 2.4 does not support Big Sur yet

R The front page of a CRAN site has a link ‘Download R for (Mac) OS X’. Click on that, then download the file R-4.0.3.pkg and install it. This runs on macOS 10.13 and later on Intel CPU20 (High Sierra, Mojave, Catalina, Big Sur, …).

RDKit All seems fine (Note: -Python 2.7 is no longer supported - use Python 3 instead)

Samson SAMSON 2020 R3 (the latest release) works on Big Sur.

Schrodinger Upgrading to macOS 11 will cause existing Schrödinger Suite releases to fail to run. We are hard at work to address this incompatibility and expect to extend support to macOS 11 in an upcoming Schrödinger Suite release

SeeSAR now updated to support Big Sur.

Sketch With version 70 release, we’re excited to introduce a UI redesign that fits right in with the new macOS Big Sur design language. It’s the same Sketch you know and love, but with every detail reconsidered — from a full-height sidebar, to a refreshed Inspector, and all-new iconography throughout the app.

Spartan There are a few interface issues, tab highlighting on selection is unreliable, not a showstopper but irritating.

SPSS The current release IBM SPSS Statistics 27.0.1 and the current IBM SPSS Statistics Subscription release build 1.0.0.0.1447 will run on MAC OSX 11 Big Sur in translation mode.

Stardrop We haven't yet completed a full test cycle, but we have not seen any issues and don't anticipate any.

Swiss-PdbViewer Swiss-PdbViewer is a 32 bits application and will * NOT * run.

TensorFlow and TensorFlow Addons This pre-release delivers hardware-accelerated TensorFlow and TensorFlow Addons for macOS 11.0+. Native hardware acceleration is supported on Macs with M1 and Intel-based Macs through Apple’s ML Compute framework.

UCSF Chimera ChimeraX v1.1 does not work on MacOS 11.0 (Big Sur), but this problem has been fixed in v1.1.1 and the daily build.

UCSF ChimeraX works on 10.14, 10.15, and 11.0 (Big Sur).

VMD there interface issues under Big Sur

VMD

VMWare In preparation for the next major version of macOS 11.0 Big Sur, VMware has made full use of Apple’s hypervisor and other APIs, removing the need for kernel extensions and supporting macOS 11 as both host and guest.

Vortex Vortex works perfectly on Intel Macs under Big Sur, and on Apple Silicon

WINE

Wizard In general works fine, some issue with older work books.

wxMacMolPlt

Xcode need to update to latest version. Remember to reinstall command line tools

XQuartz OpenGL and OpenCL are still here, even on Apple Silicon Macs

I’ll add more updates later, feel free to contact me and thanks for the comments to date.

Last update 17 January 2021

Comments

Coronavisrus stats online.

 

If you are a using a UNIX based operating system (such as Mac OS X) just type this command in a Terminal window

curl https://corona-stats.online/

coronavirus

Looks to be about 12 hours behind latest data.

From https://twitter.com/nixcraft.



Comments

Scientific Applications under Catalina: 2500 views

 

I just checked the analytics data and the Scientific Applications under Catalina has now been accessed around 2500 times.

It is a fair bit of work putting the data together so I'm delighted to see it is viewed by so many people. Many thanks to all who contributed.

Comments

Custom Accessibility Keyboard Panels

 

Anyone who is interested in AppleScript or automator workflows on a Mac will have heard of Sal Soghoian, Sal joined Apple Inc. in January 1997 to serve as the Product Manager of Automation Technologies. These technologies include AppleScript, Services, the Terminal, Apple Configurator and Automator, among others. Since he left Apple he has continued to develop automation and describe them on his website User Automation.

This website is dedicated to informing individuals about the tools at their disposal that can be used by them to control the devices they engage with and rely upon every day. I hope you find this information useful. — Sal Soghoian

In a recent video Sal describes how to use an accessibility feature hidden deep within macOS and turn an iPad into a completely customizable control panel for a Mac.

Full details are here https://userautomation.com/article/blog0003.html.

userautomation

It requires a Luna Display dongle since Apple’s Sidecar technology won’t work because it doesn’t allow touch input on the iPad when it’s acting as a Mac screen.

Comments

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




Comments

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.


Comments

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.


Comments

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


Comments

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.