The global pandemic is having a devastating impact on all charitable bodies and I'd like to give a mention to a group close to my heart. Inspiring the next generation of scientists is essential for our long term future in these challenging times.
The UK’s network of charitable Science and Discovery Centres deliver inclusive science and technology experiences to children across the country, reaching families and schools in some of our most socio-economically disadvantaged communities. They play a crucial role in inspiring young people with STEM, creating the environmental and science innovators we need for our future, and ensuring the UK stays at the forefront of global R&D and innovation.
- The UK has a vibrant network of 60 Science and Discovery Centres, including Science Museums, Science Centres, Discovery Centres, Natural History and Environment Centres and Learned Societies.
- Every year 25 million people visit UK Science Centres and Museums.
- Over half are girls and women, and over half are school-age children.
- 12.3 million people each year visit their local Science and Discovery Centres or Science Museum outside London in the hearts of cities and regions across the UK.
- About half of the network are independent charitable Science and Discovery Centres (whereas the other half are museums and learned societies).
- Eight million schoolchildren and adults visit the Science and Discovery Centres that are excluded from applying for central government grants (those open to heritage, museums, theatres and the arts) and are at risk.
- Before Covid-19, Science Centres were successful, innovative enterprises, earning their own income from ticket sales and science events.
You can read the Open Letter to Prime Minister and Chancellor asking for support, if you can offer support in any way please do so.
The UK Association for Science and Discovery Centres are also on twitter @sciencecentres
A while back I described how to add a custom chemistry dictionary. There have been a few changes so I thought I'd post an update. If you are creating scientific documents you probably find that many of the scientific terms, chemical names and drug names are underlined by a red squiggle. You can add these words individually to the dictionary or you can edit the dictionary to add a batch of appropriate words all in one go.
To uncover the file you want to edit first open a Finder window, then hold down the Option key and click on the "Go" in the Finder top menu bar, this will give access to the Library folder.
Now navigate to the "Spelling" folder, the file that you need to edit is "LocalDictionary". Open this file in a text editor (not a word processor), I used BBEdit. This file should contain any words that you have added, you can now add any scientific terms you want directly.
Over the years I've accumulated nearly 200,000 items in this file, you can download it here http://macinchem.org/blog/files/LocalDictionary.zip. Feel free to add these items if you feel they would be useful.
Now if I could find a way to add them to my iOS devices……
General Issues with Catalina
If you want an overview of Catalina I'd recommend the excellent ars-technical's review.
According to Wikipedia Santa Catalina is a rocky island off the coast of the U.S. state of California in the Gulf of Santa Catalina.
Apple has officially confirmed that the following Macs are compatible with Catalina:
- MacBook (Early 2015 or newer)
- MacBook Air (Mid 2012 or newer)
- MacBook Pro 13"/15" (Mid 2012 or newer)
- Mac mini (Late 2012 or newer)
- iMac (Late 2012 or newer)
- iMac Pro (2017 or newer)
- Mac Pro (Late 2013 or newer)
There are a number of changes to the security, in particular installation into the root folder is not allowed. After upgrade you may find it moves items into a folder on your desktop called “Relocated Items,” in the Security folder.
zsh is the new default shell for new users (bash is the default shell in macOS Mojave and earlier), so if you are upgrading you may want to change your default shell to zsh. There is an Apple Support page giving details
zsh is highly compatible with the Bourne shell (sh) and mostly compatible with bash, with some differences. For more about zsh and its comprehensive command-line completion system, enter man zsh in Terminal.
You might also like to look at oh-my-zsh
A delightful community-driven (with 1,300+ contributors) framework for managing your zsh configuration. Includes 200+ optional plugins (rails, git, OSX, hub, capistrano, brew, ant, php, python, etc), over 140 themes to spice up your morning, and an auto-update tool so that makes it easy to keep up with the latest updates from the community.
This book might also be useful Moving to zsh.
I suspect many users will now see more Notarization warnings.
Notarization gives users more confidence that the Developer ID-signed software you distribute has been checked by Apple for malicious components. Notarization is not App Review. The Apple notary service is an automated system that scans your software for malicious content, checks for code-signing issues, and returns the results to you quickly. If there are no issues, the notary service generates a ticket for you to staple to your software; the notary service also publishes that ticket online where Gatekeeper can find it.
You can notarize several different types of software deliverables, including:
- macOS apps
- Non-app bundles, such as kernel extensions
- Disk images (UDIF format)
- Flat installer packages
Beginning in macOS 10.14.5, all new or updated kernel extensions and all software from developers new to distributing with Developer ID must be notarized in order to run. Beginning in macOS 10.15, notarization is required by default for all software.
You can still use the software but you need to go to the Systems and Privacy pane in the System Preferences, form there you get the option to open the application anyway, it should be remembered so you only have to do this once.
Apple have been warning for several years now that all support for 32-bit apps would end, Apple has a page describing the reasons for moving to 64-bit. In addition support for the legacy Java 6 has finished. Catalina does include Python 3 by default, where older versions of the operating system only included Python 2.7
Anyone tried running 32-bit apps using emulation (Parallels or VMWARE?).
I've contacted all developers I know and their responses to date are shown below.
4-Peaks no issues reported
alvaDesc software is completely 64 bit and it is ready for Catalina.
Amsterdam Modeling Suite the latest update works under Catalina. However there are still some minor issues (e.g. vtk bug on windows maximizing, should be sorted soon).
Anaconda Anaconda’s default install location in the root folder is not allowed, suggestion is Start fresh with a new Anaconda installation. Pay attention during installation to make sure that your install path is a subfolder of your home folder, such as /Users/me/anaconda3. You may be able to move the Anaconda folder from "Relocated Items" to a new location but be aware it may include hard coded paths. More discussion here.
APE A plasmid Editor If you are having trouble with crashing in Mojave or Catalina, re-download to get the latest update.
Avogadro no issues reported
BBEdit version 13 is compatible with macOS Catalina
BioSolveIT report SeeSAR and infiniSee have been tested successfully on Catalina
Brainsight Brainsight 2.4b6 and later have been tested against Catalina and there are no known problems.
ChemAxon Most of our software in general requires Java, so as long as the appropriate Java version is installed, there should be no problem. However maybe notarisation issues first time using. More info.
We are pleased to inform you that the MarvinSketch installers are notarized from version 19.26. When you download our latest Marvin installer for mac OS, GateKeeper will know that the software is safe and allow you to install it without any problem
ChemDoodle ChemDoodle v9 and ChemDoodle 3D v4 are fully supported, signed for Gatekeeper, and notarized by Apple on macOS Catalina. There is only a single reported issue from some users, where either program will fail to fully startup on Catalina if they were installed prior to upgrading the OS to Catalina. In these cases, removing the “ChemDoodleSettings” folder or the “ChemDoodle3DSettings” folder in the user’s Documents folder and restarting the application will resolve the issue. We have no other known issues on Catalina at this time.
Conquest and Mercury from CCDC CSD software from the CCDC. The full CSD software suite, including Mercury, ConQuest, Mogul, GOLD, CSD-CrossMiner and other components, have been tested and are working on Catalina. Whilst our applications are all signed, due to the new "notarisation" feature on Catalina, users may need to authorise the software via the Security option in System Preferences at the point of installation. Our next major software release, the 2020.0 CSD Release which will be available before the end of 2019, will be formally supported on macOS 10.15 Catalina, as well as 10.14 Mojave and 10.13 High Sierra.
Cresset all works fine but there are notarisation issues.
CrystalDiffract 6.8.3 is a 64-bit “Cocoa” app and works fine.
CrystalMaker X 10.4.6 - another 64-bit app “Cocoa” app - also runs seamlessly with “Catalina”
SingleCrystal 3 is a 32-bit app and so won’t run. However…
SingleCrystal 4 PUBLIC BETA works beautifully on Catalina. More information - including a sign-up form - can be found at:
SingleCrystal 4 PUBLIC BETA will run until the end of December and is free to eligible users. All applications are code-signed and officially “notarized” by Apple.”
CYLView 1.0 does not work under Catalina.
Delta Delta V5.3.1 is not supported by Apple macOS 10.15 Catalina. Delta will not install or operate under macOS 10.15 Catalina. We are working on an update for Delta to run on macOS 10.15 Catalina and will post it as soon as it is available.
DEVONagent here's a minor incompatibility that keeps the application's splash screen from being closed. You can expect a free maintenance update for DEVONagent that addresses this issue later this month.
DEVONthink version 3 is 64-bit compliant
Elemental We have a new one. Think it got stuck in “notarization”. Will appear on the support site in a few days hopefully.
EndNote EndNote X9 for macOS will be extensively updated for compatibility prior to the launch of Catalina.
EnzymeX no issues reported
EverNote No issues with Evernote but Safari extensions dropped so no Evernote Web Clipper
Findings seems to be working fine, no issues reported.
Fujitsu ScanSnap If you own one of the older Fujitsu ScanSnap scanners like the S300M, S500M, S510M or S1500(M). Fujitsu has announced that they will not update the ScanSnap Manager software that drives these scanners to make them compatible to macOS Catalina; only the newer ScanSnap Home will be available for current and future versions of the Mac operating system.
Gaussaian All 64-bit versions of Gaussian 16 for macOS will work fine with macOS Catalina.
Homebrew some issues reported, brew update / brew upgrade seems to resolve many. Probably need to have updated Xcode to version 11.x
All the ICM products are compatible with Catalina:
Other products that are compatible include:
IDL Through beta testing, we have identified an issue that requires a patch to IDL 8.7 in order to run on this new OS X release. The issue is caused by the existing 32-bit applications used in IDL (Applescripts and IDLSnapFileOpen), and they will be replaced with 64-bit versions. Other related concerns on this OS X release will also be addressed. This patch to IDL will be available very soon after the release of Catalina.
Igor Pro With Catalina, Apple dropped support for 32-bit applications, dropped the QuickTime framework that Igor uses to support most movie features, and added strict security features that prevent XOPs from running without special security certification ("notarization"). We recommend that you avoid Catalina if you need to use Igor Pro. However, we expect Igor Pro 8.04 (currently in beta) to work with the caveats explained below. We do not consider any version of Igor Pro 8 to be supported on Catalina, though we will do our best to fix Catalina specific bugs. Igor Pro 6 will not run because Catalina supports 64-bit applications only. The 64-bit Igor Pro 7 application (Igor64.app) may run, but WaveMetrics and/or third-party XOPs may not load. Igor Pro 7 is no longer maintained and will not receive any changes to improve Catalina support. Workarounds for Catalina XOP Problem has been described, both workarounds require that you "bless" a particular XOP (.xop file), meaning that you tell the OS that it is OK to run the XOP.
iNMR iNMR has been recently recompiled with Xcode 10.3. iNMR is a 64-bit app since 2012. No issues reported.
KaleidaGraph is currently still a 32-bit application and will not run under Mac OS 10.15. A 64-bit version is under development, although it will not be released before Catalina and we do not have a release date at this time. We will notify registered users as soon as a beta version is ready for testing.
KNIME most recent version of KNIME Analytics Platform is notarized and, hence, works with macOS Catalina.
Matlab R2019b supports Catalina
Mathematica Wolfram products based on Wolfram Language 12.0 or later are fully 64 bit on macOS, and are therefore compatible with macOS 10.15, as well as earlier versions.
Mendeley Mendeley Desktop does not support OSX Catalina. If you choose to upgrade to OSX Catalina you may be unable to install or access Mendeley Desktop. You should alternatively use https://mendeley.com/library
Microsoft Office To provide you with the best experience, Office for Mac supports Apple’s three most recent versions of macOS. With the release of macOS 10.15 Catalina, Office 365 for Mac and Office 2019 for Mac support macOS 10.15, 10.14, and 10.13.
Mnova Mnova 14.1 is compatible with Catalina OS.
MOE MOE is now fully compatible with Catalina. Remember if you change to using zsh instead of BASH you will need to copy things from your BASH profile over.
MOPAC no issues reported.
Papers We have gotten a few reports of crashes happening on the new Mac OS 10.15(codename Catalina) for Papers 3. We have developed a fix and you should be able to update your Papers 3 to the new version. If you updated to Catalina before updating Papers 3 you can download the new version here
Parallels Parallels Desktop 15 for Mac is the fastest, easiest, and most powerful application for running Windows applications on a Mac without rebooting. Parallels Desktop 15 now supports Catalina, Sidecar, and DirectX 11.
PGOPHER not yet supported by PGOPHER. (Apple no longer supports 32 bit programs, and the required uderlying 64 bit library required has only recently become available in a useable state, and some development work is required for this to work with PGOPHER.)
pro Fit the latest version of pro Fit, version 7.0.15, runs on Catalina.
PYMOL The +python37 variant of pymol runs fine under its Qt interface on Catalina
QMForge 2.4 apparently doesn't work on Catalina, hoping to get a fix in the coming weeks.
R In general works fine but with >20,000 packages available there may be issues with some.
RDKit no reported issues
Schrodinger Unfortunately, MacOS Catalina is not yet supported by Schrödinger products and is being tested. We are planning to start supporting it from our 19-4 release.
- Spartan’18 Parallel Suite
- Spartan’18 (single core)
- Spartan Student Edition v.7
- Odyssey Instructor Edition v.6
- Odyssey Student Edition v.6
Are all compatible with Catalina.
SPSS We’ve spent weeks testing against the beta and now the generally available operating system. Overall, SPSS Statistics and Catalina are compatible.
Stardrop is compatible.
Swiss-PdbViewer is a 32 bits application and will * NOT * run on OSX Catalina. If you absolutely need it, refrain from updating, boot from an older OSX version, or use the PC version within a virutal machine. I currently have no plan to update it to run on OSX 10.15
VMD is a 32-bit app and will not run under Catalina. While VMD has supported 64-bit platforms for 20 years, the "catch" in support for 64-bit MacOS X is that 64-bit MacOS X requires different graphical user interface APIs in 64-bit mode than it does in 32-bit mode, resulting in some ongoing stability problems for the FLTK and Tk libraries that VMD depends on. The issue is that we have to create a specially modified version of FLTK (which is not written by us) to be compatible with both Catalina and Tcl/Tk. As yet we don't have any ETA to provide users at this time. We are working on building a version of VMD for MacOS X Catalina, using patched versions of FLTK/Tk that resolve their MacOS X-specific 64-bit incompatibilities, but as yet this work is still ongoing. From VMD mailing list https://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/31208.html.
I have put together a binary for VMD 1.9.4a38 (from the source dated 2019-10-17) which I would like to invite you to test. - You can download the app at https://www.dropbox.com/s/700vi9kkpglf6m6/VMD%201.9.4a38.zip?dl=0. - Install it into your Applications folder before running it. Please let me know if it works for you, or if some things are broken.
Vortex Should just work. Isn’t notorized yet though so right click Open if it complains. You only have to right click Open once.
WINEIn downloading WINE devel portable from https://dl.winehq.org/wine-builds/macosx/ , you can run the wine64 binary through the terminal, with ‘$ wine64 wine cfg’ to configure it and ‘$wine64
Wizard has been tested to work with Catalina.
wxMacMolPlt The currently available (64 bit) binary does run on Catalina. However, while it is “signed” it is not “notarized” so you do have to jump through a couple hoops to convince the OS to launch it the first time.
Xcode need to update to version 11.x
XQuartz some users reporting issues, seems to be a mixture of enhanced security and/or folders moved to relocated items. Best solution seems to be to reinstall XQuartz.
A few people have reported issues using xterm under Catalina
cd documents ls ls: Operation not permitted
However if you try the same commands in the Terminal all works fine.
The solution was described here:-
solution was to give "Full Disk Access" to /bin/bash. This is a bit counter-intuitive, since I actually use /bin/tcsh for my shell (yeah, I know, I'm a luddite). I'm not sure whether bash is involved because my tcsh is a descendant of a bash process, or because the ls command is using bash in some way. But it is certainly true that I can toggle whether "ls ~/Documents" works by checking/unchecking bash in the Full Disk Access panel.
Dr. Burkhard Schmidt from Max-Planck-Institut provided an insightful explanation
Indeed giving Full Disk Access to /bin/bash is the correct solution. Why? Well, assuming the standard location for XQuartz, look at /Applications/Utilities/XQuartz.app/Contents/Info.plist. Under the key CFBundleExecutable you will find the value X11 which is /Applications/Utilities/XQuartz.app/Contents/MacOS/X11. The command ?file /Applications/Utilities/XQuartz.app/Contents/MacOS/X11? returns ?/Applications/Utilities/XQuartz.app/Contents/MacOS/X11: Bourne-Again shell script text executable, ASCII text?, so X11 is actually not a binary but a shell script. Open it with your favourite text editor. The first line reads ?#!/bin/bash?, so eventually /bin/bash is executed upon opening (double-clicking) XQuartz. All further X11 processes are child processes to it and inherit the Full Disk Access right.
This applies not only to Xterm but to all applications using X11 (thinking of grace, xfig, gimp and friends).
I’ll add more updates later, feel free to contact me and thanks for the comments to date.
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 Mojave, High Sierra, Sierra, El Capitan, Yosemite it is apparently a useful resource.
I'll start compiling a list over the weekend but I thought I'd mention a couple of things. One of the key features is that 32-bit applications will no longer be supported, Apple has a page describing the reasons for moving to 64-bit.
Apple's transition to 64-bit technology is now complete. Starting with macOS Catalina, 32-bit apps are no longer compatible with macOS. If you have a 32-bit app, please check with the app developer for a 64-bit version.
The easiest way to check for 32-bit apps is to click on the Apple icon (top left of screen) and select "About this Mac", then click the system report button. Then select "Applications" and details of 32/64-bit are in the rightmost column.
When you attempt to open a 32-bit app, you will see an alert that the app is not optimized for your Mac, or that the developer needs to update it to work with this version of macOS. There may also be drivers that need to be updated.
Techrader has also been tracking installation problems.
As ever feel free to send me any information on scientific applications under Catalina and add them to the list.
A slightly different post.
The Bank of England are looking for nominations for who should be on the new £50 note and you can make your nomination here.
You can nominate as many people as you like. But anyone who appears on the new £50 note must: have contributed to the field of science, be real – so no fictional characters please, not be alive - Her Majesty the Queen is the only exception, have shaped thought, innovation, leadership or values in the UK, inspire people, not divide them.
Firstly I'm delighted to see a scientist be suggested and reading the comments in various news outlets I'm staggered by the number of scientists who have been suggested.
Whilst this website is aimed at providing a resource for Mac using chemists regular readers will know that much of the content is platform agnostic and includes much code/software that will be of interest to all scientists.
I recently got a rather sad email
It seems that Third Street Software quietly disappeared, breaking the syncing for Sente (reference management).
I've also heard about a couple of other smaller software developers who are finding life very tough and it started me thinking about the status of scientific software, after exchanging emails with a number of people in the industry (many thanks for their input) I thought I'd collect a few thoughts on my blog.
You can read it here https://www.macinchem.org/reviews/scientificsoftware/software.php.
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.
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".
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
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 18.104.22.168 and this seems to fix the problem.
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
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
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.
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