Macs in Chemistry

Insanely Great Science

Annual Site Review

 

At the end of each year I have a look at the website analytics to see which items were the most popular.

Over the year there were 90,006 visitors, an increase of 28% over 2019, spending an average of 2.5 minutes per session, looking at the regular visitors there are around 4000 who visited 20-200 times per year. The US provided 28% of the visitors and the UK 8% with Germany, India, China and Japan around 5%. As might be expected 57% of the visitors were using a Mac, but 23% of the visitors were Windows users, 9% iOS and 6% Android, also 4% Linux. There has been a gradual increase in the number of visitors using mobile devices.

Again the most popular page was Fortran on a Mac which has been updated a couple of times this year with reader suggestions. Other popular pages include the Reviews and the Hints and Tutorials. The page describing the update to iBabel was particularly popular.

viewerTab

The post about Scientific Applications under Catalina made it to number 4 in the years listing and elicited a significant amount of reader feedback.

The Mobile Science site has seen increased visitor numbers.

The most popular apps viewed were.

Merck PTE
IBM Micromedex Drug Info
PocketCAS: Mathematics Toolkit
The Periodic Table Project
Periodic Table

Also popular were

Python3IDE Human Anatomy Atlas 2019
ChemTube3D.
Molecular Constructor

The Twitter feed @macinchem has steadily attracted new followers and currently has 993 followers.

The most popular tweets were

IOData: A python library for reading, writing, and converting computational chemistry file formats

and

Google Colab is very cool. .


Comments

Mac OS now available on AWS

 

Amazon’s cloud division announced the availability of new virtual computing instances for software developers that run Apple’s MacOS operating system. They will be using Apple’s Mac Mini computers, featuring Intel Core i7 chips, to deliver EC2 virtual-computing instances with MacOS.

Powered by Mac mini hardware and the AWS Nitro System, you can use Amazon EC2 Mac instances to build, test, package, and sign Xcode applications for the Apple platform including macOS, iOS, iPadOS, tvOS, watchOS, and Safari. The instances feature an 8th generation, 6-core Intel Core i7 (Coffee Lake) processor running at 3.2 GHz, with Turbo Boost up to 4.6 GHz. There’s 32 GiB of memory and access to other AWS services including Amazon Elastic Block Store (EBS), Amazon FSx for Windows File Server, Amazon Simple Storage Service (S3), AWS Systems Manager, and so forth.

Full details of how to access it are here.

Apple M1 Chip – EC2 Mac instances with the Apple M1 chip are already in the works, and planned for 2021.

In further news an AWS engineer puts Windows 10 on Arm on Apple Mac M1 – and it thrashes Surface Pro X


Comments

xterm problems under Catalina

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.

fulldisc

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).

More info on Scientific Applications under Catalina here.

Comments

Scientific Applications under Catalina: Update 13

 

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.

1280px-Santa_Catalina_Island_California_Panorama

By Thomas Pekin - Thomas Pekin, CC BY-SA 2.5

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.

Notarization

I suspect many users will now see more Notarization warnings.

notarisation

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.

SysPrefSecurity

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?).

Scientific Applications

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.
Update

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

ChemDraw I've posted question on forum but no response yet. A reader reported "ChemDraw 18.2 appears to run with no new issues".

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.

CrystalMaker

  1. CrystalDiffract 6.8.3 is a 64-bit “Cocoa” app and works fine.

  2. CrystalMaker X 10.4.6 - another 64-bit app “Cocoa” app - also runs seamlessly with “Catalina”

  3. SingleCrystal 3 is a 32-bit app and so won’t run. However…

  4. SingleCrystal 4 PUBLIC BETA works beautifully on Catalina. More information - including a sign-up form - can be found at:

    http://crystalmaker.com/singlecrystal4/

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.

DataWarrior

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.

GAMESS

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.

Manuscripts

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.

SeeSAR

Spartan

  • 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

UCSF Chimera

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 ’ to run a .exe. The only issue here is that Apple’s new notorisation system means that every file executed by wine64 will need to be manually allowed in the macOS security settings, which the first few times can take a lot of clicking, but after all is said and done, things are surprisingly stable, so long as the windows .exe is also 64 bit. It’s also possible to create an Automator application to launch the application, by using the “bash script” module, so that the windows application can be launched like any other.

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.

Comments

macOS Installation

 

Just had news of an update to a popular book macOS Installation, useful reading if you have to admin multiple Macs.

With the introduction of macOS High Sierra Apple and Secure Boot on the iMac Pro has profoundly changed the workflows for installing and deploying macOS on a large scale. In addition new technologies and services like MDM, DEP and VPP need to be configured and used correctly. This books explains all the different terms, services and technologies and suggests workflows for Administrators to deploy and manage macOS in education, business, enterprise and other organisations in this new “post-imaging” world.


Comments

Getting ready for Catalina

 

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.

GetReadyCatalina

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.

Comments

Mac backup options

 

We now have so much of our digital life on a hard drive including photos, music, emails from friends and family. In addition it is always worth having a current backup prior to a major OS upgrade, and with macOS Catalina on the horizon now would be a good time to review.

This page reviews backup options including external or network hard drives, and cloud storage, in addition to the software tools available.

Backup Options for Mac.

cloud-computing-1990405_1280


Comments

MacOSX Market Share

 

I occasionally get questions from scientific software developers about MacOSX market share visiting my site, it currently runs at 55% MacOSX, 23% Windows, 13% iOS, 4% Android, 4% Linux. However I am aware that readership is very scientific focussed audience and does not represent worldwide use. So I occasionally have a look at Statcounter to get a more general view as shown below.

StatCounter

The mobile market is of course much larger and there are an increasing number of Mobile Science apps but at the moment it looks like Desktop/Laptop still dominates science.


Comments

Easy Markdown updated

 

Easy Markdown has been updated to version 1.8.

A text written in Markdown is a plain text which looks correctly to humans as text and automatically translates in a correctly web pages coded in html. In Easy Markdown the window is split in two parts. As you type plain text on the left, you see on the right the resulting web page as it will be seen on the web.

There are many other Markdown editors here detailed here


Comments

Macs in Chemistry Annual Site Review

 

At the end of each year I have a look at the website analytics to see which items were the most popular.

Over the year there were 70,000 unique visitors with 25% visiting the site on multiple occasions. The US provided 30% of the visitors and the UK 7% with Germany, India and France around 5%. As you might expect the majority were Mac users (56%), but there were also Windows (25%), iOS (12%), and Android (2.5%) users.

Of the Mac users, 51% are now using 10.14 (Mojave), 27% 10.13 with all older versions each well below 10%.

Chrome and Safari were the preferred browsers with both around 40%.

The most popular web pages were (other than the main page)

The popularity of the Fortran on a Mac page has continued for several years now and it has been updated several times with user provided information.

The most viewed blog pages in 2018 were

The update to Mojave seems to have been another daily smooth transition, with most software developers reporting no major issues.

A couple of recent additions have generated significant interest.

As has an article I wrote on my thoughts on scientific software

Comments

Which versions of Mac OS and iOS are in use?

 

I'm occasionally approached by developers asking about the versions of Mac OS or iOS the visitors to the site are using. Whilst you can get general information from sites like NetMarketShare or Mixpanel I guess it is useful to know what versions scientists might be using.

Over the last month the operating systems used by visitors are 60% Mac, 21% Windows, 12% iOS, 4% Linux, 2.8% Android.

Of the Mac users, 43% are now using 10.14 (Mojave), 35% 10.13 with all older versions each well below 10%

For the visitors using iOS, 71% are using 12.x, and 16% using 11.x

These figures would suggest that visitors to the site are probably among the early adopters, and that Chemistry software developers should try and ensure they support the latest versions of operating systems as early as possible.


Comments

Apps at discount prices

 

A summer promotion is offering 12 applications at discount prices, pick and choose the ones you want.

Here is the list of participating apps:

iOS apps:

  • Mindnode by IdeasOnCanvas GmbH (AUT) → now 10,99€/$9.99 (30% OFF)
  • Notebooks by Alfons Schmid (AUT) → now 4,49€/$3.99 (40% OFF)
  • Inko by Creaceed SPRL (BEL) → now 14,99€/$13.99 (30% OFF)
  • Prizmo Go by Creaceed SPRL (BEL) → now 3,49€/$2.99 (40% OFF)
  • Grafio by Ten Touch Ltd. (BGR) → now 8,99€/$7.99 (20% OFF)
  • PocketCAS by Daniel Alm (DEU) → now 4,99€/$3.99 (50% OFF)
  • Money by Jumsoft (LTU) → now 1,09€/$0.99 (65% OFF on Standard IAP)

Mac apps:

  • Mindnode by IdeasOnCanvas GmbH (AUT) → now 29,99€/$26.99 (30% OFF)
  • Notebooks by Alfons Schmid (AUT) → now 9,99€/$8.99 (50% OFF)
  • Prizmo by Creaceed SPRL (BEL) → now 38,99€/$32.99 (30% OFF)
  • Remote Buddy by IOSPIRIT GmbH (DEU) → now 19,99€/$17.99 (20% OFF)
  • PocketCAS by Daniel Alm (DEU) → now 9,99€/$8.99 (50% OFF)
  • Findings by Findings Software SAS (FRA) → now 32,99€/$29.99 (40% OFF)
  • PDF Watermarker by seense (FRA) → now 8,99€/$7.99 (60% OFF)
  • Money by Jumsoft (LTU) → now 16,99€/$14.99 (40% OFF on Standard IAP)
  • Studies by The Mental Faculty B.V. (NLD) → now 21,99€/$19.99 (30% OFF)
  • Workspaces by Apptorium (POL) → now 6,99€/$5.99 (35% OFF)
  • FiveNotes by Apptorium (POL) → now 3,49€/$2.99 (40% OFF)

Comments

Scientific Applications under High Sierra (Update 3)

 

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 Sierra, El Capitan and Yosemite it is apparently a useful resource. The major change with High Sierra is the update to the file system so hopefully this will be a benign update, but a Time Machine backup is always a good idea.

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

High Sierra is a major download 5GB and a couple of people have asked if it is possible to keep the installer and then use it on multiple machines.

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. You must make a copy of this to another location; otherwise if you launch the installer and it completes the High Sierra update, it'll be deleted.

When you upgrade to macOS High Sierra, systems with all flash storage configurations are converted automatically. Systems with hard disk drives (HDD) and Fusion drives won't be converted to APFS. You can't opt-out of the transition to APFS.

AppleScriptObjC there are a couple of bugs, because the issues stem from the .bridgesupport file, they will potentially pose problems in other languages that use the scripting bridge.

Avogadro 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 has just been released which bring full High Sierra 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

ChirysView no issues to date

Cresset No issues to date, more detailed testing underway.

CrystalMaker no problems

DataWarrior no issues to date

Findings no issues

iBabel no issues to date

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

MarvinView no issues

Microsoft have already announced the results of preliminary testing of the Office suite.

Office version 15.35 and later, Word, Excel, PowerPoint, Outlook, and OneNote will install and run on 10.13, but there maybe some issues

Office 15.34 and earlier. These versions are not supported on 10.13. In some cases, you may not be able to launch the Office apps.

Office for Mac 2011. Word, Excel, PowerPoint, Outlook and Lync have not been tested on macOS 10.13 High Sierra, and no formal support for this configuration will be provided.

Mnova lite no issues reported

MOE There seem to be no problems running MOE 2016.0804 or higher on MacOS 10.13.

Please note that all of our Mac users should upgrade to MOE 2016.0804 due to bugs identified in earlier versions. You can download the patch to 2016.0804 http://www.chemcomp.com/support/12/moebin_2016.0804.tgz

The default python is

 ~ /usr/bin/python
Python 2.7.10 (default, Jul 15 2017, 17:16:57) 
[GCC 4.2.1 Compatible Apple LLVM 9.0.0 (clang-900.0.31)] on darwin
Type "help", "copyright", "credits" or "license" for more information.

PyCharm no issues

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

Vortex no issues reported.

xQuartz "I would like to report that xquartz now works in the latest macOS 10.13". Download here https://www.xquartz.org.

Updated 14 October 2017


Comments

Microsoft Office and High Sierra

 

Apple have announced a major new update of Mac OS X, version 10.13 High Sierra has a number of significant changes and it is likely that applications may need to be updated. Beta test versions of the operating system have been available for a while now and the more proactive developers have already been testing their software. Unfortunately there will always be developers who seem to refuse to test their applications until the new Mac OS has been officially released.

Microsoft have already announced the results of preliminary testing of the Office suite.

Office version 15.35 and later, Word, Excel, PowerPoint, Outlook, and OneNote will install and run on 10.13, but there maybe some issues

Office 15.34 and earlier. These versions are not supported on 10.13. In some cases, you may not be able to launch the Office apps.

Office for Mac 2011. Word, Excel, PowerPoint, Outlook and Lync have not been tested on macOS 10.13 High Sierra, and no formal support for this configuration will be provided.


Comments

APFS in macOS High Sierra

 

Apple have updated the online support documentation to give more details about the new file system (APFS) that is coming with the next generation of the operating system High Sierra. Apple File System (APFS), is the default file system in macOS High Sierra for Mac computers with all flash storage, it is designed to scale from an Apple watch to a Mac Pro.

Apple File System is a new, modern file system for iOS, macOS, tvOS, and watchOS. It is optimized for Flash/SSD storage and features strong encryption, copy-on-write metadata, space sharing, cloning for files and directories, snapshots, fast directory sizing, atomic safe-save primitives, and improved file system fundamentals. APFS replaces HFS+ as the default file system for iOS 10.3 and later, and macOS High Sierra and later.

A few things that might be important to note.

  • When you upgrade to macOS High Sierra, systems with all flash storage configurations are converted automatically. Systems with hard disk drives (HDD) and Fusion drives won't be converted to APFS. You can't opt-out of the transition to APFS.
  • FileVault volumes are converted from HFS+ to APFS, just like unencrypted volumes.
  • Devices formatted as HFS+ can be read and written to by devices formatted as APFS.
  • Devices formatted as APFS can be read and written to by any APFS-formatted devices but only by HFS+ formatted devices running macOS 10.12.6 or later.
  • Volumes formatted with APFS can't offer share points over the network using AFP. SMB and NFS are supported when using APFS. The option to enforce only SMB-encrypted share points is also available.

What are the advantages?

  • APFS supports 64-bit inode numbers, supporting over 9 quintillion files on a single volume
  • APFS is optimized for SSD storage, it will work with traditional hard disk drives as well.
  • No need to repartition, APFS allows Space Sharing, which lets multiple file systems share the same underlying free space on a physical volume rather than use a fixed amount of space for each file system.
  • APFS supports sparse files, extended file attributes and TRIM operations, as well as using a copy-on-write metadata scheme to ensure that updates to the file system are crash-safe.
  • Apple File System supports encryption natively, both single key encryption and multi-key encryption (where each file is encrypted with a separate key, and metadata is encrypted with a different key).

It is almost certain that any third party disc utilities will need to be updated. Once upgraded to APFS the only way to return to HFS+ is to erase the disc losing all data.

APFS implements normalization and case insensitivity according to the Unicode 9.0 standard; this enables APFS to support a wider range of languages for these features than HFS+, which is based on Unicode 3.2. However beta testers report issues with languages that include non-Roman characters. Hopefully this will be addressed soon.


Comments

Lots of updates from Apple

 

Mac OS X 10.12.4 improves the stability, compatibility, and security of your Mac, and is recommended for all users. This update:

  • Adds Night Shift for automatically shifting the colors in your display to the warmer end of the spectrum after dark.
  • Adds Siri support for cricket scores 😄, schedules, and player rosters from the Indian Premier League and International Cricket Council.
  • Adds Dictation support for Shanghainese.
  • Improves right-to-left language support for the Touch Bar, toolbar, and visual tab picker in Safari.
  • Resolves several PDF rendering and annotation issues in Preview.
  • Improves the visibility of the subject line when using Conversation View in Mail.
  • Fixes an issue that may prevent content from appearing in Mail messages.
  • Adds support for more digital camera RAW formats.

Xcode 8.3 brings faster builds for large projects containing both Objective C and Swift. Siri support in iOS simulator. Xcode 8.3 no longer supports Swift 2.3 so you will need to update.

Also updates for Pages, Keynote and Numbers.


Comments

MacBook Pro Touchbar to open man pages

 

I can't remember seeing this mentioned but if you are using a Terminal window on the new MacBook Pro with a Touchbar, if you type

obabel

the Touchbar illuminates as shown below, if you then touch "obabel" it opens the manual page for you in another window.

IMG_1348

touchbar1

Seems to work for other command line tools also.


Comments

2016 MacBook Pro and sharing DVD drive

 

As a happy owner of a new MacBook Pro I am aware of the limitations of only having USB-C connectors. It is clear that this is the future since Apple are not the only company to make this transition. However a number of the scientific application I use regularly were supplied on DVD and I suspect others may be in a similar situation so I thought I'd mention this tip. Instead of investing in an adaptor if you have an older Mac you can use DVD or CD sharing. Open up system preferences and select "Sharing", click the checkbox for "DVD or CD Sharing".

sharing

If you now open a "Finder" window on the MacBook Pro you should find "Remote Disc in the side bar. You may need to change your preferences to display CCs, DVDs etc. (Finder:Preferences)

proshare

You can then use it as normal.


Comments

Scientific Applications under Sierra (Update 14)

 

Whilst there are many sites that track the compatibility on common desktop applications, it is often difficult to find out information about scientific applications. I’ll update the list regularly and feel free to send in information.

When I compiled a similar lists for Yosemite and El Capitan they proved very popular with 13,000 page views, I hope this page is similarly useful.

4Peaks no reported issues

Avogadro all seems OK

BBEdit version 11.6.2 and newer are compatible, recommend against using earlier versions

Brainsight requires version 2.3.3 for full compatibility with 10.12 Sierra. You could note too that 2.0 through 2.2.x will never work because 10.12 removed support for garbage collected applications. 2.3.x uses ARC

ChemDraw the official line is that it is not supported, even under El Capitan there were reports of copy/paste issues. One user reports “ChemDraw 15 is working fine for me. copy/paste, everything without issues”.

ChemDoodle no reported issues

CrystalMaker “We are pleased to confirm that all our latest software runs fine on macOS “Sierra”, as well as OS X 10.11 “El Capitan”, 10.10 “Yosemite”, and earlier.”

CYLview app launcher (icon on the desktop or the dock) does not work need to start using “Terminal”

DataDesk Data Desk 8 for Mac runs on OS X 10.7 up to 10.12

DataWarrior requires Java installation

DEVONagent has been updated to version 3.9.5 to support Sierra, in addition this update brings support for Qwant. DEVONthink has also been updated for Sierra.

EndNote From Endnote (Thomson Reuters) version 7: Message for Mac user planning to update to Sierra: In preparation for Apple's release of macOS Sierra on September 20, we have been testing various versions of EndNote. Through our testing, we discovered some issues with the EndNote PDF viewer. These issues have been reported to Apple, but in the meantime, we recommend that you DO NOT upgrade to macOS Sierra.

EnzymeX no reported issues

Evernote a bug in some versions of Evernote for Mac that can cause images and other attachments to be deleted from a note under specific conditions. We've released an updated version of Evernote for Mac, version 6.9.1, to resolve this.

Findings no reported issues

Fortran users will be happy to hear there are no reported issues with FTranProjectBuilder

GAMESS no reported issues.

Homebrew, after every update it is worth checking your homebrew installation.

Username$ brew doctor
Please note that these warnings are just used to help the Homebrew maintainers
with debugging if you file an issue. If everything you use Homebrew for is
working fine: please don't worry and just ignore them. Thanks!

Warning: /usr/local is not writable.

You should probably change the ownership and permissions of /usr/local
back to your user account.
  sudo chown -R $(whoami) /usr/local

Warning: /usr/local is not writable.
Even if this directory was writable when you installed Homebrew, other
software may change permissions on this directory. For example, upgrading
to OS X El Capitan has been known to do this. Some versions of the
"InstantOn" component of Airfoil or running Cocktail cleanup/optimizations
are known to do this as well.

You should probably change the ownership and permissions of /usr/local
back to your user account.
sudo chown -R $(whoami) /usr/local

Once corrected you can then type

brew update
brew upgrade

You may get this error

$brew update
/usr/local/Library/brew.sh: line 32: /usr/local/Library/ENV/scm/git: No such file or directory

simply retyping brew update seems to resolve the issue

If you have previously installed Openbabel using

brew install mcs07/cheminformatics/open-babel --HEAD

The "--HEAD" part means install the latest development version from GitHub. The latest version of OpenBabel is now available so type

brew uninstall mcs07/cheminformatics/open-babel
Uninstalling /usr/local/Cellar/open-babel/HEAD... (309 files, 14.6M)
brew install mcs07/cheminformatics/open-babel

You can check you have the latest version installed by type this in a Terminal window

obabel -V
Open Babel 2.4.0 -- Sep 24 2016 -- 14:01:18

iBabel seems to work fine with the latest version of OpenBabel under Sierra. One advantage to updating to OpenBabel 2.4.0 is that previews now work with Quicklook.

quicklook

IDL does run under Sierra but does require some tuning. Detailed instructions here

iPython Notebook all working fine

Lego Mindstorms At the moment everything seems to be running really great on Sierra. However, please let you readers know they are welcome to contact us via the website way you did if they run into any errors. We'd be happy to solve them!

Manuscripts no reported issues

MarvinSketch I had to reinstall Java for Mac OSX this is the last version of Java Apple created to support legacy applications, similarly MarvinSpace and MarvinView.

Matlab in general appears to be fine except for certain language localisations these languages a patch is available for download. A patch is also available for MATLAB Runtime R2016b.

Mathematica 11.0.1 has been compatibility tested with macOS Sierra and you should not run into any OS-specific compatibility issues. The font-panel is disabled, but we are actively working to address this as soon as possible.

Mendeley no issues reported

MOE working fine, XQuartz did not need reinstalling. However the MOE app launcher (icon on the desktop or the dock) does not work because Apple changed some fundamental system components which affects lots of programs not specifically compiled for the newest MacOSXs. Also you cannot double click on a file to open it in MOE. You can still start MOE from the command line

Applications/moe2015/bin/MOE

It then works perfectly. Update, just had an email from CCG support, The problem with the MOE app launcher on MacOSX Sierra has been fixed in the MOE 2016 release.

MOPAC all seems to be working fine.

osra crashed with error abort trap: 6. I uninstalled using brew then reinstalled

brew uninstall osra
Uninstalling /usr/local/Cellar/osra/2.0.1... (7 files, 1.6M)
brew install osra

Then worked fine

Pandoc depends on llvm-3.5, not supported on Sierra. Llvm-3.9 is supported, installation using Homebrew seems to be OK.

Papers Mac 3.4.7 (527) is now available! Fixes a couple of problems under Sierra. A crash that can occur when switching PDFs, The search in PDF functionality is restored

R latest version (3.3.1) all seems fine

rdkit installed using home-brew works fine.

Readcube Version 2.22.13732 is Mac OS Sierra (v10.12) compatibility update.

Scansnap Note for using ScanSnap or ScanSnap Applications on macOS Sierra In order to avoid the ScanSnap compatibility problems, please do not use ScanSnap or ScanSnap applications on macOS Sierra in the following manner as doing so may cause some pages to be deleted or to become blank. Do not use [ScanSnap Organizer], [ScanSnap Merge Pages], or [CardMinder] Do not use Excellent mode when scanning A3 (11.7 in. x 16.5 in.) documents No image data will be lost nor any blank pages produced when content that has been scanned in the A4 (8.3 in. x 11.7 in.), Letter (8.5 in. x 11 in.), Legal (8.5 in. x 14 in.), or smaller sizes is saved.

Schrodinger a reader sent in this response. We received your query regarding MacOS Sierra. Unfortunately our current, 2016-3 release, do not yet support MacOS Sierra but we have plans to include support for this OS for the upcoming 2016-4 release of our software.

SeeSAR version 5.3 now, 5.4 will come out shortly. No compatibility issues observed/reported.

Studies no reported issues

UCSF Chimera version 1.11.1 seems to be working fine

Wizard worked great with the developer pre-releases, no reported issues

Vortex no problems so far, the embedded chemical drawing app Elemental appears to have no issues.

XQuartz did not require reinstallation :-) however there are reports of an intermittent display not found error when launching apps from a Linux box.

Allow applications downloaded from anywhere in macOS Sierra, if you open the security panel in the Settings the default options in Sierra are as shown below. There is no longer the option to open applications from Anywhere.

appstore

Apple have removed this function on macOS Sierra, but you can re-enable it running this in terminal

sudo spctl --master-disable

appstore2

You can restore it back to the default setting using

sudo spctl --master-enable

I’ll add more updates later.


Comments

Mac@IBM

 

IBM’s Fletcher Previn delivered an update on the company’s rollout of Macs at the Jamf Nation User Conference this week. IBM plans to reach over 100,000 Macs by the end of the year and is now deploying 1300 a week on average.

“I can confidently say every Mac that we buy is making and saving IBM money” said Previn. IBM is saving a minimum of $265 (up to $535 depending on model) per Mac compared to a Lenovo PC, over a 4-year lifespan.

More details on Computerworld and 9To5Mac

Comments

Mac Market Share Data

 

The latest market share data is available from NetMarketShare.com, Mac market share has been rising over the last few years and in April hit a peak of 9.20%, largely at the expense of Windows.


Comments

El Capitan Review in Guardian

 

http://www.theguardian.com/technology/2015/sep/29/os-x-el-capitan-review-apple-laptop-desktop-operating-system

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

Comments

Mac OSX installer for Coot

 

A reader sent me a link to a posting on the brilliant Crystallography on OS X website highlighting the availability of a stand alone version of Coot for Mac OSX

With considerable help from Nat Echols, we can now build coot automatically every night a new revision is available. I have two versions, built on two different computers. The 10.6 version should run on 10.6.8 or greater. The 10.9 version is for 10.9 or later.. The package installer will install everything in /Library/Coot. Unfortunately, it breaks if you move it. A wrapper shell script called "coot" will reside in /usr/local/bin/coot when you are done.

Coot (Crystallographic Object-Oriented Toolkit) is for macromolecular model building, model completion and validation, particularly suitable for protein modelling using X-ray data.

Coot displays maps and models and allows model manipulations such as idealization, real space refinement, manual rotation/translation, rigid-body fitting, ligand search, solvation, mutations, rotamers, Ramachandran plots, skeletonization, non-crystallographic symmetry and more.

I've also added a link on the Spectroscopy page.

Comments

Shazino software

 

I recently became aware of a new company specialising in software for scientists Shazino have developed a number of interesting applications for both Mac OS X and iOS.

The best known app is PaperShip an iPad, iPhone, and Mac application designed to help you keep your articles organized with your Mendeley or Zotero library. However they also provide a couple of smaller apps that make life easier in the lab.

Laboratory Timer, Fast Counter and SciKey a scientific keyboard.

The latest addition is an electronic labNotebook called Hivebench, this is available for both MacOSX and iOS. Looking at the website it seems to be aimed at molecular biologists/biochemists, and there is a free version that allows unto 10 scientists to collaborate.

mobile_devices_hero-a3f5971a11bba4791e0b09df3e8a5993

Comments

Rack mounted MacPros

 

've posted a couple of entires where I've been looking at the computing power of the new MacPros however this site caught my eye because it shows how the MacPro can be rack mounted.

imgix is an image processing and delivery service that provides a supremely flexible, high performance, ultra–reliable solution to the problem of serving images on the modern internet. We operate our own hardware, run our own datacenters, and manage our own network infrastructure. At imgix‘s scale, maximizing efficiency and performance in image processing is critical for success. For this reason, we decided to incorporate Mac Pros in planning the build of our next generation image renderers. Because no existing Mac Pro server rack suited our needs, we designed and built our own.

macpro1

macpro2

The rack mounted Mac minis also look pretty impressive.

macpro3

Photo Credit to: Miguel A. Cardona Jr. / imgix

Comments

Replacing Photoshop With NSString

 

A really clever way to create icons using ascii art. It is open-source and released under the MIT license on GitHub.

I think one of the real advantages of this is you can actually see the image you want to create in the code.

asciiart

is rendered as..

asciart2

You can read more here

Comments

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

Comments

Scientific Applications under Yosemite

 

I've continued to update the Scientific Applications under Yosemite we are now up to the 18th update. Many thanks for the people who have contributed.

With over 5,000 people viewing the page it is clearly pretty useful.

Comments

OS X Source code

 

Apple has released the Darwin source code for OS X 10.10 here.

Comments

Clipboard Managers

 

This is an update to a blog post from early 2013 incorporating some valuable readers comments.

For many years I’ve used the excellent Clipboardsharing to exchange the clipboard contents between my laptop and desktop machines, it also supports multiple clipboards. However it is not supported under Mac OS X 10.7.x (Lion) and the developer website seems to have disappeared. I spent a while looking at various alternatives and I thought I’d summarise my findings.

Comments

A comparison of clipboard managers