The much-awaited CrystalMaker 10.4 is now shipping - complete with full “Dark Mode”.

CrystalMaker and CrystalDiffract are real 64-bit Mac programs, written in Cocoa/Objective-C, with beautiful real Mac interfaces. They’re not Windows or Unix applications reskinned via Qt, Java, wxWidgets they’re the real deal: 100% pure Mac. Thus they are able to offer:-

• Retina display
• Multi-touch
• Force touch
• Haptic feedback
• Touch bar interface (MacBook Pro)
• Dark Mode
• Full-screen mode and Spaces
• Quick Look
• Finder thumbnails
• QuickTime video
• Apple Help
• Code-signed, sandboxed, with “hardened runtime” for maximum security

CrystalMaker 10.4 has over 60 new features, of which the most-important are probably:-

1. Dark Mode
2. Sleek new structures library with integrated CrystalViewer (1,100 structures; fully customizable)
3. New energy-modelling engine: makes designing your own molecules quick and easy, with vibrational spectra simulation.
4. Live powder diffraction: link CrystalMaker 10.4 with CrystalDiffract 6.8 so that editing a crystal in CrystalMaker automatically updates its simulated powder diffraction pattern in CrystalDiffract.
5. Interpolate Structures command - makes animating structural behaviour smooth and seamless.
6. Customizable Atoms Inspector and coordinates display.
7. Spring-loaded sidebars: move the mouse to the edge of the screen to show the relevant sidebar (works great in full-screen mode).
8. Powerful video sizing/compression options.
9. Fat sticks display option (great for emphasising structural channels).
10. Advanced control over axial vectors with scaling, fonts, positioning, inset etc.

More details are available from the download page http://crystalmaker.com/crystalmaker/

They also have a set of video tutorials available.

CrystalMaker X lets you import data from over 40 different formats: with instant display and powerful customization. CrystalMaker can handle including multi-structure files such as DL_POLY HISTORY - use CrystalMaker's synchronization and animation capabilities to rapidly understand structural behaviour, lattice dynamics, or visualize the trajectory of a simulation. CrystalMaker X can also handle truly massive structures. Take advantage of our unique "Depth Profiling" tool, to rapidly scan ares of interest in massive structures - ideal for characterizing the results from computer models.

 

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)

• Fortran on a Mac
• Cheminformatics on a Mac
• Data Analysis Application on a Mac
• iBabel
• ChemDraw 17 review
• LaTeX and MathML support in Pages

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

• Xcode 9.0 is available for download
• Scientific Applications under Mojave
• Mac OSX installer for Coot
• Scientific keyboards for iOS
• Tools for Mac Fortran Programmers

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.

• Cheminformatics toolkits - A listing of Cheminformatics toolkits

• Data Science Libraries - A list of useful python libraries for data science

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

 

Well worth a read.

Executing AppleScript in a Mac app on macOS Mojave and dealing with AppleEvent sandboxing

Over a weekend recently I built a tiny Mac app (more on that later). What I was trying to achieve required executing AppleScript, like so many things on macOS. It seemed simple enough, but of course new app sandboxing restrictions in macOS Mojave got in the way.

 

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.

 

BBEdit 12.5 requires Mac OS X 10.12.6 or later, and is compatible with macOS 10.14 "Mojave".

If you are using macOS 10.13 "High Sierra", please make sure that you have updated to the latest available OS version (10.13.6 or later).

If you are using macOS 10.14 "Mojave", please make sure that you have updated to the latest available OS version (10.14.1 or later).

There are a number of new additions

• There is a new command on the "Go" menu: "Commands...". This brings up a modal panel which lists everything that you can do from a menu in BBEdit: menu commands, clippings, scripts, stationery, text filters, as well as open text documents and recent file.
• You can now generate lipsum, using the "Lorem Ipsum" command on the Insert submenu of the Edit menu.
• Added support for Grep patterns to Canonize. This can be turned on using the check box in the "Canonize" dialog box; or by using a mode line in a Canonize data file.
• Multi-File Search results windows now get a "reload" button, which you can use to repeat the search using the same settings.

Full details are in the release notes.

 

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

 

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

A desktop app to draw chemical structures and reactions, and to organise your data in convenient spreadsheet-like files. The Molecular Notebook is designed from the ground up to leverage the macOS platform, integrating seemlessly and making presentation quality graphics just one drag away.

The Molecular Notebook desktop app for chemical structure & data content creation has a refresh on the iTunes AppStore: it now responds to the dark-mode preference.