Macs in Chemistry

Insanely Great Science

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