Macs in Chemistry

Insanely Great Science

PyCharm

 

I must admit I’m a big fan of BBEdit for all my text editing, Markdown and python programming but I still keep an eye out for interesting alternatives. I was recently sent a link to PyCharm a Python IDE. PyCharm’s code editor provides support for Python, JavaScript, CoffeeScript, TypeScript, CSS, and a number of other languages. What caught my eye was the recently added support for iPython notebooks, with PyCharm 4 you can perform all the usual IPython Notebook actions with *.ipynb files. Everything you’re used to doing with the ordinary IPython Notebook is now supported inside PyCharm.

ipythonnotebook

Another very useful features for scientific programming is the NumPy array viewer to easily get a graphical view of a NumPy array and support for matplotlib.

There is a really comprehensive support section that includes demos and screencasts .

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Chemistry Keyboard for iOS

 

With iOS 8 Apple now support third party custom keyboards

A custom keyboard replaces the system keyboard for users who want capabilities such as a novel text input method or the ability to enter text in a language not otherwise supported in iOS.

The Chemistry Keyboard allows users to enter chemical formulae, equations etc without having to struggle entering subscripts etc. Whilst the chemistry keyboard is an app in itself it also allows you to use the custom keyboard with other applications.

You can read more details here.

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Scientific Applications under Yosemite (Update 15)

 

Whilst there are many sites that track the compatibility on common desktop applications, it is often difficult to find out information about scientific applications. Given that this seems to be such a major upgrade I thought I’d set up a spare machine to test applications before I update my main machine. I’ll update the list regularly and feel free to send in information.

I have a number of applications/libraries/toolkits installed using Homebrew and installed in usr/local, this is known to cause extended installation times for Yosemite. So don’t worry if it appears the install is stuck at 1 min remaining.

If you do use Homebrew then it is worth updating

brew update
brew upgrade

Aabel 3 appears to be working fine

BBEdit version 10.5.13 and newer are compatible with Yosemite

Beaker all seems OK

ChemBioDraw versions 12, 13 and 14 all function as before. In particular round-trip editing still works! There are a couple of issues emerging * Sometimes it becomes "almost" unresponsive. Quiting and reopening the application usually fix the problem. * There is a frequent crash on quit. * Sometimes the popup window for "save as" is too large and the "save" and "cancel" buttons get outside the screen.

ChemDoodle all seems to work fine

Chimera aka UCSF Chimera versions 1.10 and higher are working on Yosemite.

Conquest and  Mercury from CCDC works fine but you may need to reinstall Quartz (see below)

COMSOL 5.0 works out of the box on Mac OS X 10.10 Yosemite. We now have instructions and a patch for installing and running COMSOL 4.4 Update 2 on Mac OS X 10.10 Yosemite. You can find the instructions at www.comsol.com/support/updates/comsol44p3 COMSOL 5.0 works out of the box on Mac OS X 10.10 Yosemite.

Cresset report that after testing that Torch, Spark, Forge and Blaze appear to be compatible with Yosemite, the only cosmetic issues are due to a couple of as yet unresolved bugs in QT here.

Cytoscape 3.1.1 seems to be working fine

DataWarrior no issues

EndNote X7.2 works well with Yosemite.

Findings Electronic Notebook no issues, only small issue is that the ‘+’ button of the window does not trigger full-screen, though it can still be done via the Window menu.

IDL 8.2 and earlier gags on a missing reference in libPng.dyld, but IDL 8.3 and later is OK

Igor Pro version 6.3.5.5 works fine

iNMR no problems reported

LabQuest Viewer has preliminary support for Yosemite.

MacVector 13.0.6 No significant issues reported

Marvin Marvin, Instant JChem, and JChem suite all work but require Java 7 (available here http://support.apple.com/kb/DL1572

Mathematica no issues reported

Matlab 2014b works fine, 2012a thru 2014a need patching (directions available from Mathworks support site. Older versions will not run at all..

MOE works fine but you may need to reinstall Quartz (see below), no problems reported with running the license server under Yosemite.

OpenBabel no issues so far

Opsin all works fine

OSRA no issues

Papers Current version is compatible but not optimised, they hope to have a beta out of a substantially redesigned version next week.

Pro Fit 6.2 appears to work fine.

Pybel no issues reported

PyCharm works fine

Pymol All these are confirmed to work:

  • MacPyMOL 1.7.2.3
  • MacPyMOLX11Hybrid 1.7.2.3 after XQuartz reinstall (see below)
  • Open-Source PyMOL with homebrew

Known issues with MacPyMOL: - Movie export broken. Edu-only-PyMOL (free Student version) Does not work.(Now updated to work with Yosemite)
No reports so far about about - Other legacy versions (0.99 etc.) Apparently progam will not open - Open-Source PyMOL with fink or macports

PyRx 0.8 for docking works fine

RDkit no issues reported

SeeSAR all seems to be working fine

Sente 6.7.8 seems to run fine, except that it cannot open a reference library from the File > Open... dialog box. Workaround is to open from Finder.

SMARTCyp downloaded app runs fine.

Spartan 14 does not work because the Sentinel drivers are broken in Yosemite. The problem is NOT with Spartan, it is with the SafeNet developed Sentinel Run-Time Environment driver (the license manager). SafeNet has not given a definitive date when they will release an updated driver with Yosemite compatibility, but they are working on this. Best advice is to not upgrade but if you have to then contact support@wavefun.com for a temporary alternative license procedure.

Torch no issues

VarSeq no issues

Vortex Upgraded when the developer preview came out.  All works fine

The VVI products work well enough on Yosemite, but I'd like to achieve a higher level of quality for Yosemite (and iOS/iPad). There is an ongoing beta program for this product: https://itunes.apple.com/us/app/graph-ide/id904733611?mt=8 which is Graph Builder reincarnated on the iPad. There is also a beta program ramping for Graph Builder on Yosemite: https://itunes.apple.com/us/app/graph-builder/id470597599?mt=12 but a last minute interaction bug with Yosemite has delayed that for perhaps a few days. Please feel free to broadcast this information as you see fit. Beta program participation should be directed to support@vvi.com

VMD no issues reported

WHICHCyp downloaded app runs fine

Wizard Pro is fully Yosemite compatible

XQuartz it seems the Yosemite installer deleted the symlink between /opt/X11 and /usr/X11; you can either reinstall Quartz or try "ln -s /opt/X11 /usr/X11"

Updated 19 November 2014

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Papers 3 for teams

 

I’ve just added Papers 3 for teams to the mobile science site. This app has been designed for teams, departments, companies and institutions to offer the same flexibility and easy management of Papers 3 to users with iOS devices as there is with desktop volume licenses

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A late night call

 

Whenever I get a late night call I always fear the worst, I guess it is one of the unexplained features of being a parent. This night it was a very despondent child “My laptop has been stolen”. After confirming that they were OK and that nothing irreplaceable had been stolen I immediately logged into the Undercover website and logged the laptop as stolen and waited…

I think I first met Peter Schols the developer at WWDC in 2005 and heard about his idea for an application to trace stolen Macs, when the application became available I installed it on all my families machines. As time has gone on we have replaced machines and upgraded the software without any need to actually activate it until now.

The machine was stolen on a friday night from typical university accommodation, always people around, but you can never be sure if anyone has a copy of a key. We got an automated email from Orbicule saying the they were sorry to hear about the laptop and that they would inform me when the laptop was next online. They also asked me to fill in a form with the police incident information and contact details for the officer in charge of the case.

Nothing happened for several days and we were beginning to think the machine was lost for good when suddenly I got an email saying the machine was online. I quickly logged onto the Undercover website and within a short while we had the location, IP address, together with a series of photographs of the user. The police officer went around but unfortunately the culprit was out, over the next few days it was possible to build up a picture of the culprit’s working routine and to get screenshots of their bank account, ebay activities and much more personal information. Orbicule were then able to provide with a detailed evidence package to the police and they were able to target a time when the culprit would be at home.

The police were then able to arrest the culprit and recover the laptop!

The police were stunned by the detailed evidence that Orbicule were able to provide, I don’t think they had ever seen such a comprehensive evidence package.

As I said I’ve had Undercover installed for years and it will be the first thing that is installed on any new machine.

undercover-logo


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