Macs in Chemistry

Insanely Great Science

DIRAC18 released

 

The DIRAC program computes molecular properties using relativistic quantum chemical methods. It is named after P.A.M. Dirac, the father of relativistic electronic structure theory.

I can be downloaded from the zenodo repository.

New features are described here.

DIRAC, a relativistic ab initio electronic structure program, Release DIRAC18 (2018), written by T. Saue, L. Visscher, H. J. Aa. Jensen, and R. Bast, with contributions from V. Bakken, K. G. Dyall, S. Dubillard, U. Ekström, E. Eliav, T. Enevoldsen, E. Faßhauer, T. Fleig, O. Fossgaard, A. S. P. Gomes, E. D. Hedegård, T. Helgaker, J. Henriksson, M. Iliaš, Ch. R. Jacob, S. Knecht, S. Komorovský, O. Kullie, J. K. Lærdahl, C. V. Larsen, Y. S. Lee, H. S. Nataraj, M. K. Nayak, P. Norman, G. Olejniczak, J. Olsen, J. M. H. Olsen, Y. C. Park, J. K. Pedersen, M. Pernpointner, R. Di Remigio, K. Ruud, P. Sałek, B. Schimmelpfennig, A. Shee, J. Sikkema, A. J. Thorvaldsen, J. Thyssen, J. van Stralen, S. Villaume, O. Visser, T. Winther, and S. Yamamoto (available at https://doi.org/10.5281/zenodo.2253986, see also http://www.diracprogram.org).


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Most popular Python IDE, Editors

 

I always keep an eye out for the polls on KDnuggets, the latest one looks at Python editors or IDEs, over 1900 people took part and the results are shown below (users could select up to 3). There is more detail in the linked page.

poll-top-python-ide-468

I've become a great fan of Jupyter, and not only for Python.



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Wolfram|Alpha

 

Wolfram|Alpha has been updated, to include support for the iPhone XS max and bug fixes.

Remember the Star Trek computer? It's finally happening--with Wolfram|Alpha. Building on 25 years of development led by Stephen Wolfram, Wolfram|Alpha has rapidly become the world's definitive source for instant expert knowledge and computation. IMG_2014


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RSC CICAG Interest Group

 

Royal Society of Chemistry members will be getting their annual subscription details around now. Can I remind people that your membership entitles you to membership of up to THREE Interest Groups. Apparently only around 25% take advantage of this option so I'd urge you to have a look at the groups available

In particular I'd like to highlight:-

86 Chemical Information and Computer Applications Group

The Chemical Information and Computer Applications Group (CICAG) is one of the RSC’s many member-led Interest Groups, which exist to benefit RSC members and the wider chemical science community, and to meet the requirements of the RSC’s strategy and charter. The storage, retrieval, analysis and preservation of chemical information and data are of critical importance for research, development and education in the chemical sciences. All chemists, and everybody else who works with chemical substances, need tools and techniques for handling chemical information.

If you have already submitted your form you can make a request to join a group via email (membership@rsc.org) or telephone (01223 432141).

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If you want to find out more about CICAG activities the newsletters are available here and if you have ideas for future activities feel free to contact the committee.


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Installing Osprey 3.0 under Mac OS X

 

A recent publication described OSPREY 3.0: Open-Source Protein Redesign for You, with Powerful New Feature DOI.

We present Osprey 3.0, a new and greatly improved release of the osprey protein design software. Osprey 3.0 features a convenient new Python interface, which greatly improves its ease of use. It is over two orders of magnitude faster than previous versions of osprey when running the same algorithms on the same hardware. Moreover, osprey 3.0 includes several new algorithms, which introduce substantial speedups as well as improved biophysical modeling. It also includes GPU support, which provides an additional speedup of over an order of magnitude. Like previous versions of osprey, osprey 3.0 offers a unique package of advantages over other design software, including provable design algorithms that account for continuous flexibility during design and model conformational entropy. Finally, we show here empirically that osprey 3.0 accurately predicts the effect of mutations on protein–protein binding.

Osprey 3.0 is available at http://www.cs.duke.edu/donaldlab/osprey.php as free and open‐source software GPLv2.

The source code is available on GitHub https://github.com/donaldlab/OSPREY3/.

Unfortunately the installation instructions do not include Mac OSX but there are instructions for "Debian-like Linux" which seemed promising. With the invaluable help of Nathan Guerin I was able to get OSPREY installed.

Read more…..


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