Macs in Chemistry

Insanely Great Science

Stellarium

 

Every looked into the night sky and wondered what a bright object might be? If so then this is the app you need, Stellarium is a Mobile Sky Map is a fully-featured planetarium for your phone. It shows a realistic and accurate night sky map, just like what you see with the naked eye, binoculars or a telescope.

  • a catalog of over 600,000 stars displayed as a real time zoomable sky map
  • a catalog of many nebulae and galaxies, with pictures for some of them
  • asterisms and illustrations of the constellations for several sky cultures
  • artificial satellites, including the International Space Station
  • realistic Milky Way
  • realistic landscape and atmosphere with sunrise, sunset and light pollution simulation
  • accurate simulation of stars extinction, and atmosphere refraction
  • 3D rendering of the major solar system planets and their satellites
  • night mode (red)
  • GPS positioning, accelerometers control of the direction of view in the sky

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iOS Human Interface Guidelines

 

For all you iOS app developers, here are the iOS Human Interface Guidelines a set of guidelines and resources that should help developers build high quality, intuitive and consistent apps.


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CompTox Mobile

 

CompTox Mobile allows the user to find chemical structure instantly by exact mass (m/z), ¹³C NMR chemical shifts, structure name or CAS Registry Number in a database of about 720,000 EPA CompTox structures.

Within the Chemistry Dashboard, users can access chemical structures, experimental and predicted physicochemical and toxicity data, and additional links to relevant websites and applications.

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PyMOLProbity

 

Just heard of a new PYMOL plugin, created by Jared Sampson, called PyMOLProbity which allows a PyMOL user to visualize MolProbity-style structural validation data directly in a PyMOL session. PyMOLProbity is a plugin allows the user to produce MolProbity-style visualization of atomic interactions within a structure (e.g. H-bonds, van der Waals interactions and clashes) directly within a PyMOL session.

The plugin runs local copies of several executable programs from the Richardson Lab at Duke University, authors of the MolProbity software, parses the output, and displays the results in the PyMOL viewport. There are both a graphical user interface (GUI) for general point-and-click use, and a command-line interface (CLI) suitable for scripting.

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Chen et al. (2010) MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallographica D66:12-21 DOI.

Full installation instructions are here

The Reduce, Probe, and Prekin executables are only available for Linux and MacOS, PYMOL is available from Schrödinger and also available via Homebrew, you will need to install XQuartz first.

There are detailed instructions on how to install a variety of chemistry/cheminfomatics/biology packages on a Mac here.


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Several ways of scripting Name to Structure

 

Too often I come across datasets that Chemical names or identifiers but no actual molecular structure, recently Dan at Dotmatics suggested I look at OPSIN. There are also several web services for converting names to structure and I've highlighted a couple of options here and described three scripts that allow them to be used from within Vortex.

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There are many more scripts on the Hints and Tutorials Page.


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