Macs in Chemistry

Insanely Great Science

Bookends Updated

Bookends 12 has been rewritten from the ground up. It includes configurable spell checking, database journaling, integration of the built-in browser with the library window, enhanced formatting options,.

The full release notes are here

There is a page of reference management applications here



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Molegro Virtual Docker Update

An update to the Molegro Virtual Docker has been announced. It includes new data analysis tools that are now available directly from within Molegro Virtual Docker. Some of the new features include:

  • New and powerful regression features: Support Vector Machine regression and Partial Least Squares
  • Classification using either K-Nearest Neighbors or Support Vector Machine classification
  • Automated fine-tuning of regression and classification model parameters
  • Spring-Mass Maps for visualization of high-dimensional data
  • Clustering of data sets and subset selection
  • Principal Component Analysis
  • Outlier Detection



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MacPro

I was just looking at a few of the images of the internals of the new MacPro, I wonder how long it will be before someone produces a replacement transparent cover and subtle lighting for illumination. Could look pretty cool.

MacPro2



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ChemDoodle Updates

IChemLabs have announced a couple of updates

ChemDoodle Web Components 5.2.2 has been released, this is a minor update This update fixes some issues, and most notably stabilises the WebGL text system. They have updated a few of the demos to show off this feature:

2D to 3D Coordinates
MolGrabber 3D
PDB Ribbons

ChemDoodle mobile 1.4.1 is also now available from the App Store, the release notes include.

  • Support for the iPhone 5
  • IUPAC Naming
  • 3D coordinate generation and viewer
  • Added empirical formula to calculations
  • Added rotatable bond count to calculations
  • Added total electron count to calculations
  • Added vdW volume to calculations
  • Added complexity to calculations
  • Fixed slow performance issues on iPad in landscape mode
  • Fixed MolGrabber search issues
  • Fixed issue where the back button wouldn’t appear on the last help page
  • Fixed login issues
  • Performance improvements
  • General improvements and fixes



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OpenEye updates

OpenEye have announced updates to a couple of their products

OMEGA v2.5 is designed to produce high quality multi conformer databases.

Highlights from this release include: OpenMPI version 1.6 is supported on all platforms. The -mpinp and -mpihostfile flags are now used to run OMEGA and makefraglib in MPI mode. These new flags replace the oempirun script. PVM (parallel virtual machine) is no longer supported. An option has been added to allow hydrogen atoms in -OH, -SH, and amines to take part in conformational sampling. This new option can be enabled via the -sampleHydrogens parameter. By default, hydrogen atoms are not sampled. Now using -fixsmarts without -fixmol will rematch for every input structure. Previously, this would only match the first input structure and reuse that match for the rest of the calculation. Using both -fixsmarts and -fixmol will continue to match against the fixmol and use that match for the entire calculation.

EON v2.2. compares electrostatic potential maps of pre-aligned molecules and determines the Tanimoto measures for the comparison.

Highlights from this release include: OpenMPI version 1.6 is supported on all plafforms. The -mpinp and -mpihostfile flags are now used to run EON and makefraglib in MPI mode. These new flags replace the oempirun script. PVM (parallel virtual machine) is no longer supported. The default hitlist format has been changed from sdf to oeb for increased functionality and decreased filesize. The output format is adjustable with the -oformat parameter. Now SD tags are prefixed with EON_. The tags are optional with the -sdTags parameter. Additionally, any existing ROCS tags will not be removed because ROCS and EON tags no longer conflict



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