Macs in Chemistry

Insanely Great Science

OEDocking v3.2 released

 

OpenEye have announced the release of OEDocking v3.2. This is an upgrade that adds new features and fixes several bugs.

NEW FEATURES

  • POSIT is now integrated with the OEDocking suite. A POSIT license is still required to run POSIT.
  • POSIT‘s clash detection algorithm has been enhanced. It now ignores clashes with the protein on a per atom basis if the crystallographic ligand makes these same clashes.
  • OpenMPI version 1.6 is now supported on all platforms. The -mpinp and -mpihostfile flags are now used to run FRED, HYBRID and POSIT in MPI mode. These new flags replace the oempirun script.
  • PDB2RECEPTOR now incorporates all of MAKEPOSERECEPTOR functionality. MAKEPOSERECEPTOR is no longer supported.
  • PDB2RECEPTOR now supports the identification and selection of a desired ligand in a protein-ligand complex.
  • MAKERECEPTOR, PDB2RECEPTOR, APOPDB2RECEPTOR, DOCKINGREPORT, RECEPTORSETUP and RECEPTORTOOLBOX now all accept either a POSIT or FRED2 license.

  • Support for Mac OS X 10.9 and 10.10 was added.

  • Mac OS X 10.6 and 10.7 are no longer supported.

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Tabula is awesome!

 

I recently needed to download the supplementary information provided with a publication, my heart sank when I saw it was provided as a PDF file. My worst fears were justified when I tried to simply copy and paste SMILES strings together with 5 columns of data into a spreadsheet, no chance of it copying across in an ordered manner!

Then I tried Tabula a tool for "liberating data tables locked inside PDF files". It worked perfectly, nearly 2000 rows of data spread over 11 pages converted to a csv file in a couple of mouse clicks. This is wonderful and should be part of any data scientists toolkit.

It is included on the Data Analysis Tools page but really deserves a special mention.


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Unicon and Mona

 

I've just added Unicon and Mona to the alphabetical listing of applications.

UNICON is a command-line tool to cope with common cheminformatics tasks. The functionality of UNICON ranges from file conversion between standard formats SDF, MOL2, SMILES, and PDB via the generation of 2D structure coordinates and 3D structures to the enumeration of tautomeric forms, protonation states and conformer ensemble.

Mona is an interactive tool that can be used to prepare and visualize large small-molecule datasets. A set centric workflow allows to intuitively handle hundred thousands of molecules.


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WEBMO VERSION 16 RELEASED

 

WebMO version 16

WebMO version 16 has been officially released and is available for FREE download at http://www.webmo.net/download

New features in WebMO version 16 include:

  • Support for both iOS and Android WebMO free apps
  • Support for the newest versions of ORCA, PSI, and Q-Chem
  • Support for hydrogen bonds in the WebMO editor
  • Improved support for building/cleanup of fused aromatic rings
  • Incorporation of modern HTML5 user interface elements including: drag-and-drop of jobs between folders, fewer pop-up windows, live updating of output files while jobs run, and expandable results page
  • Support for unlimited number of user folders and sub-folders (Pro)
  • Enhanced support for resource specification with external batch queues (Enterprise)
  • Various bug fixes

Important changes in the previous version include:

  • Java security warnings are reduced/eliminated with new signed applet
  • Support for the newest versions of GAMESS, MOPAC
  • Lookup feature to build structures by name (type "aspirin" or "vancomycin")
  • Links to external databases to lookup molecular properties, spectra, and data
  • Huckel molecular orbital calculations from within Build Molecule page (Pro)

WebMO is the most popular interface to computational chemistry programs, with over 22,000 unique WebMO licenses issued to date!

WEBMO iOS AND ANDROID APPS

WebMO has released a new Android app and updated its popular Apple iOS app!

The WebMO apps for portable devices are FREE.  

The Android and iOS WebMO apps provide equivalent features including:

  • Standalone molecular editing, optimization, symmetry, and orbital calculations
  • Integrated web lookup of molecular properties, spectra, and data
  • Access to WebMO servers (Free, Pro, and Enterprise versions of WebMO 16 and higher)

The WebMO apps supports all chemistry courses by calculating and displaying:

  • VSEPR structures for General Chemistry
  • 3-D structures to replace model kits for Organic Chemistry
  • Data and properties for Analytical Chemistry
  • Point group and symmetry elements for Inorganic Chemistry
  • Small proteins and bimolecules for Biochemistry
  • Molecular orbitals and vibrations for Physical Chemistry
  • WebMO calculations for undergraduate and graduate level Research

Thousands of students and scientists use the WebMO apps on their smartphones and tablets each month.  You can join them today for free!

WEBMO SUPPORTS CLOUD COMPUTING

More computational services are moving away from local hardware and into the "cloud".  Cloud computing requires zero upfront capital outlay, eliminates hardware maintenance, and can dramatically lower the cost of computing.

WebMO now supports installation on cloud computing platforms.  In less than 10 minutes, you can use your web browser to create a virtual machine, run the WebMO SITC ("Server in the Cloud") script, and have a functioning WebMO 16 server.

The cost of a WebMO cloud server can be amazingly low: <$1 per day for a WebMO server capable of running jobs on standard ab initio chemistry engines, and just $0.12 per day for a WebMO server running MOPAC!  And when you don't need it, you just turn it off.

Complete documentation is available at http://www.webmo.net/cloud/sitc.html

Since Google Compute Engines are free for the first 60 days, so there is no cost or risk to try cloud computing today.


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BBEdit 11.5

 

BBEdit 11.5 has been released.

BBEdit 11.5 adds a variety of new features, and includes changes to existing features and behaviors as well as fixes for reported issues.

Of particular note are

BBEdit now supports the use of iCloud Drive for sharing application support and setup items. This works similarly to the existing Dropbox support: in your "iCloud Drive" folder, create a folder named "Application Support", and then within that create a folder named "BBEdit". You can populate that folder with the contents of your /Users/USERNAME/Library/Application Support/BBEdit/ folder.

BBEdit now supports the use of iCloud Drive for a shared backup folder: in your "iCloud Drive" folder, create a folder named "BBEdit Backups", and if you have turned on Use Historical Backups, BBEdit will use this folder.


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