Dear Consortium Members and Affiliates,
It's April in New England and after a week of tragedy and drama all around us, we're eager for some humdrum routine, with plans to dodge some raindrops and fight off the fever of spring that lures us from our desks. In this month's update we have several interesting bits of news to pass along.
SHELX-2013 was recently released and requires registration for inclusion in your SBGrid software suite. If you would like this application included in your installation, please register on the SHELX website (http://shelx.uni-ac.gwdg.de/SHELX/register.php) then send your registration confirmation to us at email@example.com.
If you missed the xia2 webinar presented by Graeme Winter or Paul Sanschagrin's recent webinar demonstrating our new docking and fingerprint tools, you can find the links to replay these presentations on our webinar archive.
To complement the docking tools described in Paul's webinar, we now have LigPrep'd versions of the commercially-available compounds found in the ZINC free database. The in-stock subsets of these compounds reside on the SBGrid cluster and can be found in /programs/local/databases/zinc-ligprep/
Next up on the webinar front is a presentation by Steven Lewis of the Richardson Lab at Duke on May 16th at 11:00am EST. He will introduce the application "ERRASER for RNA structure error correction." Our website posting includes more information on ERRASER and how to join the webinar.
Be sure to check out our April SBGrid Tale featuring Stephen Harrison, with a look at how computing has changed during his career, both limiting and expanding the scope of his research.
We've also just added a new position posting from Genzyme. Check out this advertisement and others posted on our Member Job Postings page.
The March 20th software update included new versions of PHENIX, XIA2, CCP4mg, 3DNA, CCP4 updates p18 and p19, as well as two new applications: Fiji and istHMS.
Notable Software Changes
CCP4MG (Molecular Graphics) is used to prepare images and movies of macromolecules. This application provides a slick and intuitive interface and several tutorials are available on the CCP4MG website. Release 2.7.2 improved OpenGL support (e.g. better shadows and performance fixes) and it fixed the undo/redo option and problems with starting up COOT/refmac from within CCP4MG. Dozens of other minor changes were also included.
3DNA package added a new module: Defining Secondary Structures of RNA (DSSR). PDB coordinates can now be searched for canonical and noncanonical Watson-Crick base pairs, triplets, quadruplets, and higher order structures. Please visit the 3DNA website for more details.
CCP4 was upgraded to release p019. Most notably, this upgrade improved the molrep molecular replacement scoring system. In addition, the applications Gesant and Superpose can now print superimposition matrices in fractional coordinates.
Phenix was upgraded to the nightly release 1320 and includes a new automatic search for elemental ions (e.g. Mg, Cl, Ca, Zn, etc). This search option works best with anomalous data for which users can provide an explicit list of atoms to search.
An application using an Iterative Soft Threshold algorithm was developed by Sven Hyberts at Harvard Medical School: ist@HMS. This application uses a poisson gap sampling method to perform forward maximum entropy reconstructions. According to the Wagner lab, this new approach results in fewer artifacts.
We have added a new software package, Fiji, which enhances ImageJ by improving the menu structure and adding extensive documentation. Dozens of Fiji tutorials are available on the Fiji website.
Please note that not all software applications are available to every SBGrid member type. If you see an application that you would like to use, but is not included in your software tree, please contact us to find out what options are available for access.