Consortium Update for May

Dear Consortium Members and Affiliates,

May has arrived and our Boston spring has been a beautiful one. We now await the end of the school year, when our streets and sidewalks are fleetingly empty, after the students depart and before the summertime tourists arrive. Before we indulge in this brief respite, we have several bits of news to pass along.

We have 4 active positions from SBGrid member labs on our Job Postings page. Please take a look here if you are considering a change, or send us (help@sbgrid.org) your position description if you have an opportunity to advertise.

For those of you that are moving on to an independent position, please remember that SBGrid has a special program for Jr. Investigators to offer help determining your computing needs in your new environment. If you are preparing to set up shop, please contact us for a complimentary consultation.

Last week Jane Richardson and Steven Lewis gave SBGrid members a primer on ERRASER, for RNA structure error correction. If you missed the presentation, you can access the playback link here. In June we will hear from Jan Brezovsky of Loschmidt Laboratories about the Analysis of Tunnels in Static and Dynamic Protein Structures using CAVER 3.0.

Borden Lacy, from Vanderbilt University, is the subject of our May SBGrid Tale. Read her story on our website and learn about some of the obstacles involved when working with high risk toxins.

Software Update

Software updates were pushed on April 23rd and May 14th. These updates included new versions of ATSAS, Coot, CCP4, CCP4mg, CS-Rosetta, FREALIGN, MAFFT, PROTOMO , PyMOL, Phenix, Bsoft, and em2em.

A reminder that SHELX-2007 has been replaced by the new version: SHELX-2013. As of July 1 we will no longer actively support the old version. If you want SHELX 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 help@sbgrid.org. As with all of our software applications, we maintain a copy of old versions that can be made available if you need to reprocess data.

Notable Software Changes

A major PyMOL update has been installed. In this new version performance is significantly improved, in some cases boosting efficiency as much as tenfold. Additional changes include the introduction of surface color smoothing and an expanded undo command.

We would like to remind you that SBGrid members have access to a special, incentive version of PyMOL. Some of the special features in this release include access to incentive documentation that comprehensively describes PyMOL's features and updates and includes narrated screencasts and step-by-step tutorials, direct export of QuickTime movies (Mac only), and built-in MTZ map reading. This special documentation is available in the PyMOL Incentive User Area. To access this section, request a login from help@schrodinger.com and mention that you are an SBGrid Consortium member. We also have a recorded webinar highlighting some of these special features that can be accessed on the SBGrid Webinar Archive.

CCP4MG, a molecular graphics application, was updated to version 2.7.3. Changes include a minor fix in drawing of text labels and improvements in the screen capture utility.

ATSAS, an EMBL suite of applications for small-angle scattering data analysis, has been upgraded to version 2.5.1. Minor fixes have been applied to several programs in the suite.

Electron Microscopy:
Frealign has been upgraded to version 8.11. New features include implementation of a single particle Wiener filter and B-factor correction of the final output map.
Changes in Bsoft, a collection of programs used in electron microscopy, include new threading algorithm in the watershed function (bflood application) and fixes in secondary structure parsing and writing routines.
em2em, a program to convert between different formats of 2-D images and 3-D volumes, has been upgraded to the latest April 2013 release. This new version incorporates support for JPEG images and can automatically detect MRC file formats.

New Members

Andre H-J Wang is our newest member, becoming the third lab from Academia Sinica to join SBGrid.

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.