We're moving! SBGrid is in the midst of relocating its offices. It's only a short move to the building next door at 240 Longwood Ave, LHRRB, 2nd floor. So if you plan to pay us a visit, keep in mind that some of us have already settled in to the new space, while others will follow in the next few weeks.
We are pleased to announce the launch of our YouTube channel SBGridTV. We will use this outlet to publish recorded webinars and other useful information for SBGrid members and the greater structural biology community. We are still working out the kinks and need to improve the sound quality of the videos and upload more of the webinars from our series, but we hope this resource will provide you with improved access.
We had a good turnout for last week's webinar to hear Jim Procter, from the College of Life Sciences at University of Dundee, talk about Jalview. No webinar is scheduled for August, but please be sure to join us in September to learn more about SHELX-2013 from Andrea Thorn.
Schrodinger Molecular Modeling Suite 2013 was included in the most recent SBGrid software update. The new features and enhancements included in this release were described in a presentation by Woody Sherman, the Schrodinger Vice President for Applications Science, which can be accessed here. Please note that this application is primarily available only to North American, academic labs.
Mark Lemmon, Chair of the Dept of Biochemistry and Biophysics at the University of Pennsylvania Perelman School of Medicine, is the focus of our July Tale. Read about how he has returned to the topic of study he originally undertook as an undergraduate, with the hope that new technologies will make possible what was formerly unattainable.
We've had eight new members join since our last publication. Gregor Blaha has become our first representative from UC Riverside and the University of Zurich has become a bright spot on our member map with seven new members: Amedeo Caflisch, Raimund Dutzler, Martin Jinek, Ohad Medalia, Andreas Plueckthun, Markus Seeger, and Ben Schuler.
Welcome to our new members!
Our June 25th software update included the new versions of the following titles: XDS, Xplor-NIH, Schrodinger, CCPNMR, IPLT, PyMOL, HKL2000, Fiji, and ImageJ.
Notable Software Changes
XDS was modified to include more comprehensive support from multi-segment detectors.
The new version of xplor-NIH introduces dozens of new helper scripts, including a new tool called scriptMaker that provides graphical interfaces to generate xplor scripts. The xplor binary now supports single quotes on the command line and standard Python -c command-line options. Example scripts ub_strDet.py and filter_data.py can be used to switch to using a torsion database and to write out backaluated R2/R1 relaxation restraints. Dozens of Python and TCL interface options were also improved. For a comprehensive list of all above changes introduced in version 2.34, please visit the developer’s website: http://nmr.cit.nih.gov/xplor-nih/Changes.txt.
The incentive version of Pymol (available to all SBGrid labs) was updated to version 22.214.171.124. This new release introduces presets for coloring by representation (Color > C > by rep) and extensive settings documentation (Settings > Edit All GUI). Molecular morphing was further improved (A > generate > morph) and multi-state morphing is supported. The mouse wheel can also now scroll the object-menu-panel and other scrollable widgets. Additional updates include improved graphics performance and surface lighting, new commands (split_chains and mse2met), and several minor changes and fixes.
The Schrodinger 2013-1 release incorporates Maestro Graphical Interface improvements (e.g. a new task tree interface, new job starting and monitoring controls). A number of improvements and changes were also incorporated in bundled applications. Most notable changes: significantly improved coverage of QM-based method, a new covalent ligand docking method, better handling of ligand-metalloprotein interactions and intramolecular ligand H-bonds, a new induce fit scoring function, several improvements to functionality in protein refinement, and a new launch panel for PrimeX X-Ray refinement.
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.