Dear Consortium Members and Affiliates,
Last month things were swinging, and activity in November continues unabated. But this month also ushers in the start of the holiday season in the US, which has combined with hurricane destruction and election mania to create plenty of distraction. We hope to help you keep your focus with an SBGrid Newsletter full of interesting tidbits and information on tools to keep your science moving forward.
We have recently expanded our Affiliate Job Postings page and now have open positions advertised from Lawrence Berkeley National Labs, UT Southwestern, Harvard Medical School, Biogen Idec, and the Okinawa Institute of Science and Technology. SBGrid Affiliates can post positions free of charge, so be sure to email Michelle Ottaviano with any new job opportunities you want to announce, and check back often to see the latest postings.
This month the SBGrid spotlight is on University of York Professor, Eleanor Dodson. Read about her dedication to collaboration and her involvement in the development of CCP4 in our November SBGrid Tale.
We had two successful webinars since our last publication. Ronan Keegan introduced the newest version of CCP4 and SBGrid's own Jason Key gave a primer on accessing the SBGrid computing clusters available for Schrodinger virtual screening. These presentations are included in our Webinar Archive and are available for playback. Don't forget to join us on Thursday, December 20th to learn about PiMS, a Protein Information Management System. A few of our SBGrid member labs have expressed an interest in this system and we are currently investigating options for hosting this application for SBGrid members.
Write to us! You can suggest future webinars, nominate PIs and developers to be interviewed for structural biology tales on the SBGrid website, refer new members or suggest how to further expand our support. Members can write directly to Michelle Ottaviano, our relationship associate, or contact us through firstname.lastname@example.org.
We are also now collecting nominations for the Annual SBGrid Software Award. SBGrid members may vote in our annual poll to select a favorite structural biology application. Paul Emsley won last year's award for his application Coot. The application of the year is chosen based on innovation, in terms of underlying software code, integration, user interface, and the frequency of use or impact on the structural biology community. If you would like to nominate your favorite application for this award, please complete the poll. Nominations from SBGrid members will be accepted until the end of November.
Buy your tickets to London today or stay in Europe after the Holidays! CCP4 would like to announce the CCP4 Study Weekend, which they will host on January 3-5, 2013 at the East Midlands Conference Centre at the University of Nottingham. This year's topic will be molecular replacement and will feature talks by leaders in the field. Associate Principal Scientist Giovanna Scapin of Merck will provide an overview of molecular replacement over the years; Thomas Terwilliger, of Los Alamos National Laboratory, will discuss approaches to enhance model building after using molecular replacement; and Piotr Sliz, of Harvard Medical School and SBGrid, will talk about using wide search molecular replacement in cases when no other approaches are feasible. In addition, the developers of Coot, Refmac, Phaser, Mosflm and many more CCP4 software packages will be giving lunchtime byte sessions where they will demonstrate the latest features and be available to help users with any problems or issues they might have.
To learn more or to register, please visit: http://www.cse.scitech.ac.uk/events/CCP4_2013/
We had two small software updates in the last month. On October 15th we pushed out the latest Schrodinger 2012-2 release and updated Swiss PDB-Viewer to version 4.1.0. We also introduced two new packages: GAMMA, a library for simulation of magnetic reasonance experiments and fpocket, a protein pocket detection tool.
The update on Novemeber 6th included Theseus 2.0.1, XMIPP 3.0 for OS X Intel and an update to HKL2000 version 704k. We again added two new packages, x3d and COMO. x3d is a tool for particle picking in cryo-electron micrographs. COMO is developed by Liang Tong at Columbia and is a tool for combined molecular replacement, which is a protocol to carry out a limited six-dimensional search, covering both the rotational and translational degrees of freedom. The combined approach can sharpen results of cross-rotation searches. COMO is the successor to the Tf/Replace package.
Notable Software Changes
Schrodinger Suite 2012 was updated to release 2, which includes several performance improvements. A full list of updates to the Maestro, Canvas and Core Hopping modules is available on the Schrodinger website. To request installation of the Schrodinger Suite on your computers please contact email@example.com.
SBGrid offers a dedicated computing cluster that can be accessed by all members of the Consortium. Please note that all users accessing Schrodinger software should join our dedicated mailing list and run more extensive computations on the SBGrid shared cluster, which will allow us to maximize access to the Consortium licenses.
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.