Dear Consortium Members and Affiliates,
I'm writing this update as I watch the snow fly with the hope that we'll be done digging out by the time this lands in your inbox. In keeping with the season, we have a blizzard of news to relay to you.
A reminder to our members that staff, post-docs, and students in SBGrid labs can access specialized computing resources via an SBGrid Consortium UNIX account. Resources include a 100-core computation cluster configured for Schrodinger jobs, dedicated GPU hardware for scientific applications, and the SHARP/autoSHARP web application. Other resources are likely to be available in the future and we are eager to hear your suggestions about resources that would be valuable to you. Users that wish to set up an SBGrid Consortium UNIX account should email email@example.com.
Hopefully many of you joined us for the recent Chimera webinar presented by Tom Goddard. If you missed the live presentation, please remember you can watch past webinars posted in our Webinar Archive. Up next will be a presentation from PyMOL developer Thomas Holder on March 7th at 1:00pm EST, which will be followed, on April 18th, by a seminar on the new automated data reduction system XIA2.
Be sure to read this month's SBGrid Tale, featuring member PI Wes Sundquist, to learn about the rich structural biology environment that has been established at the University of Utah over the past two decades.
Registration for the PyMOL Minicourse at Harvard Medical School will remain open until February 15th. Selected applicants will be notified by e-mail by February 18th.
Upcoming Structural Biology Conferences
The New England Structural Biology Association has announced that registration is open for the upcoming meeting "Protein Misfolding and Rare Genetic Diseases: From Human Genetics to Drug Discovery" to be held at Bentley College in Massachusetts on March 29th. Follow these links to register or for more information on sponsorship opportunities.
The 11th annual Analytical Ultracentrifugation and UltraScan workshop is scheduled for May 29th - June 4th 2013 at the University of Texas Health Science Center in San Antonio. With only 20 seats a available on a first-come, first-served basis, please be sure to secure your seat and register without delay.
Registration is still open for the West Coast Protein Crystallography Workshop being held in Monterey, CA from March 17th-20th.
The Keystone Meeting on Structural Analysis of Supramolecular Assemblies by Hybrid Methods kicks off March 3rd in Lake Tahoe, CA and will include a workshop on the"Reproducibility and Publishing of Hybrid Models", with a panel discussion on hybrid-computational methods intended to define a set of best practices for reporting research.
The software update on January 29th included new versions of Xplor-NIH, EMAN2, OpenBabel, GROMACS, NMRPipe, DSSP and CONCOORD as well as CCP4 patch releases 13, 14, 15 and 16, a few updated SHELX binaries, and for labs with a license, the latest versions of d*TREK for both Linux and OS X. Tim Gruene has renamed his MRPREP tool to MRTAILOR, and we incorporated the latest version of that tool as well. You can now choose to use the "nightly" version of EMAN2 with a version override.
Notable Software Changes
The new version of NIH-XPLOR features new utilities, including contactMap, a helper script to visualize molecular contacts, and ramaStrip, a script to help with a quick visual evaluation of Ramachandran scores for many structures.
Molrep, in CCP4, features a significantly more accurate packing function.
The data reduction application, d*TREK version 184.108.40.206 was relased with improved algorithms for spot finding, integration, and scaling.
Open Babel version 2.3.2, the open source chemistry toolbox, provides better support for unknown stereochemistry, direct 2D depiction to PNG files, and several other improvements and functionality enhancements.
Gromacs version 4.6 includes new free energy sampling techniques, “rotational pulling”, a Verlet non-bonded energy scheme, and several performance improvements.
This month we are welcoming four new members to SBGrid: Andre Yudin joins a large contingent from the University of Toronto, Michael Sattler becomes our third member from the Institute of Structural Biology in Germany, and we have two new institues represented by Michael Nilges at Institut Pasteur and Brian Zoltowski at Southern Methodist University.
Welcome to our new members!
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.