Dear Consortium Members and Affiliates,
It's time for the final installment of this year's SBGrid newsletter. As we say goodbye to 2012 and wish everyone Happy Holidays, we now have a dedicated 64-bit software branch, 2 software updates, a webinar reminder, a look at the history of CCP4, the SBGrid holiday schedule, and other interesting tidbits to bring to your attention. Please read on for full details.
SBGrid offices will be closed from December 24th through January 1st in accordance with the Harvard holiday schedule. We will attend to emergencies, but the small stuff will be on hold for a week. Please be sure to contact us before the 24th with any questions or concerns.
We present a brief history of CCP4 in this month's SBGrid Tale. Read about the origins of this mainstay in the crystallography software community and learn what future directions it will take.
Our Affiliate Job Postings page has been very active this past month, so be sure to take a look at all of the interesting opportunities available in member laboratories.
December's webinar will be presented by Chris Morris on Thursday, December 20th. Join us then 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.
Over the last 12 months, we have been working to add a dedicated 64-bit software branch for Linux machines, and that work is now complete. If you only have 64-bit workstations, you can save about 80 gigabytes of disk space on your server by removing the 32-bit software branch. If you want to remove the 32-bit Linux software branch from your installation, please email email@example.com with the request and include the installation name found in /programs/share/sitename.
November software updates included PHENIX nightly version dev-1208, Jalview 2.8, XIA2 0.3.5.0, CCP4 6.3.0 update 9, LigPlot+ 1.42, PyTom 0.932, 3DNA 2.1beta from 20121126, Caver 3.0 beta 4 and Rasmol 2.7.5.
Notable Software Changes
Jalview supports interactive editing, analysis and visualization of multiple sequence alignments. Version 2.8 incorporates RNA visualization features developed by Lauren Lui and Jan Engelhart during their Google Summer of Code projects. For the full listing of changes, bug fixes and new features please visit the website.
The new version of mafft supports RNA structural alignments as well as protein/DNA/RNA sequence alignments.
CAVER, a tool for analysis of transport pathways in protein structures, was updated to the most recent release. A detailed description of this application is included in a recent paper published in PLoS Computational Biology.
The PHENIX update improved hydrogen covalent bond length and vdW radii parameters for protein and nucleic acid geometry restraints for X-ray refinement.
CCP4 version 6.3.0 was updated and includes mostly small fixes. A new results viewer, QTRView, was added. We unsure how this new utility works, but are following up with the CCP4 group for more information.
Xia2 is an automated X-ray crystallography data reduction application that interfaces with XDS and mosflm. The new release offers several bug fixes. Usage instructions are available on the application website.
3DNA, a suite of software programs for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures, was updated with a nightly release. Other applications in this category include RCrane (COOT plugin developed in Anna Pyle's lab at Yale) and Enumerative Real-space Refinement ASsisted by Electron density included in Rosetta (ERRASER).
For EM laboratories:
PyTom, a cryo electron tomography toolbox, was updated to version 0.932.
We had five new members join during the past month. Three of our new members represent institues new to the Consortium: Jochen Zimmer from University of Virginia School of Medicine, Jose-Maria Carazo from Centro Nacional de Biotecnologia in Spain, and Keith Miller from Massachusetts General Hospital. The other two members hail from veteran institutes: Uhn-Soo Choo became our 5th University of Michigan lab, and Kenneth Westover the 10th from UT Southwestern.
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.