Newsletter

Dear Consortium Members and Affiliates,

With this Thanksgiving edition of the SBGrid newsletter, we'll begin with thanks to our members, whose support helped us secure a Helmsley Foundation grant award. THANK YOU! Also this month we've scheduled an ad hoc XFEL webinar, posted a new webinar on our YouTube channel, hosted an SBGrid-Schrodinger Working Group, profiled SBGrid member Kevin Corbett, pushed out a software release with 14 updates and 4 new titles, announced 2 new job postings, welcomed new members, and highlighted a few member publications.

We are pleased to announce that we recently received a grant award from the Helmsley Charitable Trust to support our new initiative - the Structural Biology Data Grid - for storing and publishing X-ray diffraction datasets (data.sbgrid.org). Thank you for your overwhelming support and eager participation in our pilot project. Read more about our initiative here (https://hms.harvard.edu/news/dropbox-structural-biologists) and please help us show our sponsor that their funds are being put to good use and deposit your diffraction datasets, new or old, previously reported or pending publication. Data deposition is quick and painless.

We've scheduled an ad hoc webinar for Monday, November 30th at 12pm EST featuring Filipe Maia from Uppsala University, who will speak about the burgeoning field of XFEL crystallography. Local members can join us onsite at SGM106 while others can connect to the live webinar. Connection details.

If you missed this week's webinar on DIALS, with speaker Graeme Winter, you can watch the recorded version on SBGrid's YouTube channel. Due to an unexpected conflict, we've had to cancel Ivet Bahar's ProDy webinar scheduled for December, but hope to get her added to the roster in the spring. Our webinar series will resume in January.

The second SBGrid-Schrodinger Working Group met last week for a fruitful discussion on Schrodinger's Docking Tools and Virtual Screening options. Our next meeting is scheduled for January 12th and will focus on the role of water molecules in protein preparation, docking, and scoring. If you haven't yet joined the working group, but would like to do so, please email Michelle Ottaviano.

Our November member tale spotlight is aimed at Kevin Corbett and his group at the Ludwig Institute for Cancer Research, UC Berkeley. Corbett describes donning his first pair of 3D glasses in a graduate school interview that set his sights on structural biology. Read more on his history and his vision for future studies to solve Spo11.

This month's software release includes updates to ALBULA, autoPROC, BUSTER, CCP4, Coot, CTFFind 4, Haddock, HKL2000, ilastik, R, relax, Rosetta, SamViewer, and Schrodinger. We also pushed out four new titles: CAVER Analyst, H5TOXDS, RStudio, and WebLogo.

Take a look at recent additions to our job postings page, with a call for a Senior Fellow or an entry level Scientist in the Department of Cancer Immunology and Virology at Dana-Farber Cancer Institute. Here at SBGrid we're also seeking a Data Management Software Developer for work on our Structural Biology Data Grid Project. Read more.

This month we welcome new members Jasim Al-Rawi from La Trobe University, who brings our Australian contingent to six, and Sebastien Granier from the Institut de Génomique Fonctionnelle in Montpellier France. We also welcome many new members from the Novartis Institutes for Biomedical Research, as we expand to provide global support for NIBR at sites in Basel Switzerland, Emeryville and LaJolla CA USA, Shanghai China, and Singapore. Welcome to our newest members!´

Member Publications

For the month of November, SBGrid received 2 new citations in member publications, one from Katya Helwein's group at Tuft's University reporting on the the Crystal Structure of the Human Cytomegalovirus Glycoprotein B and another from Rockefeller's Roderick MacKinnon on Cryo-electron microscopy structure of the Slo2.2 Na+-activated K+ channel.

Over 38 publications from SBGrid member laboratories have appeared in journals since our last newsletter. You can find a full listing on the Member Publications page of the SBGrid website. Here are some notable highlights:

• For some history on the mathematical concepts and computational approaches used in single particle cryo-EM, check out Joachim Frank's review that appeared this month in the journal Microscopy. Microscopy 2015.
• Two new studies on CRISPR-CAS9, both from Jennifer Doudna's laboratory at UC Berkeley, give us a new understanding of the "proofreading" system used when editing (Nature) and the dynamics of how the Cas9 protein moves through the cell and searches DNA (Science).
• Brandt Eichman's group at Vanderbilt University offer new insight into DNA repair in their article appearing in Nature this month. They describe an alternative pathway to DNA repair that takes place without base flipping in the glycosylase AlkD. Nature. 2015 527:254-8".
• From our undergraduate desk: Harvard Medical School student Kristen Rodrigues chose to highlight an article that appeared in the journal Vaccine from Ethan Settembre's group at Novartis Vaccines. Settembre reports on a new, more time-efficient method of isolating active HA molecules that could help speed the development of effective flu vaccines. Read about this and more on tumblr

If you're currently preparing a manuscript, please remember to follow our X-ray dataset publication guidelines to archive and publish your data along with the PDB record and journal publication. Also, please remember to cite our eLife publication (eLife 2013;2:e01456) for all projects completed with SBGrid compiled software.

Software Changes

ALBULA version 3.1.0-13 now includes an option to collect data with EIGER detectors in a simple and intuitive way.

autoPROC version 20150923 introduces the parameter autoPROC_PointlessTolerance, improves handling of inhouse (CuKa-wavlenegth) datasets when generating predictions, corrects MRFANA computations of completeness and stablizes automatic decision making about adequate high-resolution limits with use of the Bezier curve to test cutoff-criteria.

BUSTER version 20150923 fixes a a couple of MakeLINK bugs.

Note: autoPROC and BUSTER are included in the default software installation but require a license from Global Phasing for activation. Copy your license file to /programs/local/buster/autoproc_licence or /programs/local/buster/buster_licence, respectively, and the software will start working. Academic members can register for a free license on the autoPROC and BUSTER websites.

CAVER Analyst version 1.0 is new to the SBGrid install from Jiří Damborský's group. CAVER Analyst offers an intuitive GUI to calculate, analyze, and visualize in real-time the access tunnels and channels in static and dynamic protein structures.

CCP4, now at version 6.5.019 includes a number of bug fixes and updates along with a new feature in aimless to accept XDS misfits

Coot was updated to version 0.8.3-pre-revision-5722 (Linux only). With this update you'll see a dictionary-based atom name match in pyrogen, an option for ligand fragment flipping, that HOLE now exports surface points, a new map-statistics function, and that global translations towards the molecule centre were removed on model morphing. You'll also benefit from a number of bug fixes.

CTFFIND 4 version 4.0.16 includes a new command-line option, --fast, to spend less time on diagnostic output and save compute time. You'll also notice more and faster low-level optimizations and more robust background subtraction.

H5TOXDS version 1.1.0 was added to the SBGrid collection (Linux only). This tool is used by XDS to process EIGER HDF5 data.

HADDOCK version 2.2. With this version HADDOCK is compatible with CNS 1.3, which no longer wild cards in linkage files for topmar. Accordingly, all linkages are specified explicitly and only three character residues are used. You can now also mix molecule types within one molecule and utilize S3 and C4 symmetry restraints.

HKL2000 release 708c was pushed out. This release includes a Bruker format update, a resolution display for scaled datasets widgets on the project page, and a new refine option on the integration page.

ilastik version 1.1.7 includes major changes to the front and back ends of the application. Users are no longer limited by their machine's RAM during pixel classification since computations are cached and the older caches are discarded when the memory limit gets close. The Carving preprocessing interface was also simplified and objects are now segmented separately to improve speed. Also new are four new workflows: object classification, automatic tracking based on the Conservation tracking algorithm, manual tracking, and count allows users to count objects in crowded scenes.

R version 3.2.2 (code name: fire safety). This version enables package installation via HTTPS.

relax version 4.0.0 introduces a new analysis type labelled 'frame order' for studying rigid body motions. The frame order theory aims to unify all rotational molecular physics data sources via a single mechanical model and can be used for analyzing RDC and PCS data from internally aligned systems.

Rosetta 2015.38 is a weekly build that fixes some bugs in PHENIX-ERRASER.

RStudio version 0.99.473 was added for Linux CentOS7 and Mac OSX. RStudio is an integrated development environment (IDE) for R that includes a console and syntax-highlighting editor that supports direct code execution, as well as tools for plotting, history, debugging, and workspace management.

SamViewer was updated to version 15.01.

Schrodinger version 2015-4 includes overall improvements in speed and usability.

WebLogo version 3.4 was also added to the SBGrid collection. WebLogo is a command line tools for sequence logo generation.

^{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.}