Dear Consortium Members and Affiliates,
One month into 2018 and it's time for an update on SBGrid activities. Read on for details about our plan to remove large software titles from the default installation, a new lineup of webinars running from February through May, a story on SBGrid member Seth Darst, a listing of open positions in SBGrid member labs, details on the latest software updates, one new member to welcome, and three member publication highlights.
We're modifying our default software installation to reduce the size and avoid overloading servers at some of our member institutions. By not installing these more specialized, heavy-weight applications, we can save 99Gb of space (20% of the total size) for those with a combined Mac/Linux collection. SBGrid will still support these applications, and they can be added back to site installations upon request. To continue receiving one or all of the following titles, please email us by March 1 at accounts@sbgrid.org:
ACEMD ilastik
AmberTools Pomona
Anaconda Pyrosetta
CSRosetta
We've got a new lineup of webinars for the new year and will kick things off February 27th with a presentation from Debora Marks of Harvard Medical School on EVcouplings, a tool for predicting protein structure, function, and mutations using evolutionary sequence covariation. Full details on our website. Mark your calendar for this and other upcoming dates:
- February 27, 2018: EVcouplings - Debora Marks
- March 27, 2018: Cryo-EM in the Cloud - Michael Cianfrocco
- April 3, 2018: NMRFAM-Sparky - Woonghee Lee
- May: PLUMED - Giovanni Bussi
For our January member tale, we connected with Seth Darst from Rockefeller University. Darst describes how he relies on his musician's sense to see parallels in the rhythms of music and science, recognizing that the spaces between notes, like the pauses in gene transcription, are as important as the notes themselves. Read the full story.
You can read about the latest open positions in SBGrid members labs on our Position Postings Page. If you'd like us to include a new opportunity available in your lab, please email Michelle.
Our January software push includes updates to autoPROC, BUSTER, CCP4, HKL2000, MotionCor2, NMRFAM-Sparky, Phenix, Schrodinger, and SHELX, along with one new title: LocScale.
We had one new member join in the new year: Yang Li from Surrozen, Inc. Welcome to our newest member!
Member Publications
If you're currently preparing a manuscript, please remember to follow our X-ray dataset publication guidelines to archive and publish your data in the SBGrid Data Bank along with the PDB record deposit and journal publication. Also, please remember to cite our eLife publication (eLife 2013;2:e01456) for all projects completed with SBGrid compiled software.
SBGrid's eLife paper got 5 new citations in January. Many thanks to those who remembered to give us a mention: Jason McLellan at Dartmouth [Abstract], Dana Lord at Sanofi-Genzyme [Abstract], Andrew McCarthy at EMBL Grenoble [Abstract], Holger Sondermann at Cornell [Abstract], and Titus Boggon at Yale School of Medicine [Abstract].
Over 70 member publications appeared in January journals. You can find a complete listing on our website, along with a couple of notable highlights below:
- Published in Virology Journal is a new paper from Lawrence J. Stern of the University of Massachusetts Medical School evaluating a more time and cost effective method of measuring human herpesvirus 6B infection. Using an imaging-based automated cell counter, a cell size-based approach is explored and proves to be a fast, easy, and hopeful alternative for executing and achieving quick preliminary test results [Abstract].
- La Trobe University's Begoña Heras has a new publication in Acta Crystallographica this month, investigating the bacteria membrane protein DsbD. Since DsbD is a reductase found to be crucial to the survival of the Gram-negative bacterium Neisseria meningitidis, the authors strive, through biophysical & crystallization studies of DsbD's two periplasmic domains, to determine the structural and functional components of DsbD and thus potentially disrupt the viability of N. meningitidis to cause meningitis & other forms of meningococcal disease in humans. [Abstract].
- From our undergraduate desk: Harvard student Kristen Rodrigues recently highlighted a Cell Reports publication from the laboratory of Nenad Ban at ETH Zurich. Using cryo-EM, Ban's group determined the complete M. smegmatis 70S ribosome structure, visualizing two additional ribosomal proteins and suggesting new possibilities for tuberculosis drug targets. [More on Tumblr].
Software Changes
autoPROC version 20171219 includes fixes to automatic determination of non-shadowed image ranges (when re-doing initial background determination), better handling of warning messages regarding image headers, and for synchronization of parameters SEPMIN and CLUSTER_RADIUS relevant for indexing via XDS/IDXREF - the Pilatus detector now uses the same values as Eiger images (SEPMIN=4 and CLUSTER_RADIUS=2), which should help indexing very dense diffraction patterns.
BUSTER version 20171219 has many fixes and improvements to Pipedream, which now incorporates use of both pepflip and SideAide into the refinement procedure.
CCP4 is now at version 7.0.050. For a full listing of changes, refer to these release notes.
HKL2000 716.1 can handle data collected using the new Eiger 16M detector at the Shanghai Synchrotron Research Facility, beamline 17U1.
LocScale version 0.1 is new to SBGrid. LocScale uses rotationally averaged reference amplitudes from a refined atomic model to locally scale (sharpen) amplitudes of the Fourier transform of a cryo-EM potential map, keeping the phases constant.
MotionCor2 is now at version 1.0.4.
NMRFAM-Sparky was updated to the latest release 20180104 with improvements to PINE/PINE-SPARKY 2, new Hydrophobic core and flexibility detection in PINE-SPARKY 2. You'll also notice new sequence entry integration for automated tools, more available colors, labels moved to peak centers, fixes to the dummy graph/Pine graph assigner, explicit buttons in the strip plot, a new completeness counter, and an improved APES peak picker.
Phenix is now at version 1.13-2998. Improvements include better symmetry support and improved runtime efficiency in phenix.map_to_model, structural library and internal support for mmCIF in phenix.structure_search, an option to limit ligand size for search in phenix.ligand_identification, bug fixes in Phaser 2.8.1, and more and improved validation information (ligands, waters, cis/trans peptides, HIS protonation) in Structure Comparison.
Schrodinger version 2017-4 was pushed out. Check their website for a listing of new features.
SHELX was updated to version 2018-1 and includes improvements to the SHELXE chain tracing algorithms, which now work better at low resolution. SHELXL also saw improvement, with fixes to SAME_XYZ residue use and the use of chain-IDs with SAME.
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.