Dear Consortium Members and Affiliates,
September has passed in a blink and we're again sending an update, with news on recent improvements to our website, a new webinar lineup, a look at SBGrid-member Sébastien Granier, position postings in member labs, the latest software updates and a note about Mac High Sierra, new members to welcome, and a few member publication highlights.
We've made lots of improvements to our website that we hope you will find useful: a new list of recent software updates on our home page that let's you see when new software is added or updates are pushed out, a revamped listing of Supported Applications, with a new title/developer search function, an option to filter by keyword, and a redesign for individual software titles that includes more information on available versions along with links to relevant webinars and developer tales. Check out these listings for Phenix and CCP4 for a sample.
Our webinar lineup for the new academic season is coming together nicely. Mark your calendars to join us and hear about:
- SPHIRE - October 3, 2017 - with Toshio Moriya: SPHIRE: User-friendly pipeline for near-atomic resolution Cryo-EM structure determination with automatic validation mechanisms. Details here
- EMAN2 - November 14, 2017 - with Steven Ludtke
- NMRPipe - December 5, 2017 - with Frank Delaglio: Concepts in Spectral Processing of Conventional and Non-Uniformly Sampled NMR Data.
- NMRPipe - December 12, 2017 - with Frank Delaglio: Processing of Conventional and Non-Uniformly Sampled NMR Data with NMRPipe.
- SIMPLE - January 2018 - with Hans Elmund
- ORCA - February 2018 - with Frank Neese
For our September member tale we caught up with Sébastien Granier at the Institut de Génomique Fonctionnelle in Montpellier France where he continues his long-standing focus on GPCRs (they first caught his eye as an undergraduate student) and is extending his work to look at adiponectin receptors. Read the full story.
Don't forget to check out our listing of open positions in SBGrid member labs, and if you'd like to include a position posting for your lab, please email Michelle. [Job Postings Page].
Software updates in September include new versions of autoPROC, BUSTER, CCP4, PHENIX, RELION, Rosetta, and XDS. Full details in the software changes section below.
Also note that Mac 10.13 High Sierra is just out and includes a new file system. We haven't yet tested this latest release and don't recommend upgrading until we have some time to test things out. If you've upgraded already please let us know if something breaks or if things are sailing along smoothly.
September brings us three new members: Michael Holtzman from Washington University St. Louis and from the University of Virginia, Barbie Ganser-Pornillos and Owen Pornillos. Welcome to our newest members!
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 Structural Biology Data Grid 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 received three new citations in the month of September: Titus Boggon at Yale U School of Medicine in Nature Communications [Absract], Karen Anderson also from Yale School of Medicine in PNAS [Abstract], and our friends at Lawrence Berkeley and Argonne National Labs in PeerJ [Abstract].
Our publications search is on the fritz and only returned a small sampling of our members' publications for September. We'll work on getting that fixed, but in the meantime, take a look at our imperfect listing of Member Publications and a few notable highlights:
- Appearing in Nature this month is a new publication from Harvard Medical School investigator Maofu Liao, which examines the lipid flippase lipopolysaccharide and MsbA-mediated transport. [Abstract].
- Chris Hill's group at the University of Utah has a new publication in eLife that reports unexpected findings of SH2 recruitment of Spt6 to transcription sites. [Abstract].
- From our undergraduate desk: Harvard student Kristen Rodrigues chose to highlight a publication in Science Advances from Jennifer Doudna's group at the University of California, Berkeley, which looks at the Cas9 inhibitor AcrIIA4 and found that it doesn't bind directly to Cas9, but only to Cas9-sgRNA complexes. [More on Tumblr].
Software Changes
autoPROC version 20170920 is now in the tree.
BUSTER version 20170920 was pushed out.
CCP4 version 7.0.044 is out with a new coiled coil mode in arcimboldo-lite, a fix for switching between hklin files with F and I in CCP4i; a fix for the enantiomorphic spacegroup issue in crank2; a new libg semi-automated search mode, new CCP4i2 compatibility added in lorestr; and improvements to SAPTF in molrep.
The PHENIX nightly build 1.12-2829-c5 was pushed for Linux. This updates includes several new tools (phenix.secondary_ structure_validation, Structure Comparison, phenix.mtriage, phenix.real_space_diff_map); improvements to sharpening algorithms in phenix.auto_sharpen; iterative maps in phenix.map_to_model; individual mapping in phenix.map_to_object; and outlier rejection in ssm-rmsd calculation in phenix.find_alt_orig_ sym_mate. You'll notice that secondary structure restraints use angles for restraining hydrogen bonds; a new user-defined box in phenix.polder in addition to atom selection; an option for different restraints for different copies of the same ligand in the same model; better control of peptide planes and omega angles; faster calculation of clashscore; and improved handling of cis-peptides in ramalyze.
RELION 2.1.b1 was pushed out to fix a critical bug affecting half-set (gold-standard) refinement.
Rosetta was patched to account for phosphorylated residues.
XDS version 20170923 is out. Since our last update you'll find a fix in the COLSPOT step that sometimes refused too many weak spots, an input parameter CLUSTER_NODES that accepts 2048 characters for naming the nodes of the cluster, a modified forkxds shell script that uses the full path names of the invoked executables, a check that forbids negative values for the input parameter MINIMUM_VALID_PIXEL_VALUE, and a new error message that warns of incomplete parameter specification of multi-segment detectors that will prevent XDS from collapse at later stages of processing.
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.