Dear Consortium Members and Affiliates,
As we return from the Thanksgiving Holiday and turn our attention to the remaining weeks of 2016, we'd like to put in a plug for our new software installer, remind everyone to deposit their X-ray diffraction datasets in the SBGrid Data Bank, mark your calendar for next week's webinar, share a story about SBGrid member Jochen Zimmer, give details on our latest software update, welcome four new members, and highlight a few member publications.
Do you have a Top Ten list for structural biology software? Do you wish SBGrid could install and maintain a personalized list of essential software titles on your laptop? We can! Our new software installer allows users to cherry-pick their preferred applications or install the whole collection and manage new additions and updates from a simple graphical-user (Mac) or command-line (Mac or Linux) interface. Email us at firstname.lastname@example.org to register for the installer.
Please don't forget to deposit your X-ray diffraction datasets in the SBGrid Data Bank. Our collection is growing and we now have almost 300 publicly available datasets from 66 different institutions available for download. Please contribute your datasets to protect your data and support community efforts to reprocess and validate existing structures to improve existing models and help develop more advanced software.
Join us Tuesday the 6th for our December webinar featuring Abhishek Singharoy from the Beckman Institute and University of Illinois at Urbana Champaign. Dr. Singharoy will talk about the xMDFF approach and "Structure Determination of a Cell Organelle with a Computational Microscope." You can also watch the recording of our October webinar, with Willy Wriggers giving a tutorial on Sculptor, on the SBGridTV YouTube channel.
For our November member tale we talked to Jochen Zimmer at the University of Virginia. Read our webtale to learn about his work focused on understanding how cells build and secrete polysaccharides and the snapshots he is using to make a movie of the action in membrane transport.
This month's software release included two new titles - Gwyddion and Timescapes - and updates to 19 software applications: adxv, Ambertools, Buster, CCP4, Chimera, Coot, Dynamo, em2em, Geneious, iMODFit, Molprobity, Phenix, Rosetta, Sculptor, SHARP/autoSHARP, SHELX, SHIFTX2, XDSAPP, and Xplor-NIH.
Four new members joined during the month of November: Alan Roseman from the University of Manchester, UK, Miles Pufall at the University of Iowa, and from Rutgers, John Westbrook at RCSB and Wei Dai. Welcome to our newest members!
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 four new citations in member publications during the last month. Thanks to Oliver Ernst at the University of Toronto Cryst. Growth Des. 2016 16(11): 6318-6326, Ernesto Fuentes and Lokesh Gakhar from the University of Iowa Structure 2016 Oct , Stephen Blacklow and Andrew Kruse at Harvard Medical School Cell. 2016 Nov 167(4): 1041–1051, and Catherine Drennan from MIT PNAS 2016. 113(48): 13750-13755.
Over 90 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:
- A Nature Letter from Daniel Rosenbaum's group at the University of Texas Southwestern Medical Center may help explain how marijuana affects the brain with the most detailed crystal structure to date of the human cannabinoid receptor 1 and a view of the structure that reveals a ligand binding pocket that may be useful in drug discovery. Abstract
- Appearing in Nature Communications is a study from Marco Sotomayor's group at Ohio State University that gives new insight on perception of sound and movement in the inner ear, with an examination of the tip-link protein protocadherin-15, which appears to act as an elastic spring to mediate gating of hair-cell channels. Full Article.
- From our undergraduate desk: Harvard student Kristen Rodrigues chose to highlight a Nature Communications paper from Timothy Springer at Boston Children's Hospital that suggests a new model for the activation of actin-dependent integrins during T-cell migration based on studies showing that actin-dependent force or tension is necessary for integrin activity. More on Tumblr
adxv version 1.9.11 is the new default.
With Ambertools 16 binary output files are now the default, there are new specifications for choosing force fields, and there are separate leaprc files for proteins, DNA, RNA, water+ions, lipids and carbohydrates.
Buster version 20160930 fixes a regression that made gelly erroneously generate 'special position' EXCLUDE cards for grade runs.
CCP4 was updated to version 7.0.023.
Chimera version 1.11.2 fixes a few bugs and includes a new attribute assignment file for the Moon-Fleming hydrophobicity scale in the user manual.
Coot version 0.8.7 has several new features, including canvas scaling, CH3 superatoms, and atom name and index display modes in Lidia.
Dynamo is now at version 1.1.102.
em2em version 20160926 is the new default.
Geneious was upgraded to version 10.0.2. The big changes in version 10 include smarter restriction cloning, new alignment masking, an improved Plasmid Viewer, the ability to filter chimeric reads, easier access to Lineage View, and assembly improvements with added support for structural variant mapping.
Gwyddion is new to SBGrid at version 2.46 (Mac) and 2.30 (Linux). Gwyddion is a modular program for SPM (scanning probe microscopy) data visualization and analysis.
iMODFit version 1.44 is available for Linux. Speed is greatly improved with this update, thanks to the parallel band-Krylov eigensolver, and the developers have improved stability for very big and/or symmetrical macromolecular complexes.
Molprobity version 4.3, which some users access through Global Phasing tools, was added as a stand-alone application. Molprobity is a protein structure analysis platform offering quality validation for 3D structures of proteins, nucleic acids and complexes.
Phenix was updated to version 1.11.1-2575. With this update you will see improvements to geometry restraints, the NCS search, model geometry, Phaser, validation, and phenix.real_space_refine (including an added GUI). There is also simplified Rosetta installation, improved support for Amber, and new map and model-building tools.
Rosetta is now at version 3.7 and includes many new and updated applications: ERRASER now supports residues that are not canonical RNA, a streamlined RosettaAntibody protocol, and FlexPepDock and ddg-monomer for ligand compatibility. You'll also find new introductory tutorials, many new ResidueSelectors, a new score term to penalize peptide sequences that form aspartimide, and a new script for setting up the pyrosetta environment.
Sculptor is now at version 2.1.1. This release includes the new multi-scale ambient occlusion illuminatio and the DPSV and VolTrac algorithms for denoising and detecting filamentous densities (such as alpha-helices and actin filaments) in maps from EM and tomography. SHARP/autoSHARP (?) 20160324
SHARP/autoSHARP was updated to version 20160324.
SHELX was updated to include new versions of SHELXL and PDB2INS.
SHIFTX2 version 1.10 now supports calculating multiple chains and Phosphorylated Residues and includes several bug fixes.
Timescapes version 1.3 was added to the collection. From Willy Wriggers at biomachina.org, Timescapes is a Python-based program package that can be used to efficiently detect and characterize significant conformational changes in simulated biomolecular systems.
XDSAPP was just updated to version 2. Since our last update the developers have introduced a new graphical user interface, a change in the R_free reflections fraction to avoid problems with phenix.refine, and automated detection of anomalous signal and setting of "strict absorption correction" in CORRECT.
Xplor-NIH was updated to 2.43. For a complete list of changes, see the change log.
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.