Dear Consortium Members and Affiliates,
As we continue our march through the waning days of summer, we have a brief SBGrid update to include in your summer reading list. August presents its own special kind of challenge as the vacation season results in fewer user requests, but we juggle responsibilities internally to fill in for staff holidays. Please read on for details on our upcoming PyMOL webinar, a reminder about our next SBGrid-Schrödinger working group, a story on SBGrid member Oleg Tsodikov, a software push with 13 updates, a welcome to two new members, and highlights from 3 SBGrid-member publications.
We'll kick off a new season of webinars with a much-anticipated update from PyMOL. Daniel Cappel will join us on September 13th to give a general introduction to new users as well as a primer on using PyMOL for PowerPoint visualizations and rendering movies along with a glance at recent improvements and new features.
Schrödinger's new Protein Ligand Database is the topic of our next SBGrid-Schrödinger Working Group session. Join us on October 4th to learn more about this knowledge base of 3D structural data and protein-ligand interactions for idea generation and validation. Connection details here.
For our August member tale we spoke with Oleg Tsodikov, who heads the lone structural biology laboratory at the University of Kentucky College of Pharmacy, where he divides his efforts between three different drug discovery projects that focus on drug-resistant tuberculosis, the inhibition of bacterial cell division, and the molecule mithramycin, which may interfere with the progress of Ewing Sarcoma. Read the full story.
Our August software release includes updates to 13 applications, including 2dx, Anaconda, ARCIMBOLDO LITE, CCP4 EMAN2, Ghostscript, ilastik, IMOD, Jalview, OpenMM, pandas, PDBFixer, and Spider.
We had 2 new members join in the month of August: David Clapham from Children's Hospital Boston and Leemor Joshua-Tor from Cold Spring Harbor Laboratories. Welcome to our new 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 4 new citations in member publications during the last month. Thanks to those who remembered us, including Qing Fan in her eLife report on the Structural mechanism of ligand activation in human calcium-sensing receptor out of Columbia University, Carlo Petosa and Guy Schoehn from IBS Grenoble in their Science Reports paper on Fusion to a homo-oligomeric scaffold allows cryo-EM analysis of a small protein, MIT's Thomas Schwartz in a Nature paper on the Mechanism of arginine sensing by CASTOR1 upstream of mTORC1, and Roderick MacKinnon from Rockefeller in his Science article on the Structure of the voltage-gated K+ channel Eag1 reveals an alternative voltage sensing mechanism.
Over 60 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:
- In a recent Nature Immunology article, Professor Stephen Harrison from Harvard Medical School looks at the results from 5 recently published papers that reveal an antigenic relationship between the Zika and dengue viruses and highlights the necessity of understanding whether exposure to one virus increases the risk of infection to others Nature Immunology 2016. 17: 1010–1012.
- Catherine Drennan's group at MIT describes the process of self-destruction that occurs in the enzyme LipA to insert sufur and produce lipic acid. Read the full story in PNAS.
- From our undergraduate desk: Harvard student Kristen Rodrigues highlights a paper in Science with SBGrid member Terunaga Nakagawa from Vanderbilt University as co-author, that examines β-neurexin 1 and expands our understanding of the role of glutamate receptors in synaptic signaling. Read more on Tumblr.
2dx version 3.5.1 includes a new tool to automatically switch between maps and references, parallel processing of images in 2dx_merge, weighted backprojection instead of Latline fitting, movie mode processing for direct electron detectors, an option to sharpen maps using bead models, B-factor sharpening scripts, new volume refinement methods, new kernel tools for major operations on EM-Volume, and radiation damage measurement for movie-mode processing along with improvements to the GUI and performance and many other bugfixes.
Anaconda has jumped from version 2.4.1 to 4.1.1 in an effort to avoid confusion with the versions of Python included in Anaconda. The highlights of this release include a new Navigator GUI for managing conda environments and applications and the addition of Jupyter Notebook Extensions.
ARCIMBOLDO LITE is now at version 20160224.
The latest from CCP4, version 7.0.18, includes many updates and changes, a full listing of which you can find on their Updates Page.
In EMAN2 the most recent version 20160805 includes a new Tophat filter in e2refine_easy.py: --tophat. This option was added to satisfy the call for a 'sharper' map, despite Ludtke's mixed feelings about the appropriateness of the filter.
Ghostscript version 9.19 is the new default. This software has had a number of releases since our last update and a full listing of changes can be found in their release notes.
ilastik version 1.2.0 includes a new IIBoost Synapse Detection workflow along with better support for reading multi-dimensional TIFF datasets many performance enhancements, a Camera" Export button to export image views exactly as they appear in the window, a new object statistics window, improved object counting, and numerous bug fixes and performance improvements.
IMOD was updated to version 4.8.54. No release notes are available.
Jalview version 2.9.0b2 is a major new release with bug fixes and general improvements galore as well as new options for alignment, editing and analysis of proteins linked to coding sequences; discovery and retrieval of 3D Structure Data from the EMBL-EBI's PDBe query services, publishing and exchange of data and visualizations on the Web with BioJS-MSA, UCSF Chimera and VARNA session storage in Jalview Projects, and secondary structure prediction with Jpred4.
OpenMM is now at version 7.0.1. Major improvements include improved performance, flow control in custom integrators, extrapolated polarization, writing PDBx/mmCIF files, and compound integrators.
pandas version 0.18.1 is a minor release that includes an enhancement to .groupby(...) to provide convenient syntax when working with .rolling(..), .expanding(..) and .resample(..) per group, an option to assemble dates from a DataFrame using pd.to_datetime(), and method chaining improvements, along with the usual bug fixes.
New features in PDBFixer version 1.3 include reading PDBx/mmCIF files and creating non-rectangular solvent boxes. This version requires OpenMM 7.0, which was updated this month as well.
Spider version 23.03 is the new default for Linux. This update includes several new operations, including DOC SLICE to put a slice from one document file into a new document file, DIS to convert SPIDER image to JPEG , RI R and RI RV to examine positions of rings in power spectra or CTF images, CP TO STK to merge a series of stacks into a single new stack, and FSC NEW to find FSC and resolution. You'll also find that the Three Dimensional Reconstruction protocol for single particle reconstruction now incorporates a 'gold standard resolution' workflow.
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.