Dear Consortium Members and Affiliates,
Happy spring to all (even if we are expecting snow showers all weekend). For our transition to spring we have news on last week's EM Data Processing Workshop, a webinar to watch and one to add to your calendar, a profile on Kay Diederichs, a software push with 10 updates and 4 new titles, 3 new members to welcome, two new citations for SBGrid, and three member publication highlights.
We had a great turnout last week for our Relion/EM Data Processing Workshop. Thanks to all who participated, to Björn Forsberg and Dari Kimanius from Stockholm University/SciLifeLab in Sweden for presenting, and to Susan Shao for co-hosting and helping to organize. Slides and handouts are available from the SBGrid Wiki.
We also just finished uploading Frank Murphy's webinar on RAPD for Automated MX Data Analysis. Up next is an introduction to ChimeraX with Tom Goddard from the UCSF Resource for Biocomputing, Visualization, and Informatics. Tune in Tuesday, April 11th.
Kay Diederichs is the focus of our web tale for the month of March. Diederichs gave us some background on his work as a structural biologist and methods developer who has seen a transformation in the field as software has taken over the tasks that physicists once tackled in structure determination, and explained how CC1/2 data quality indicators have the potential to replace experience.
Our March software release included updates to CCP4, Coot, DIALS, EMA2, NMRFAM-Sparky, O, PyMOL, Pytom, UNIO, XDS, XDSCC12, and XDSGUI along with 3 new software titles: Focus, infernal, and PLIP.
Three new members joined SBGrid in the month of March: Geoffrey Greene from the University of Chicago, Trevor Moraes from the University of Toronto, and Dongyan Tan from Stony Brook University. 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 two new citations during the last month, one from Lynne Howell's group at U Toronto appearing in PNAS [Abstract] and a second in Nature Structural and Molecular Biology from Lawrence Stern's group at UMass Medical School [Abstract].
Over 88 publications from SBGrid member laboratories appeared in our latest monthly search. You can find a full listing on the Member Publications page of the SBGrid website. Here are some notable highlights:
- Christopher Garcia's lab at Stanford University School of Medicine reported in Cell on a stem cell factor variant his group engineered that impairs c-Kit dimerization and truncated downstream signaling amplitude and shows a preference for activating hematopoietic progenitors over mast cells. [Abstract].
- Appearing in the Journal of Biological Chemistry this month is a report from Galina Lepsheva's group at Vanderbilt University on CYP51, a target for drugs fighting fungal pathogens, and provide a comparative structural analysis to identify a new approach to combat drug resistance. [Abstract]
- From our undergraduate desk: Harvard student Kristen Rodrigues chose to highlight a paper in the journal Nature, from Ohad Medalia's lab at the University of Zurch. Medalia's group used cryo-electron tomography to get a first glimpse at nuclear lamins and the surprising ways in which they are organized. [More on Tumblr].
Software Changes
CCP4 version 7.0.033 includes a new BALBES pipeline and fixes a bunch of bugs.
Coot has gone through a few iterations since our last update. At version 0.8.8 several new features have been added including API and GUI ligand percentile scoring, a function - closest_atom_simple_py(), which returns the closest atom to the centre of the screen (without CA substiution), chemical feature clustering, an "Outliers Only" mode in the Ramachandran plot, canvas scaling and CH3 superatoms name and index display modes for Lidia, multi-thread multiple map contouring using C++11 compilers, and a new 3D menu item.
DIALS version 1.4.5 fixes a few bugs.
EMAN2 version 2.2_20170322 was pushed out.
FOCUS 0.9.1, 20170325 is new to SBGrid. FOCUS is an interface for cryo-transmission electron microscopy (cryo-EM) data collection with computer image processing allowing users to import and manage data recorded by direct electron detectors and perform elemental image processing tasks in a high-throughput manner, while new data is being acquired at the microscope.
infernal version 1.1.2 was added to the collection. infernal (INFERence of RNA ALignment) is for searching DNA sequence databases for RNA structure and sequence similarities. It is an implementation of a special case of profile stochastic context-free grammars called covariance models (CMs). A CM is like a sequence profile, but it scores a combination of sequence consensus and RNA secondary structure consensus, so in many cases, it is more capable of identifying RNA homologs that conserve their secondary structure more than their primary sequence.
NMRFAM-SPARKY was updated to version 20170320.
O has been updated to version 15. With this release users will find new commands, including: HKL_signal, which shows the anisotropy present in a structure factor HKL project, QDS_extract for stereo-chemistry of an existing residue to generate an initial QDS molecule, Auto_extend to extend the results generated by Auto_2ry, and DB_average, for averaging the values selected for an atom ODB. Additional new functionality includes updates to the NDP and stereo-chemistry dictionary to allow the generation of classical secondary structures for DNA and RNA, and QDS master menu and data ODB updates.
PLIP version 1.3.3 is another new SBGrid title. PLIP, a (Protein-Ligand Interaction Profiler) is used for automated detection and visualization of relevant non-covalent protein-ligand contacts in 3D structures.
PyMOL was updated to version 1.8.6. This update includes support for Fast MMTF load and chromadepth ray tracing and introduces smooth surface edges.
UNIO is now at version 2.0.2.
XDS version 20170215 fixes a few bugs.
XDSCC12 was updated to version 20170112.
XDSGUI version 20170131 now works with Eiger HDF5 by selecting the *master.h5 file in the FRAME tab.
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.