Dear Consortium Members and Affiliates,
For our April newsletter, we have webinar updates, with a presentation from GROMACS on the horizon, a new monthly Schrodinger Data Club and Training Subgroup, some background on the science happening in Michael Sattler's Munich laboratories, a note about nightly releases and a reminder that you can override the version for almost any application installed by SBGrid, a security alert for Mac users, two new members to welcome, publication highlights from six member laboratories, and a software push with 3 new applications and 14 updates.
We had a few wrinkles in our recent webinar recordings, but have ironed those out and you can now find the recordings for iMosflm, Relion, and EMAN2 posted to the SBGridTV YouTube channel. Please take a look if you missed the original presentations. Molecular dynamics will be the focus in May, with a presentation from the folks at GROMACS scheduled for May 19th at 12:00. June will bring a webinar from Willy Wriggers on SITUS, an application for modeling atomic resolution structures into low-resolution density maps.
For members in North America and Australia that access Schrodinger through SBGrid, we will be establishing a monthly Molecular Simulations Data Club and Training Subgroup. Participants will discuss workflows and hear from Woody Sherman, a Vice President for Schrodinger Application Science, about software updates and how to improve your computational results.
Beginning with our July renewal, participation in this monthly meeting will be mandatory for all users accessing Schrodinger software, as we make an effort to improve project convergence and maximize the benefits of the SBGrid-Schrodinger collaboration. To sign up for continuous access to the Schrodinger Suite and join our Molecular Simulations Subgroup, please complete this Google Form.
For our April webtale, we talked with Michael Sattler, with laboratories at the Technical University Munich and Helmholtz Zentrum München. Sattler's groups are highly invested in using integrated structural biology methods -- X-ray crystallography, NMR, and small angle scattering -- to form a more complete picture of the structures he is studying. Read the full story in the member tales section of our website.
For several software packages we provide so-called 'nightly' releases. These are bleeding-edge releases that have the most up to date features, but are also untested and often have bugs. In some cases, we make a selected 'nightly' release our default version based on the number of user requests or new software features. To deliver nightly releases more rapidly and with minimal impact to users who prefer a stable platform, we will no longer set nightlies as the default version. To use the nightly version of a title, set a version override to 'nightly' or specify the version directly. Read on for more info on overrides.
Would you like to use a software version other than the default version installed by SBGrid? You can! How to do a version override is a question that users ask us every week. Users can usually access the last 3 versions for each software title. To find out the available versions, run the sbgrid -l command. You can then create a version override file to define the version you want to use. Detailed instructions can be found on our support forum.
Want an even older version? We have a collection of previous versions that goes back several years, so we may have it. Drop us an email to inquire.
Mac users, note that there is serious security flaw in all versions of MacOSX since 10.7 that allows arbitrary privilege escalation, i.e. any user (or malicious program) can gain administrative 'root' control on the machine. This vulnerability is patched in 10.10.3, but will not be patched on other versions of the OS. Please consider upgrading, particularly for macs in multiuser environments.
We had two members join in the last month. Robert Kingston became our second member from Massachusetts General Hospital and Kenton Swartz is our sixth from the NIH (National Institute of Neurological Disorders and Stroke). Welcome to our newest members!
April's software push includes updates to Bsoft, CARA, CCP4, CMView, CTFFIND, EMAN2, IMOD, Maxit, Phenix, relax, Relion, Schrodinger, Spider, and Theseus, and 3 new applications: Arcimboldo_Lite, Assemble2, and RSRef. Read additional details below.
SBGrid member labs published over 58 manuscripts during the last month, a full listing of which can be found on the Member Publications page of the SBGrid website. Here are some notable highlights:
- For those of you interested in Single-Particle Cryo-Electron Microscopy, check out this Primer, authored by Yifan Cheng, Niko Grigorieff, Pawel Penczek, and Tom Walz, published in Cell this month.
- Guy Schoehn's group from Grenoble reported on a 4.3 angstrom cryo-EM structure of the helical measles virus nucleocapsid in the April 16th edition of Science.
- At UC Berkeley, John Kuriyan's laboratory has a new PLos One publication detailing the crystal structure of the FLT3 kinase domain bound to the inhibitor Quizartinib.
- Nenad Ban's group from ETH Zurich published an article in Science describing the 3.8 angstrom resolution structure of the 55S mammalian mitochondrial ribosome using cryo-electron microscopy and chemical cross-linking/mass spectrometry.
- Axel Brunger's Stanford laboratory, in collaboration with Qing Zhong from UTSW, determined the structure of ATG14, an essential autophagy-specific regulator of the class III phosphatidylinositol 3-kinase complex. ATG14 promotes membrane tethering of protein-free liposomes, and enhances hemifusion and full fusion of proteoliposomes reconstituted with the target (t)-SNAREs, syntaxin 17 and SNAP29, and the vesicle (v)-SNARE VAMP8. Read the full story in Nature.
- Jamie Kate's UC Berkeley group used PAR-CLIP to identify human transcripts that interact with eIF3 in an April 6th Nature publication.
If you have news from your lab that you would like to share with the community, please let us know by emailing Michelle Ottaviano or communicating with SBGrid on Twitter (@SBGrid).
ARCIMBOLDO_LITE is new to the SBGrid collection. This application is for crystallographic Ab Initio protein solution below atomic resolution. This LITE version runs on all cores of a single machine, without requiring a grid, supercomputer, or database.
Assemble2, another application new to SBGrid, allows you to design your RNA 2D structure interactively and to create and assemble the corresponding RNA 3D modules directly in UCSF Chimera. Read more on the Assemble2 website.
Bsoft version 1.9.0 was pushed out. This update is a big one with further conversion to C++ syntax and new programs that do fast cross-correlation searches (bfcc), reconstruct tomographic particles and estimate resolution (btompart), symmetrize hexagonal tubes (btube), reconstruct a cross section based on helical parameters (bhelcross), estimate filament width (bfilwidth), support single particle reconstructions (bspr), calculate regional density averages (bdens), and manipulate plane models (bplane).
CARA is now at version 1.9.0. This version includes new variants with arguments for spec.createPeakList() and spec.openPeakList() and a new requirement to define the home of the peaklist.
CCP4 version 6.5.008 is the new default. In addition to a bevy of bug fixes, this version includes improvements to multi-copy search in Molrep, handling of nucleic acids and increased dimensions in ccp4-progs, updates to the autosharp interface in ccp4i, and in ARP/wARP, a new solvent search run from ccp4i, changed file name length in the ligand search, and an option to select MTZ column labels for protein model building.
CMView was updated to version 1.1.1.
CTFFIND 4 version 4.0.13 is a new version of ctffind that should run significantly faster than CTFFIND 3 and may give slightly improved results when processing data from detectors other than scanned photographic film.
The EMAN2 2.1 nightly update was installed, currently only for Linux users.
The IMOD 4.7.13 release fixed robust fitting with whole contours that aren't cut into pieces, a problem when running SIRT with binned K2 data, an error in the last interpolation region between strips in Ctfphasefli, and a bug in Imodauto if there are empty boundary contours.
Maxit version 8.2 is now the default version.
Phenix is now at nightly build dev-2027.
relax version 3.3.8 is a minor bugfix release that allows the relax GUI to be used on screens with the low resolution of 1024x768 pixels.
For Relion Linux version 1.3, we pushed out a bug fix build.
RSRef version 0.4.2 (currently only for Linux) was added to the collection. RSRef comes from Michael Chapman's lab at the Oregon Health and Science University and can be used for the fitting of atomic models into electron density maps derived from x-ray crystallography or electron microscopy by stereochemically-restrained refinement.
The Schrodinger 2015-1 release include a new tool in BioLuminate for predicting protein titration curves. Also in BioLuminate, peptide docking can now be done with non-standard residues. The covalent docking panel has been redesigned in Glide and a number of other significant improvements have been included.
SPIDER version 22.09 includes a new procedure for aligning raw frames from a direct capture camera using multiple linear regression for frame alignment.
Theseus version 3.1.1 includes minor tweaks to the help page, updates to the man page, a slightly improved algorithm, a corrected marginal likelihood calculation, a change to include average structure in same reference frame as the superposition, and fixed a bug in the PCA output. Please note, Theseus is now distributed with CCP4 and may be removed as a stand alone application soon.
Please don't forget to cite our eLife publication (eLife 2013;2:e01456) for all projects completed with SBGrid compiled software.
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.