Dear Consortium Members and Affiliates,
The New England weather continues to yo-yo between 55 and 85 degree days as the academic season winds down and we wrap up May with another SBGrid update. This month you'll find tips on how to make SBGrid work using modules or on Amazon EC2, a profile on Karolin Luger at U Colorado Boulder, a June webinar on Scipion, a big software release with 21 updates and two new titles, two new members to welcome, and three member publication highlights.
Interested in using SBGrid with modules or on Amazon's EC2? For those of you with an existing module/lmod setup, we now have module files for loading and unloading the SBGrid environment in our programs tree that can be used to load and unload the entire SBGrid environment. Learn more at https://sbgrid.org/wiki/modulefiles. And Amazon EC2 users can use our installation client to easily add the same software used in the lab with the familiar SBGrid environment. See https://sbgrid.org/wiki/AWS for more information.
Our May member tale brought us to Colorado and the laboratory of Karolin Luger at University of Colorado Boulder, where her scientific path is meandering and has shifted from examining static structures to catching them in action. Luger emphasizes two key principles in her approach to science: fresh perspectives and really listening to what the results are saying. Read the full story.
Thanks to Giovanni Bussi and Massimiliano Bonomi for joining us last week to give a webinar on "analyzing and enhancing molecular dynamics simulations with PLUMED." If you missed the tutorial, you can watch it on our YouTube channel. Next we'll look at "Using Scipion for Stream Image Processing at Cryo-EM Facilities," with José Miguel de la Rosa Trevin at the SciLifeLab, Stockholm University. Full details here.
This month's software release includes updates to autoPROC, CCP4, Chimera, BioXTAS RAW , Buster, DIALS, Geneious, Global Phasing Suite, OpenMM, Modeller, Mosflm, NMRPipe, PHENIX, ProDy, STAMP, Staden, SIMPLE, vmd-xplor, XDSGUI, XDSSTAT, XPLOR-NIH. We also added two new titles: gmconvert, gmfit.
Two new members joined in the month of May: Jennifer Bridwell-Rab from the University of Michigan and Cristina Paulino from the University of Groningen in The Netherlands. 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 SBGrid Data Bank 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's eLife paper got 6 new citations in May, with acknowledgements from Ryan Hibbs at UT Southwestern in his new Nature publication [Abstract], Katya Heldwein from Tufts Medical School in Nature Structural & Molecular Biology [Abstract], Vanderbilt University's Terunaga Nakagawa in Journal of Biological Chemistry [Abstract], Jonathan Abraham at Harvard Medical School in Nature Communcations [Abstract], La Trobe University's Marc Kvansukal in Nature Communications [Abstract], and Jacqueline Cherfils from École Normale Supérieure (ENS) Paris-Saclay France in bioRxiv [Abstract].
More than 50 member publications appeared in March journals. You can find a complete listing on our website, along with a few notable highlights below:
- In cryo-EM, as in most aspects of life, balance is key as researchers endeavor to find the yin and yang of exposure versus damage. In a new paper in Structure, Tamir Gonen's group at UCLA assesses the radiation damage in cryo-EM of two crystalline samples: the proteinase K and a prion hepta-peptide. The originator of the MicroED method, the Gonen group demonstrates that controlled exposure is important for results integrity and that radiation damage in cryo-EM parallels the problems in X-ray crystallography. [Abstract].
- In a new publication published online in Nature Structural and Molecular Biology, Katya Heldwein of Tufts University School of Medicine solves the structure of the fusogen gB of the herpes simplex virus, highlighting the players involved in membrane anchoring with the cytoplasmic domain (CTD) playing a key role in the fusogenic refolding of gB. A better understanding of how the fusion of the viral envelope with host cell membranes occurs could aid in the development of new methods for treatment and infection control. [Abstract].
- From our undergraduate desk: Harvard student Kristen Rodrigues chose a new publication in Nature Neuroscience that SBGrid member Steve Brohawn co-authored, where researchers engineered a new opsin that exerts more precise control over spatiotemporal manipulation of neurons. [More on Tumblr].
autoPROC was updated to version 20180515.
CCP4 version 7.0.057 includes minor fixes to Coot, updates to Pointless and mrbump, interface improvements to refmac, lorestr, prosmart, Phaser MR in ccp4i and crank2 in ccp4i2. In dui there is a new workaround for the FPE issue, and in truncate, the Global Phasing team helped with a serious issue with F/sigF.
Chimera's latest version was pushed out. In version 1.12 you'll notice changes to the tools Add Charge and Morph Conformations and several new command options along with some general updates and bug fixes.
BioXTAS RAW version 1.4.0 is a major feature release with the big news that users can now use the DENSS method to calculate electron density from SAXS scattering. Full details are at http://denss.org/. This version also include the often-requested error calculation for Guinier fits, available whenever you open the Guinier panel.
Buster is at version 20180515, which includes improvements and fixes to Pipedream along with improvements to statistics for high-resolution bin, new support for equal-observation-number binning in rvalue, a fix to aB_covalent_ligand when atom names in ligand and protein are duplicated, new options in the 'fetch_PDB' tool -- -nomerge/-notruncate/-nouniqueify, improvements when working with hydrogenated models in combination with occupancy refinement, a command-line option to explicitly specify the linkage name used in the resulting dictionary, improvements to the automatic test for duplicated restraint definitions, and an update to "pdb2occ" to generate Gelly command files that only automatically exclude hydrogens with OCC=0.0 and not any atom with OCC=0.0. Other minor changes and bug fixes you can find in their change log.
DIALS version 1.9.3 includes support for scan-varying beam models, a fix for crashes on Ubuntu 14.04 (#513), an update to dials.image_viewer, which will now work with large Nexus files, improved error reports, and changes in xia2 to improve processing error messages.
Geneious 11.1.4 introduces a number of fixes and improvements.
gmconvert was added at version 20180516. gmconvert converts 3D density maps and an atom models into GMM (gaussian mixture model). An expectation maximization algorithm is employed for conversion into GMM. The program gmconvert also has many other useful functions to handle GMM. From Takeshi Kawabata in Osaka, Japan.
gmfit is another new title, at version 20180516. gmfit superimposes molecular subunits into the density map of their complex. The program is designed to superimpose multiple atomic models of subunits into a low-resolution 3D density map, however, it is also applied to superimposing two 3D density maps or two atomic models. To reduce computational costs for the superimposing, both subunits and complexes are transformed into GMM (Gaussian Mixture Model).
Global Phasing Suite is at version 20180515. This suite is available only to commercial members with a valid license.
OpenMM version 7.2.1 was pushed out. In this version you'll find that OpenMM is now built against CUDA 9.0, new support for the Amber14 and CHARMM36 force fields, new routines for building lipid membranes in the Modeller class including support for POPC and POPE lipids, a new class - CustomCVForce - for applying forces based on collective variables, new flexibility when defining virtual sites with the LocalCoordinatesSite class, a new CustomIntegrator that lets you define tabulated functions and use them as part of your integration algorithm, a handy new feature called Context.reinitialize() with an option to preserve state within the context.
Modeller version 9.19 was pushed out. Primarily a bug-fix release, this version has an update to the automodel-generated PDB or mmCIF files, which now point to the alignment file used to generate them, a new bundled version of HDF5 updated to 1.8.18, a fix to ensure that whitespace is removed in alignments with gaps so there is no erroneous mapping to the '.' residue type, and a fix to automodel to output SSBOND and CONECT records for any disulfide bridges.
Mosflm is now at version 7.2.2.
NMRPipe was updated to version 20180523.
PHENIX dev-3139 is available as a version override.
ProDy was bumped a couple of versions to 1.10.7. The newest features include newt showAtomicLines() and showAtomicMatrix() functions to improve visualization and a networkx option to showTree() so that the user can choose to use networkx to visualize a given tree. Users can also now associate an MSA object to the PDBEnsemble class and use a new pairwise option to Ensemble.getRMSDs() to obtain an RMSD table of every pair of conformations in the ensemble. Also new are methods and classes for obtaining data from CATH and Dali and new functions for Uniprot and Pfam, such as queryUniprot() and parsePfamPDBs().
STAMP version 4.4.1 is the new default. With this version the manual was updated to reflect some minor changes in the STAMP output format and the bundled SCOP domain databases have been updated to SCOP release 1.75.
Staden version 2.0.0b11 brings the software one step closer to the asymptoptic approach of version 2.0, with the primary changes to Gap5. This release is still a beta release since documentation updates are still needed.
SIMPLE version 2.5 includes a DDD movie pre-processing program unblur based on Grigorieff’s program of the same name, but with two important differences: automatic weighting of the frames using a correlation-based M-estimator and stochastic continuous optimisation of the shift parameters. This enables analysis of movies with severe pathologies due to radiation damage or extreme drift. Also new is a unblur_tomo for movie processing of tomographic tilt-series. You also may notice improvements to simultaneous 2D alignment and clustering with prime2D using a hybrid extremal/stochastic hill-climbing search approac, ab initio 3D reconstruction from class averages using stochastic neighborhood hill-climbing for initialization of the 3D orientation search, serial CPU code optimization through data re-organization and pipelining, parallel CPU performance through load balancing, high-level workflows for 2D analysis and initial 3D model generation that automate initialization, update of search parameters and dynamic down-scaling of the images for improved performance.
vmd-xplor versions 1.9.1/1.11 are now available.
XDSGUI version 20180427 fixes the bug so that the INTEGRATE tab will now update when XDS runs. Starting with this version the developers will no longer make 32-bit Linux binaries.
XDSSTAT updates were pushed out for Mac 20171011 and Linux 20180223.
XPLOR-NIH version 2.48 is the new default. This version updates to PREPot to allow correlation target type where the prefactor to 1/r^6 is not considered in the energy, posDiffPot, adding a planarFit option to allow free rotation/translation within a plane while restraining orientation and translation relative to the plane surface, and RepelPot to fix a bug when usiong overlapping non-equivalent selection pairs. New helper programs - jupyterXplor, energyPlot and calcPRE - were also added.
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.