Newsletter

Dear Consortium Members and Affiliates,

As May comes to a close and Phase 1 reopening begins in Massachusetts and at Harvard, most SBGrid staff will continue to work remotely, and will be available for support as you continue at home or begin your ow . Read on for a bevy of webinar updates, a large software push with 14 updates and 3 new titles, 3 new members to welcome, some technical notes on bugs and changes from our software team, an SBGrid-member position posting, and 3 member publication highlights.

We've had another great month of talks from speakers in our weekly webinar series. In May, Karin Reinisch of Yale gave us some insights on lipid transfer, and on the software side of things we heard from Kay Diederichs on XDS/XDSGUI, Ellen Zhong on CryoDRGN, Kelly Brock and Thomas Hopf on EVcouplings, and Colin Palmer on CCP-EM. We also had two rounds to trainee talks with speakers from 5 different member labs: Goran Bajic of Harvard Medical School, Ryan Feathers and Mike Fenwick of Cornell, Liron David of Boston Children's Hospital, and Mayukh Chakrabarti of Johns Hopkins. Many thanks to all who have participated! Catch what you missed on SBGrid's YouTube channel.

We have a big software push this month, with 14 updates  -  BioXTAS RAW, CCP4, ChimeraX, Cinderella, Coot, crYOLO, DIALS, HKL2000, NAMD, NMRFAM-Sparky 0., Phenix, .3.5AmberTools202RStudio, ScÅtter, and SRAtoolkit - and 3 new titles: the R package Bio3D R, ConCavity, and HARUSPEX.

May brought us three new members: Hening Lin from Cornell University, Ray Blind from Vanderbilt and Jens Mieler, opening a new lab at Universität Leipzig . Welcome to our newest members!

Technical Notes from our Software Team

LICENSE CHANGES: for Schrödinger users, please note that we recently updated our license configuration, so please make sure to update your installation to the most recent configuration.

CENTOS-OS6 GOODBYE: as of Nov 30, 2020 CentOS 6 will no longer receive updates. We recommend that you migrate to CentOS 7 or 8, which will receive updates until 2024 and 2029, respectively.

CCP4 7.1 bugs: a few users have reported that 3d Stereo is not working properly for the 0.9 version of COOT included in CCP4 7.1. Users may benefit from sticking with COOT version 0.8.9 version while we resolve the issue.

Community Announcements

Vertex has a new position posting for a Computational Structural Biologist to join their computational research team:  Vertex pharmaceuticals is looking for a dynamic scientist in the area of Cryo-EM protein modeling and structure determination to join their computational sciences group at one of three research locations: Boston, MA, San Diego, CA or Oxford, UK. Experience in Cryo-EM structure analysis in the context of understanding dynamic motion and lead optimization is sought and this individual would be expected to interface between our structural biology and computational chemistry groups. [More details].'

If you'd like to advertise a new position in your laboratory, please send an email to Michelle at ottaviano@hkl.hms.harvard.edu

Member Publications

Over 50 new member publications appeared in journals this month. You can find a complete listing on our website, along with a couple of notable highlights below:

If you're currently preparing a manuscript, please remember you can publish your datasets in the SBGrid Data Bank along with your PDB record deposit and publication submission to preserve your primary experimental datasets. We also recommend the following boilerplate language in all publications that report results obtained with SBGrid supported software:

Members cited SBGrid's ELife paper in nine publications this month, including Ramachandran Murali of Cedars Sinai in a bioRxiv preprint: RIPK2 Stabilizes c-Myc and is an Actionable Target for Inhibiting Prostate Cancer Metastasis; Niraj Tolia's Washington University School of Medicine, St. Louis laboratory in Nature Communications Biology: Tetracycline-inactivating enzymes from environmental, human commensal, and pathogenic bacteria cause broad-spectrum tetracycline resistance; Harvard Medical School's Suzanne Walker and Harvard University's Daniel Kahne's in a bioRxiv preprint: Structure and reconstitution of a hydrolase complex that releases peptidoglycan from the membrane after polymerization; Lynne Howell at The Hospital for Sick Children in Toronto published in Nature Communications: Structural and biochemical characterization of the exopolysaccharide deacetylase Agd3 required for Aspergillus fumigatus biofilm formation; Diana Tomchick of University of Texas Southwestern Medical Center in an article from Nature Structural and Molecular Biology: A distinct inhibitory mechanism of the V-ATPase by Vibrio VopQ revealed by cryo-EM; Bing Chen of Boston Children's Hospital and Shaun Rawson at Harvard Medical School in a bioRxiv preprint: Distinct conformational states of SARS-CoV-2 spike protein; Eva Nogales's preprint from her University of California, Berkeley laboratory in bioRxiv: The cryo-electron microscopy structure of the human CDK-activating kinase; an mBio article from the laboratory of Katya Heldwein at Tufts University Medical School: Conserved Outer Tegument Component UL11 from Herpes Simplex Virus 1 Is an Intrinsically Disordered, RNA-Binding Protein; and Eric Fischer's Dana-Farber Cancer Institute laboratory in the journal Cells: Tubulin Resists Degradation by Cereblon-Recruiting PROTACs.

Software Changes

Bio3D is new to SBGrid. Bio3D is an R package containing utilities for the analysis of protein structure, sequence and trajectory data.

BioXTAS RAW 2.0.0 is the new default and brings with it Python 3 compatibility, a conversion to pyFAI for radial integration, a new .deb prebuilt installer for Debian/Ubuntu, .hdf5 - a new series save format, and .hdf5 that other programs can easily read and is ~50-70% smaller than the previous format. You'll also notice new information windows above the control panel, options to align DENSS and DAMMIF/N outputs to PDB files, and a new series adjustment panel that lets users easily adjust the scale, offset, and q range for all profiles in a series. 2.0.0 also works with ATSAS 3 on all platforms.

CCP4 7.1, aka Skipton, is a complete rewrite including an upgrade to C++-11, updates to many packets, and many other improvements and new features.

ChimeraX version 1.0 includes a new option to open CCD entries as structures, a convenience tool to show chain sequences in the same way that a structure's chain table in the log displays them, use the ​shape command to create geometric shapes as surface models, and the ​build start peptide command to construct peptides from scratch. Note: version 1.0 is a release candidate available via version override. 0.93 is the default.

Cinderella version 0.6.0 fixes an issue for classes in mrcs format.

Coot is now at version 0.9. See this presentation for a summary of what to expect in 0.9: A Coot for Cryo-EM: 0.9 (pre-release)

ConCavity version 0.1 is new to SBGrid. ConCavity is a tool for ligand binding site prediction from protein sequence and structure.

crYOLO 1.6.1 will allow users to filter particles according to their size when using the general model, and now writes the estimated size and picking confidence distribution to disk.

DIALS version 2.2.3 is now available.

Haruspex is another new tool. Haruspex is a Convolutional Neural Network capable of recognizing and predicting secondary structure elements and nucleotides in Cryo-EM reconstruction density.

NAMD version 2.14b was pushed out. This version includes improvements to alchemical free energy calculation and hybrid QM/MM simulation, an updated collective variables module, featuring a more flexible colvars scripting interface, geometric path collective variables, and volumetric map-based variables. You'll also notice an update to random acceleration MD (RAMD) 5.0.5 and to Charm++ 6.10.1, enabling improved scaling on the InfiniBand via ucx network layer, improved multi-copy on POWER via pamilrts network layer, a clean exit with non-zero status for many failures, and support for CUDA versions 8.0-10.x on Kepler or newer GPUs.

NMRFAM-Sparky is at version 20200408.

Phenix 1.18 is the new default. This version allows the automatic creation of Amber files in the phenix.refine GUI and provides a new AmberPrep GUI. It has Engh & Huber restraints (2001) for cis-peptides, new FeS restraints, and a change so the metal coordination library defaults to Zn+2 and FeS clusters. There is a new global Ramachandran score for identifying protein structures with unlikely stereochemistry in CLI, new cryo-EM denisty modifications - a model-based density modification with automatic model generation and optimized defaults. Real-space refinement has added the NQH flip option and no longer includes hydrogen atoms in the map target function, which improves fit. There's also a new tool for ordered solvent picking in cryo-EM maps (phenix.douse), a new map and model superposition tool (phenix.match_maps), a new FindProgram to find any Phenix program with a text search, and a new project details button for opening the README file for tutorials

2.3.5AmberTools2020

RStudio 1.2.5042 fixes a crash when debugging with R 4.0+, a crash in rserver that sometimes occurs when a port proxy request fails to connect, and a display issue for configured Launcher session limits. It also allows users to select the R version in Global Options and elsewhere, and fixes a failure to start R sessions when multiple values are present in www-frame-origin

ScÅtter 4.0 was pushed out.

SRAtoolkit 2.10.5. You can find a full change log on Github

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.

This newsletter is sent to you because you are a member or affiliate of the SBGrid Consortium, the Structural Biology Grid computing consortium.

More information about the SBGrid Consortium is available at http://sbgrid.org

Report software bugs: sbgrid.org/bugs