Dear Consortium Members and Affiliates,
Greetings from the SBGrid crew. We're scattered about Greater Boston, but happy to find that we and Consortium members are as busy as ever, even if the tasks at hand have changed somewhat. Read on for the latest on our now weekly webinar series, a profile on Yuh Min Chook of UTSW, 1 new member to welcome, a reminder of remote resources at your disposal, 3 member publication highlights, and a software release with 4 new titles and 9 updates.
We've had an enthusiastic response to our expanded webinar series, with talks on software and science from developers, PIs, and trainees. We are grateful to the speakers who have contributed their time and to everyone for joining us online. We'll have the first of our trainee talks on Friday, featuring Harvard Medical School's Goran Bajic and Ryan Feathers from Cornell University. During the last month we heard from Pavel Afonine on Phenix refinement and validation, Dorothee Liebschner on Phenix cryoEM tools, Daniel Panne on genome folding by CTCF and cohesin, Pablo Conesa on Scipion, and Tristan Croll on ISOLDE. These webinars are up on SBGrid's YouTube channel.
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Upcoming SBGrid Weekly Webinars
May 1: Trainee talks - Goran Bajic, PhD (Harvard Medical School); Ryan Feathers (Cornell). Note: trainee talks may not be recorded.
May 5: Prof Kay Diederichs on XDS
May 8: Carol Herre and Jason Key with SBGrid technology updates
May 12: Dr. Debora Marks on EVCouplings
May 15: Ellen Zhong on CryoDRGN
May 19: Trainee talks - Mayukh Chakrabarti (Johns Hopkins); Liron David, PhD (Boston Children's Hospital), Mike Fenwick, PhD (Cornell)
May 22: Colin Palmer on CCP-EM
See the full webinar lineup and let us know if you'd like to share a story from your lab.
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Yuh Min Chook is the subject of our April member tale. We spoke to her at home, socially distanced from her University of Texas Southwestern Medical Center laboratory, where she was cooking up ideas for how her group might study the molecular mechanisms at work in Selinexor, a drug her laboratory helped to develop and which has potential therapeutic use in COVID-19 (a clinical trial is in the works). Almost as interesting: what Chook's actually cooking, as this foodie finds herself with much more hands-on time in her kitchen. [Read the full story]
Our April software push includes 4 new titles - cryoID, cryoDRGN, deepTools, and Numbat - and updates to these 9 applications: AmberTools, bedtools, ChimeraX, DSSR, DivCon Discovery Suite, Homer, ISOLDE, Modeller, and MoRDa. See Software Changes below for complete details.
Kuang Shen from University of Massachusetts Medical School is our newest SBGrid member. Welcome to the Shen lab!
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Resources for Remote Work
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We've heard from many SBGrid members during the last month who are struggling to get their home environments set up for productive work. Please check out these resources and contact us at accounts@sbgrid.org if you have questions.
TIPS FROM OUR ADVANCED RESEARCH COMPUTING (ARC) TEAM
We asked SBGrid's ARC team, who provides systems administration support for Boston-area labs, for some tips on how to combat common problems when working from home. They offered these potentially useful tidbits, with the caveat that these are but a few ways to tackle these issues and should not be considered an official endorsement. Contact our ARC team for additional information at help@sbgrid.org
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Slow or unstable network connections to your lab computers getting you down? Consider implementing persistent console and desktop sessions or combining graphics programs running locally with remote data access. |
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Awkward passage through your firewall? You might try configuring jump hosts in your local ~/.ssh/config file; password-less authentication using an ssh-agent; or tweaking the configuration of the VPN option for your existing firewall |
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Better yet, why not make some of these solutions work together? |
SOFTWARE INSTALLER: Our software installation client is probably our most popular tool these days. The installer has a graphical interface for Mac and command-line options for either Linux or Mac. It allows users to pick-and-choose subsets of applications to install on multiple machines and kick off updates when convenient. To give it a try, complete our installer registration form.
SBGrid WIKI: You'll find many answers to common questions on our wiki, including instructions for getting started with our installation client, how to implement version overrides, work-arounds to use SBGrid with Mac 10.15 Catalina, and how to get the v2 beta release of our command line installation client.
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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:
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Yale University's Anna Pyle describes her investigation of the reverse transcriptase MarathonRT, its demonstrated processivity, and its ability to efficiently sequence complete long RNAs in a new publication in Journal of Molecular Biology. MarathonRT's utility in assisting structure determination on long RNAs using SHAPE and DMS-MaP, and in detecting natural post-transcriptional modifications, contribute to its appeal as a powerful new investigative tool for RNA research. [Abstract]
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In a new paper in Structure, Michael Cianfrocco of the University of Michigan reports on an automatic, robust workflow crafted to ease the challenge of preprocessing for single-particle cryo-EM, a user friendly pipeline for multiple experience levels. [Abstract]
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From our graduate student desk, Harvard student Kristen Rodrigues highlighted a new Cell publication from Stephen Cusack's EMBL Grenoble laboratory, in which the authors visualize cryo-EM structures of transcription elongation, termination, and recycling states of influenza polymerase, providing a foothold for researchers designing drugs targeting the influenza polymerase inhibitor. [Read more].
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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:
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Structural biology applications used in this project were compiled and configured by SBGrid [1].
[1] A. Morin, B. Eisenbraun, J. Key, P. C. Sanschagrin, M. A. Timony, M. Ottaviano, and P. Sliz, “Collaboration gets the most out of software.,” Elife, vol. 2, p. e01456, Sep. 2013.
Link to article: https://elifesciences.org/articles/01456.
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3DNA 2.4.4 has a fix to bug in reported base-stacking areas. Find a full listing of recent updates on the 3DNA website.
AmberTools 19 is the new default. This version includes CUDA-enabled pbsa updates and major updates to the packmol_memgen tool for building lipids and bilayers. You'll notice faster tree-code analysis and support for periodic systems in rism3d, better pathways for complex transformations and support for pmemd in FEW. Check out sander for constant redox potential simulations, directional pressure scaling, and QM/MM interface to Fireball;
moft for volumetric analysis of water/ion densities using Lapacian analysis; and cpptraj for new extensions and improved scripting options.
bedtools 2.29 adds support for the “=” and “X” CIGAR operations to bamtobed, has a new -C option to the intersect tool that separately reports the count of intersections observed for each database (-b) file given, a new -L option to L`imit the output of the `complement tool solely to the chromosomes represented in the -i file, and fixes a number of bugs.
ChimeraX version 0.93 generates cartoons up to 6X faster, saving session files uncompressed (20X faster save, 3X faster restore, 2X bigger files). Users will also find that commands are speedier (show, hide, color, select, style, size, transparency) when acting on all objects, open2 and save2 commands were rolled out to replace open and save, toolshed is now based on Python 3 and supports the ~= compatible release operator in dependencies, and a new option to us .gz to save a compressed file.
cryoID version 1.0 was added to SBGrid. cryoID is a graphical user interface for identification of proteins from cryo-EM maps.
cryoDRGN is new to SBGrid 0.2.0. cryoDRGN is a neural network-based algorithm for heterogeneous cryo-EM reconstruction.
deepTools 3.3.1. is another new tool. deepTools is used to map reads data for multiple quality checks, creating normalized coverage files in standard bedGraph and bigWig file formats, which allows comparison between different files (for example, treatment and control).
DSSR 1.9.9 includes a new --nt-mapping option so users can specify how modified nucleotides are mapped to their canonical counterparts. The DSSR-PyMOL interface was also refined for producing the characteristic block schematics.
DivCon Discovery Suite version 7.5 is a significant re-write, focused on improvements to QM/MM-based crystallographic refinement and analysis tools including XModeScore and Phenix/DivCon. New features include integrated crystallographic protonation and tautomer/protomer characterization, speedier (~140-fold) CPU time for QM/MM calculations, expanded parallelism with PBS and SGE integration, and integrated density-driven docking (using MOE) for scoring fragment/ligand binding modes. Also new is a tool for crystallographic "water picking" using a Phenix/DivCon with MOE:3DRISM.
HOMER is now at version 4.9. We'll be pushing out additional updates to this tool soon.
ISOLDE version 1.0b5 was pushed out. New optimizations improve speed (~20x) when choosing the initial map contour levels and the MDFF coupling constant, a new option to explicitly specify the GPU to use for simulations with the command "isolde set gpuDeviceIndex {a number}" is available for multi-GPU machines, a new command - "isolde set timeStepsPerGuiUpdate" - to adjust the number of simulation steps between GUI updates, and a reminder that ISOLDE is now fully compatible with ChimeraX's session save/restore.
Modeller 9.24 is primarily a bugfix release, but users may notice an option to label single-chain models 'A' by setting automodel.blank_single_chain to False, a change to treat MEX and ABU residue types as other ligands so they are no longer automatically converted to CYS, regardless of the setting of env.io.convert_modres, and an update to the bundled version of HDF5 to 1.10.5.
MoRDa 32 is the new default.
Numbat version 0.999 was added to the SBGrid collection. NUMBAT is a new user-friendly method built for automatic Δχ-tensor determination.
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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 | |
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