Dear Consortium Members and Affiliates,
As with much of the country, and the world, July brought many new procedures and a return to the laboratory for some Harvard researchers. Most of our SBGrid team will continue to work from home for the foreseeable future, and we have the usual round of news as the month draws to a close, with new webinar recordings online and planning for the fall lineup, an SBGrid tale featuring Priyamvada Acharya from the Duke Human Vaccine Institute, 7 new members to welcome, 10 software updates, and 3 publication highlights.
We wrapped up our webinar series in July with a presentation from Tom Goddard on the cutting edge work in ChimeraX for augmented reality videos. We also heard updates on the science happening in several structural biology laboratories from Mike Sheedlo in Borden Lacy's group at Vanderbilt, Makaia Papasergi-Scott in Georgios Skiniotis's Stanford lab, Evan Worden from Cynthia Wolberger's group at Johns Hopkins, and Brent Nannenga at Arizona State University. You'll find most of these presentations posted on the SBGrid YouTube channel. Link to webinar details. [Webinar details here].
Priyamvada Acharya from the Duke Human Vaccine Institute is the subject of our monthly SBGrid Tale. Movement is what brought her to structural biology and what allowed her lab to stay open through the pandemic. Acharya was quick on her feet, quickly pivoting and applying her knowledge from 15 years of research into HIV to SARS-CoV-2 . She is encouraged by signs that SARS-CoV-2 is not nearly as nimble as HIV, and leaves itself more vulnerable to attack. [Read the full story].
This month's software push included updates to these 10 titles: ATSAS, BioXTAS RAW, CCP4, ChimeraX, crystFEL, crYOLO, DIALS, Geneious, ProFit, XDSGUIccp47.1.002. See Software Changes below for complete details.
July brought seven new members to SBGrid, a welcome sign that science is still proceeding in the face of (and in response to) the pandemic, including several new members from institutions and countries we have not previously supported: Evangelia Chrysina from the National Hellenic Research Foundation in Greece, Ji-Joon Song from Korea Advanced Institute of Science and Technology in South Korea, Aneel Aggarwal from Icahn School of Medicine at Mount Sinai, Alex Vecchio at University of Nebraska, Franziska Bleichert of Yale University School of Medicine, Chi-Min Ho at Columbia University, Adam Middleton from Otago University, and Mark Bathe of MIT. Welcome to our newest members!
Over 100 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:
ATSAS version 3.0.2 is available.
BioXTAS RAW version 2.0.2 was pushed out. This version fixes a bug in loading SAXSLAB images, allows loading of .dat files that are comma separated and from WAXSiS.
CCP4 version 7.1.002 is available.
ChimeraX version 1.01. With the bump to 1.0 users will notice a new options to color a surface from an image file, and open Chemical Component Dictionary entries as structures, show chain sequences in the same way that a structure's chain table in the log shows them, create geometric shapes (sphere, ellipsoid, cylinder, cone, triangle, etc) as surface models, construct peptides from scratch using the Build Structure tool.
CrystFEL was bumped to version 0.9.1 (Linux only), and is primarily a bug fix release.
crYOLO 1.7.4 makes the switch from multiprocessing to multithreading permanently. We removed the option --use_multithreading due to problems with the program freezing.
DIALS version 220.127.116.11.3 is available.
Geneious is now at version 2020.1.2. See the full release notes for details.
ProFit version 3.3 adds support for reading individual models from a PDB file by adding %n to a filename (where n is the model number): pdb2kqn.ent%2 will read MODEL 2.
XDSGUI 20190417 is the new default.
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.
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More information about the SBGrid Consortium is available at http://sbgrid.org
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