Dear Consortium Members and Affiliates,
To close out 2022 we have a mini-newsletter with a reminder of SBGrid holiday closures, webinar news, three new members to welcome, and a mid-month software push.
SBGrid offices will officially close from December 22 through January 2. During the holiday break, we'll be on the look out for emergencies, but other requests will be on hold until January 3rd. Happy Holidays and see you in the new year!
At last week's webinar we heard from Thomas Simonson on Proteus, software for physics-based protein design. If you missed the live presentation, the recording will be up on the SBGrid YouTube channel soon. We'll start the new year with a presentation from Chris Waudby, Group Leader at University College London, on TITAN: Getting the most from NMR titration experiments with two-dimensional lineshape analysis. Join us January 10th - register here!webinar front - general link to YouTube channel
Our December mid-month software push includes updates to ChimeraX, cryoCARE, NMRPipe, PDBFixer, PyTOM, and XPLOR-NIH, plus 3 new titles: ESMFold, ModeRNA, and TM-Align. See Software Changes below for complete details.
Three new members joined us in December: Mark Yeager from University of Miami, Nami Tajima of Case Western Reserve University, and Jailson Brito Querido from University of Michigan. Welcome to our newest members!
Position postings: Alexandra Deaconescu's laboratory at Brown University has openings for two postdoctoral researchers and one technician funded by a new multi-year grant from the NIH. The laboratory's interests lie primarily in stress responses, with particular emphasis on responses to DNA damage and the mechanochemistry of large macromolecular machines. [See full details]
ChimeraX 1.5 is out with an update to v4 for AlphaFold database searches, colored lines that show AlphaFold residue-residue errors, Axes/Planes/Centroids tool to define objects, a surface transform command to scale, shift, or rotate surface coordinates, a new add hydrogen GUI, an addcharge command that looks up Amber force field charges for standard residues, a new dockprep command, a new tool to renumber residues and change chain IDs, new crosseye and walleye stereo modes for the camera command, improvements to the close session command that restores more startup settings, updates to UniProt, a new DICOM browser that shows patient-study-series hierarchy in medical image data.
cryoCARE 0.2.1 adds a GPU ID selection option and updates sample jsons.
ESMFold is new to SBGrid at version 1.0.3. ESMFold harnesses the ESM-2 language model to generate accurate structure predictions end to end directly from the sequence of a protein.
Julia 1.8.3 includes bug fixes and improvements to documentation.
ModeRNA 1.7.1 is another new title. ModeRNA is used for comparative modeling of RNA 3D structures.
NMRPipe 20221123 is the new default.
PDBFixer was bumped to version 1.8.1.
PyTOM 1.0a is available for Linux.
TM-Align is new to the SBGrid collection. TM-Align is an algorithm for sequence independent protein structure comparisons.
XPLOR-NIH 3.6 includes the addition of Darwin_arm64-native architecture for M1-based Macs, new helper programs calcPr and calcTrace, for computing a pair-distance distribution and the corresponding DEER trace, added facilities (atomProbHeight, maxHeight) to aid in the use of height data in structure calculation, and a number of other bug fixes and improvements.
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 https://sbgrid.org
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