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Dear Consortium Members and Affiliates,
With the close of June, we come to the close of our annual subscription period and a flurry of activity. In this monthly update you'll find information about renewals, our upcoming Animation Workshop, a software push with 11 updates and 5 new titles, one new member to welcome, a technical note on accessing the PyMOL license file, new features for CryoEM facility management of multiple software collections, open position postings from our community, and three member publication highlights.
It's time for our annual July renewals so please be on the lookout for a renewal invoice in your inbox. We are not permitted to accept payment prior to July 1, but please rest assured that SBGrid support will continue uninterrupted. We are transitioning to a new system, so the invoice may look a bit different than in past years and we appreciate your patience as we work through a few bugs that caused some extra delays this year. A few notes to keep in mind for renewals: |
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We're excited to host our first in-person workshop in over two years with Janet Iwasa of The Animation Lab joining us for a 5-day, intensive Animation Workshop that will run from August 1-5 in Boston. We've had a few of cancellations due to travel issues, so we are accepting PI/Group leader nominations for a couple of open seats. Experience using Chimera and PyMOL for animations or figures is required. One nomination accepted per lab and approved on a first come, first served basis. Complete nomination form.
Our June software push includes updates to AlphaFold, AutoPROC, BioXTAS RAW, BUSTER, ChimeraX, CCPEM, Coot, crYOLO, emClarity, EVcouplings, and GPHL suite, along with these five new software titles: Assembline, GHECOM, globus-cli, OpenFold, and Relion block-based reconstruction. See Software Changes below for complete details.
We have one new member to welcome for June: Martin Pilhofer of ETH Zurich.
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Technical notes from our Software Team |
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PyMOL: The SBGrid “incentive PyMOL” license is updated annually in June and is included in the software distribution. The license does not need to be updated manually in PyMOL, but if your application reports an expired license, please check that you are using the latest SBGrid release. Also check your ~/.pymol directory, which may contain an expired license file which takes precedence. Please let us know if you have questions or problems at bugs@sbgrid.org.
CryoEM Facility Members: We’ve rolled out some new features to help CryoEM facility staff manage multiple software collections for different user types. Facilities managers can utilize UNIX credentials for controlling access to a collection. For additional information, please see our CryoEM Facility Management Overview or contact us at bugs@sbgrid.org.
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Community Announcements |
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Navaratnam Laboratory, Yale School of Medicine The Navaratnam Lab has an opening for a postdoc who would like to expand his/ her/ their horizons in CryoEM. The lab has new funding for five years to investigate the voltage dependent structural changes in the membrane motor protein prestin that is responsible for outer hair cell electro-motility. They are seeking a motivated and enthusiastic person to work on this project and hope to build on recently published cryoEM structure of prestin in detergent. The wider cryoEM group at Yale is large, deep and nurturing. Contact the Navaratnam Laboratory to apply.
ModeX Therapeutics Focused on developing flexible, multi-specific antibody technology platforms with broad targeting and functional capabilities for multiple disease areas, ModeX Therapeutics has the following open positions:
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Member Publications Highlights |
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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:
Deposit your experimental datasets: If you're currently preparing a manuscript, please remember that, while you're making the PDB record deposit and publication submission, you can also preserve your primary experimental datasets with deposits to the SBGrid Data Bank.
Acknowledge SBGrid: SBGrid operations are funded with member fees and grants, so we are grateful when you are able to acknowledge SBGrid in your presentations and publications.
Please use this SBGrid logo on the acknowledgements slide of your presentations.
We recommend the following boilerplate language for inclusion in publications that report results obtained with SBGrid supported software: |
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SBGrid citations: SBGrid's eLife paper received two new citations in the month of June, from these SBGrid-member laboratories: Walter Chazin of Vanderbilt University in Biochemistry: Modification of the 4Fe-4S Cluster Charge Transport Pathway Alters RNA Synthesis by Yeast DNA Primase; Hao Wu of Boston Children's Hospital in Science: Structure of cytoplasmic ring of nuclear pore complex by integrative cryo-EM and AlphaFold.
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Software Changes |
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AlphaFold 2.2.2 fixes a bug introduced in v2.2.1
Assembline is new to SBGrid at version 1.03. Assembline is a multi-step protocol for integrative structural modeling of macromolecular complexes based on electron microscopy, cross-linking mass spectrometry, and other data.
AutoPROC 20220608 now supports images that follow the CBF/mini-cbf v2.0 specification, gzipped mini-cbf files "out of the box", based on the xds-zcbf plugin developed at EMBL-Hamburg. Users also have additional control over image metadata to better support in-house data, and a new tool (aP_suggest_xds_parameters) to assist with parallel processing decisions when using XDS.
BioXTAS RAW was bumped a couple of releases to 2.1.3, which includes a prebuilt version for arm64 chips on MacOS, support for Eiger2 images from BioCAT, improved handling of multi-image files, a new dependency on mmcif_pdbx to read mmcif files, and many other bug fixes. Note that RAW is not compatible with pre-release version of ATSAS 3.1.0
BUSTER 20220608 includes a number of new features and improvements, including a new automatic refinement tool ("aB_autorefine") that make it easier to get started by running a series of standard BUSTER refinements and providing a graphical summary of all steps from initial rigid-body to normal refinement with TLS, occupancy and ADP refinement including hydrogens (if appropriate). The developers have also improved the method for automatic adjustment of (relative) X-ray weight to use a resolution-dependent formula for better balance between X-ray and geometry part. Users can select three different
ChimeraX 1.4 allows users to search/retrieve ~1 million structures from EBI AlphaFold DB, display AlphaFold predicted aligned error (PAE) plots, use Google Colab for AlphaFold prediction of multimers (of limited size), use mouse mode for independent centers of rotation, join models with Build Structure tool or command, define axes for display and/or use in measurements, increase/decrease VDW radii relative to their current values, switch PDB residue numbering scheme, align sequences with Clustal Omega or MUSCLE, and calculate % identity in sequence alignments.
CCPEM 1.6.0 is out and is the last release that will include Python 2.7, Coot 0.9 and RELION 3.1. Future CCP-EM versions will use Python 3, Coot 1 and RELION 4. It is also the last release that will support Red Hat / CentOS 6 or similarly old Linux versions.
COOT 1.005 is out for Linux. Note that non-default, live interactions with REFMAC and Phenix are not working in this build.
crYOLO 1.8.3 fixes a dependency problem of pystardb.
emClarity 1.6.1 fixes a bug interfering with higher-order symmetry, adds: support for Nvidia Ampere architecture natively, saves unmasked halfmaps for EMDB deposition, and saves XML FSC plot for upload to emdb.
EVcouplings 0.1.1 is out. Please be sure to update your config files to include new mandatory parameters. New features include integration of a novel logistic regression-based model to assign globally comparable probabilities to ECs. Users should select scoring_model: logistic_regression in the couplings section of your monomer config. To use the previously scoring models choose "skewnormal" or "normal." There are improvements to contact map plotting that show alignment coverage, missing structural coverage, and used PDB IDs. This release also fixes deprecations causing problems with pandas and improves database syncing of results for EVcouplings webserver (available at https://v2.evcouplings.org).
GHECOM 20211201 is new to SBGrid. GHECOM finds multi-scale pockets on protein surfaces using mathematical morphology.
globus-cli 3.6.0 is also new. Using this stand-alone application users can access the Globus service. It also allows the use of wildcards.
GPHL suite 20220608 is out. This suite is the Global Phasing Limited collection of software available to for-profit groups with a license.
OpenFold 0.1.0 is, you guessed it, another new title. OpenFold is a faithful PyTorch reproduction of DeepMind's AlphaFold 2.
RELION Block-based-recontruction 20220512, is a RELION fork with block-based reconstruction modifications that is now available as a separate application.
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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 https://sbgrid.org Report software bugs: sbgrid.org/bugs
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