Dear Consortium Members and Affiliates,
It's JULY, and time for our mid-summer update on what's new at SBGrid. Read on for a reminder about July renewals, our monthly tale featuring Montserrat Samso of Virginia Commonwealth University, a software push with 8 updates and one new title - AlphaFold! - a welcome to 10 new members, position postings at the University of Leicester and right here at SBGrid, and 2 member publication highlights.
July 1 marks the beginning of our fiscal year and our common renewal date for all SBGrid members. All members should have received an email with a link to an invoice. Many thanks to all those who have already processed the payment. If you have not received the invoice for your renewal, or if you have any questions about payment options, please contact us at email@example.com.
For our July SBGrid Tale we connected with Montserrat Samso, from Virginia Commonwealth University, for whom mountains figure prominently, from the Catalonian range that is her namesake, to those she treks in her off-hours, to those mountains of the ion channel world - ryanodine receptors - that are the focus of her research. [Read the full story].
This month's software push includes updates to CCP4, ChimeraX, COOT, DIALS, ORCA, PyMOL, and SAMtools, and one new, and highly anticipated, title: AlphaFold. See Software Changes below for complete details.
July has our technical team doing some virtual globe-trotting with 10 new members: Edmund Ndip from Hampton University, Matthias Baernthaler from Max Perutz Labs in Austria, Tomas Kouba from the Institute of Organic Chemistry and Biochemistry in Prague, Pontus Gourdon at the University of Copenhagen, Maria Spies and Sandipan Chowdhury at University of Iowa, Feng Zhang of the Broad Institute, Adrian Keatinge-Clay from University of Texas, Austin, Rick Page from Miami University, Ohio, and Vincent Tagliabracci of UT Southwestern.
Welcome to our newest members!
Technical notes from our Software Team
July is the month of software licensing and SBGrid member renewals, and this year we have some additional logistical hurdles with a couple of new add-on options, the transition to an opt-in model for licensed software, and a new and improved version of our software installation manager. Please email us at firstname.lastname@example.org if you are encountering any problems or are unsure how to access the requested software.
Licensed Software: For those of you who opted in for access to Schrodinger or Geneious, we’ll be in touch soon with new credentials for continued access to these tools.
Installation Manager: Many users rely on our software Installation Manager, with graphical and command-line options for Mac and Linux, to install a subset of the SBGrid software collection on workstations at home or in the lab. If you are not already using this tool (freely available to users in SBGrid member labs) and would like to try it out, register for an account at www.sbgrid.org/registration/register/.
For some labs that were early adopters, users will need to do an account migration to ensure that all new features are available. The migration is quick and painless and we'll contact you soon with migration instructions.
For those looking for a change of pace or to share with your communities, we have a couple of new position postings to highlight, one from SBGrid member Daniel Panne at the University of Leicester and another for our own SBGrid team:
LINUX SYSTEM ADMINISTRATOR
SBGrid Consortium at Harvard Medical School in Boston MA is in need of a full-time, potentially remote, Linux System Administrator to support our structural biology and software curation environments. [Job posting]
POSTDOC – STRUCTURAL BIOLOGY OF GENOME REGULATION
The Panne Group at University of Leicester is seeking a postdoctoral fellow with a background in Biochemistry, Biophysics or Molecular Biology with a track record in conducting internationally competitive research who is creative and ambitious with good communication skills and keen to work on challenging projects. Experience in biochemistry of protein complexes, insect cell expression systems, X-ray crystallography or cryo-electron microscopy would be particularly beneficial. [Job posting]
Over 70 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:
AlphaFold is eagerly anticipated and new to SBGrid. This version is an implementation of the inference pipeline of AlphaFold v2.0 using a completely new model that was entered in CASP14. Running this package requires a couple of extra steps, downloading the databases (>2TB) and running the wrapper script. See our AlphaFold usage notes on our Wiki for more information.
CCP4 version 7.1.015 includes updates to shelxe with -O3 side chain tracing (give rootname.seq file with fasta format for each chain), new RVAPI histogram function, and gemmi was updated to version 0.4.6.
ChimeraX is now at version 1.2.5.
COOT version 0.9.6 includes several new features: middle-mouse and double-clicking enabled for moving atoms, -P mode added to pyrogen, model_correlation_stats_per_residue_range() added to the API, molecular (i.e. not crystallographic) symmetry added, coot-find-ligand mode to generate conformers, new API function to flip the side-chain of the active atom of the moving atoms: side-chain-flip-180-intermediate-atoms, and coot-identify-protein, a new program for identifying proteins from a poly-ALA fragment and a set of sequences.
DIALS 3.5.2 fixes the display of spot-finding intermediates and updates dials.image.viewer so stacking images no longer gives incorrect results for multi-sweep data.
ORCA 5 is a major new release with an overhaul of the core engine of the program, which is now leaner, more efficient, and more able to adapt to extensions in an ever shifting hardware landscape. Part two of this overhaul is planned for 2022, but Orca 5 includes a bevy of new features detailed in this forum post (note, you will need to register to view this post). We bumped the version to 5.0.1 for some bug fixes.
PyMOL 2.5.1 is a maintenance release with some minor bug fixes.
SAMtools 1.13 is the new default and includes new options to set and clear flags to samtools view and long option equivalents for most mam-view single-letter options. SAMtools coverage
now allows users to set the maximum depth (default is 1000000), using the -d/--depth, and SAM flag now accepts any number of command line arguments so that multiple SAM flag combinations are converted at once. SAMtools depth had a complete rewrite that improves speed and eliminates the need for a depth limit to avoid high memory usage. Users will also notice that samtools import reads one or more FASTQ files and converts them into unmapped SAM, BAM or CRAM, samtools ampliconclip now accepts the --tolerance option, which allows the user to set the number of bases (default is 5) within which a region is matched, and three new counts in samtools flagstat: primary, mapped primary, and duplicate primary.
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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