Newsletter Nov 2011

Newsletter for November, 2011

Dear Consortium Members and Affiliates,

We have posted our latest structural biology tale on the SBGrid website. Paul Emsley and a brief history of Coot is the subject of our latest missive. Click through to read a bit about Paul's motivation and desires for the future of his baby, Coot.

We have a small update planned for this month which includes new versions of SPIDER, the Schrodinger Suite, TCoffee, ctffind/ctftilt, RCrane, HKL2000, PSIPRED, WHATCHECK and Coot and a few new packages including Avogadro and Ilastik.

New Members

Four new members have joined the SBGrid Consortium this month including our first member at the UC Davis.

Jawdat Al-Bassam at the University of California, Davis.

Richard Baxter is one of three new members at Yale University, including Yorgo Modis and the Yale Chemical and Biophysical Instrumentation Center headed by Eric Paulson.

Welcome to all of our new members!

Software Updates

The following software updates will be available later tonight or tomorrow:

Linux and Mac OS X (Intel and PPC)

SPIDER has been updated to version 20.02. The exciting news about this version of SPIDER is that the latest version of 'web' now supports real 24-bit color! No more VNC hacks or tweaked out wrapper scripts forcing 8-bit color X11 set ups... yay! Release notes, docs and more are available on the SPIDER website.

T-Coffee has been updated to version 9.01. T-Coffee has a variety of excellent documention including technical docs and a nice tutorial. Requested by Harrison Lab at Harvard Medical School.

Nico Grigorieff's ctftilt and ctffind tools have been updated to the 20111001 version. Requested by Leschziner Lab at Harvard University. There is documentation and some sample data sets to play with on Niko Grigorieff's ctf website.

RCrane has been updated to version 0.9. This is the version that Kevin Keating was using in his recent webinar. You can read more about Rcrane on the Pyle Lab software page.

HKL2000 has been updated to version 0.98.703. This version should have support for all the latest detectors. There is a PDF of the HKL2000 manual online. Requested by Rich Hite, MacKinnon Lab.

PSIPRED has been updated to version 3.2.1. There's not a ton of info on this package, even on the PSIPRED download site.

Linux only

The Schrodinger Suite has been updated to version 2011 update 1. The Schrodinger website has PDF release notes listing new features and fixed bugs in the suite.

WHATCHECK has been updated to version 9.0. More info is available on the WHATCHECK website.

Coot has been updated to version 0.7-pre-1-r3697 as a part of the long slog to eradicate bugs. The Coot website has extensive resources.

OS X Intel only

ilastik is a new package for "simple, user-friendly tool for image classification and segmentation in up to three spatial and one spectral dimension." There is documentation on the Ilastik website. Requested by Guobin Hu, Hogle Lab at Harvard Medical School.

Avogadro is new package for the SBGrid distribution offering an "advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas." The Avogadro website has documentation and more. Requested by Pedro Pereria, Pereira Lab, Universidade do Porto.

Bug Reports

WHAT_CHECK was misconfigured in the i386-linux tree. Reported by Erik Debler, Blobel Lab, Rockefeller University.

HADDOCK had a syntax error related to newer versions of Perl. The perl script was fixed for compatibility with modern Perl. Reported by Sabine Abakayov, Wagner Lab, HMS.

CCPNMR was broken on OS X 10.5 systems. We recompiled the application for 10.5 support. Reported by Remy Sounier, Chou Lab, HMS.

POINTLESS was linked against a missing library in the OS X Intel branch. We updated the binary to remove the bad library dependency. Reported by Michael Lazarus, Kahne Lab, Harvard.

Thanks for reading!

Published November 1, 2011