Dear Consortium Members and Affiliates,
Newsletters are boring, don't you think? We did a software update on Tuesday this week. Hopefully it went off without a hitch, and you can continue to work on meaningful scientific projects without worrying about all the software tools that make them possible.
The PyMOL webinar that we held a couple weeks ago was our biggest to date. We had 75 online attendees and 25 more in the room. Thanks to all the participants and to our speaker, Jason Vertrees. We have fixed the audio issues that came up during that webinar; sorry about the problems!
The list of updated software for October includes PHENIX, XPLOR-NIH, CcpNmr, Modeller, XIA2, Jalview, Rosetta, PyRosetta, RnamlView, UNIO, ImageJ and the PDB Remediator from Richardson Lab.
Y'all take care now.
Mark your calendars for Afternoon Tea with SBGrid. We will finish off the year with webinars/seminars on DEN, RCrane and Phenix in October, November and December. Please see the SBGrid Consortium website for details. You can subscribe to the SBGrid Calendar to stay up to date with upcoming events.
It's curious how new members seem to join in waves. It will be quiet for a few months, and then we'll have 8 new members in a single month.
Weikai Li joins us from Washington University in St. Louis.
Peter Kwong is our newest member from the National Institutes of Health.
Tamir Gonen has a new lab at HHMI's Janelia Farm facility.
CS Raman is our first member from the University of Maryland.
Kevin Corbett is our latest member from the University of California at San Diego.
Soumya Ray has joined us from Brigham and Women's Hospital right down the street here in Boston.
Matthias Wolf is starting a new lab at the Okinawa Institute of Technology.
And we have added one new industrial member this month: Novartis Vaccines and Diagnostics in Siena, Italy.
Welcome to all of our new members!
The following software updates should be available now:
Linux and Mac OS X Intel
PHENIX has been updated to the latest release version 1.7.2-869. The PEHNIX website has excellent documentation. The PHENIX mailing list is a great place to ask questions and learn more about the software. Requested by Engin Ozkan, Rob Campbell and others.
XPLOR-NIH has been updated to version 2.29. The XPLOR-NIH website has documentation, tutorials and change log listing the bug fixes and new features of this version. Charles Schweiters, the developer, is very helpful if you into problems.
CcpNmr has been updated to version 2.2.1. The latest CcpNmr versions 2.2.x are for users who are interested in testing the newest features being developed by the CCPN team. These new features include automated bug tracking and many new features to make it easier to handle magic-angle spinning solid-state NMR.
Important: If you save a project with Analysis 2.2.* you will not be able to then run Analysis 2.1.5 on the same machine unless you have installed all of the updates for version 2.1.5. (Version 2.2 has always been able to read older projects). The EBI and BMRB deposition systems and iCing do not currently accept 2.2.x projects. The gory details are on the CCPNMR website.
Modeller has been updated to version 9.10. I don't know much about the software, but Ben Webb, the current maintainer, is very friendly. You can track him down on the Modeller website.
XIA2 has been updated to version 0.3.3.3. The XIA2 website has release notes, documentation and an example data set to help you get started. Graeme Winter rocks your socks.
Jalview has been updated to version 2.7. The Jalview website has pretty good documentation. Not yet requested by the Garcia Lab, but they would have gotten around to it if we hadn't.
Rosetta has been updated to version 3.3. To quote from Andreas Forster's post to the CCP4bb, Rosetta is "viciously obfuscated and the learning curve correspondingly steep, but once you've figured things out, it's quite powerful." Jump in with both feet on the Rosetta website. Requested by Andrew Ring, Michael Durney, Vinodh Kurella and Engin Ozkan!
PyRosetta has been updated to version 2.0beta1 to work with the latest Rosetta release. Python's powers of de-obfuscation are widely know. Read more on the PyRosetta website. Requested by Engin Ozkan.
RnamlView is a "visualization tool that displays/edits 2-dimensional diagrams of RNA/DNA secondary structures with tertiary interactions created by RNAView". There is a basic introduction to using the software on the RnamlView website. Requested by Piotr Sliz.
UNIO is another new package used for NMR. Torsten Herrmann, the developer, was very helpful in getting it set up. Find out more on the UNIO website. Requested by Adrien Favier at IBS Grenoble.
ImageJ is a versatile java-based image manipulation tool. From the docs, it can "can display, edit, analyze, process, save and print 8-bit, 16-bit and 32-bit images. It can read many image formats including TIFF, GIF, JPEG, BMP, DICOM, FITS and "raw". It supports "stacks", a series of images that share a single window. It is multithreaded, so time-consuming operations such as image file reading can be performed in parallel with other operations." We have included the BioFormats ImageJ plugin which suports numerous additional image formats used in structural biology. Requested by Brent Livesay from one of our member labs at Vanderbilt University.
The PDB Remediator tool from the Richardson Lab can convert your PDB file between version PDBv2.3 and PDBv3.2. The full description is available on the Remediator website.
Coot on some Red Hat/CentOS 5 machines was showing broken button images. Using the SVG button images from an earlier version resolved the problem. Reported by Chris Bzymek at City of Hope.
PHENIX was not detecting the new 3.0 release of the linux kernel properly. The new release fixes that bug. Reported by Rob Campbell at Queens University.
Thanks for your bug reports!