Dear Consortium Members and Affiliates,
It's officially summer time at HMS, and there is not much news to report. It's raining again in Boston, and we will have a small update later today that includes Curves+, AMIGOS II, NMRView and NMRPipe.
The following software updates will be available today:
Linux and Mac OS X (PPC and Intel)
Curves+ is the latest version of the Curves package. The Curves+ website has documentation on using Curves+ and some of the helper programs that are also installed. Note that the PDF user guides located on the download page contain accurate usage information. The examples on the website do not exactly work.
AMIGOS II is a new package from the Pyle Lab at Yale University. AMIGOS allows the user to perform interactive comparisons between RNA structures and to conduct database searches for specific RNA structures or substructures. There is a readme with instructions available in the program directory: /programs/
NMRView has been updated to version 8.0.a49. There's a long list of changes in the release announcements, but online documentation continues to be a bit thin.
NMRPipe has been updated to a version from June 9, 2009. It appears that this new version does not include TALOS+, but I can't find much other information about it.
Xmipp 2.3 was missing libjpeg on linux. Reported by Sjors Scheres, an Xmipp developer, while he was visiting the Wang Lab at Yale University.
The USF Gerard utilities are now in the standard path without their platform specific prefixes (i.e. no osx_ or lx_). Suggested by Mark Mayer, Mayer Lab, NIH and Olve Peersen, Peersen Lab, Colorado State.
Thanks for your bug reports!
This month we are pleased to welcome the Peersen Lab at Colorado State University as a new SBGrid member.
We are often asked for recommendations on suitable hardware for Linux-based structural biology workstations. We are constantly evaluating new hardware and new vendors, and our current recommendation is the Sun Ultra workstation series. The Sun workstations are reasonably priced with multiple options for hardware support and are tested by Sun to be compatible with Red Hat/CentOS. In our testing here, they have worked out of the box with both our standard CentOS operating system installation and the structural biology applications.
We have secured a quote with GovConnection that any SBGrid Consortium Lab can use to purchase the top of the line Sun Ultra 24 workstation. The base system is available for around $1300, which is a savings of about 20% off the retail price. You can contact GovConnection directly using the contact information in the quote available on our website.
As always, we recommend that you consult with your local IT group to ensure that this machine will meet any requirements they may have. If your institution has a dedicated Sun sales representative, you should ask them to assist you with a purchase, as you may be able to get a slightly better deal. If you do end up ordering one of these machines, we'd love to hear your feedback on how it has worked out for you.
This evening we'll have updates for Coot and SHELX, along with three new applications: Qnifft, Theseus and Muscle. The list of upcoming software updates includes CCP4 6.1.2, PyMOL 1.2r1, NMRViewJ 8.0b2, EMBOSS 6.1.0, SPIDER 17.15, Bsoft 1.5.7, CCPNMR 2 and Frealign 8.07.
The following software updates will be available today:
Linux and Mac OS X (PPC and Intel)
Coot has been updated to revision 0.6-pre-1-revision-2131. Paul Emsley has been keeping up his usual rapid development pace, and I expect to be updating Coot at least monthly until things slow down a bit. If there is a feature or bug fix in a particular version of Coot that you need sooner, please email bugs@sbgrid.org with your request, and I'll try to oblige. Since these are all pre-release versions, there are no formal announcements of new features or bug fixes, but you can use the change log available on Google Code to find out what's new.
SHELX 97-2 has been updated with the latest binaries from the SHELX web site. It appears to have been mostly bug fixes with few new features added. Requested by the Springer Lab at the Immune Disease Institute.
Qnifft version 2.2 is a new package this month. It is a macromolecular electrostatics program based on finite difference solutions to the Poisson-Boltzmann equation and is an outgrowth of the DelPhi macromolecular electrostatics software. This version of Qnifft is maintained by Dr. Kim Sharp at the University of Pennsylvania Medical School. There is a README file in the program directory along with some example files that demonstrate how to use the software. Requested by the D'Souza Lab at Harvard University.
Theseus version 1.4.3 is an application for maximum likelihood superpositioning and analysis of macromolecular structures. The Theseus website has additional details including PDF documentation, which is also in the program directory. This was a request by the Peersen Lab at Colorado State.
MUSCLE version 3.7 is multiple alignment software for protein and nucleotide sequences similar to FASTA or CLUSTALW, but it's supposedly faster and more accurate. This was recommended by the Theseus developer for use with the theseus_align script. The MUSCLE website has news and documentation.
No bug reports this month!? Everyone must be taking time off to enjoy the summer weather. Or I'm doing a really good job...