Dear Consortium Members and Affiliates,
I hope you are enjoying the hot summer months. With our system architect Ian Levesque participating in a two-week grid computing workshop, we are running a bit behind. Nevertheless, in the last month we still managed to resolve 165 tickets. This is more than our average 137 per month showing that most of you are still around!
We are happy to welcome three new consortium members: Mark Mayer, Loren Walensky, and Robert Oswald. In this newsletter, you can also read about our plans for Fedora Core 7 support. In the hints section, you can read about programs for displaying and manipulating graphics files on Linux and Mac OS X.
Software updates will be sent to your site tonight, Wednesday, July 18. This month, crystallographers will be receiving two new applications SGXPro and Xia2. We also have several updates this month, including the molecular graphics application MOLMOL, the MRC Image Processing System, the sequencing program BLAST, the NMR applications CARA and Ligplot, the EM applications SPIDER and PFT3DR, and the crystallography applications Phenix and Coot.
Immediately after receiving the software updates tonight, you will be using the newest installed versions. If there are any problems, please report them (http://www.sbgrid.org/bugs). You can always switch to an older version of the application while we work on your request—just use ‘sbgrid –n’ for more information. Many of these monthly updates and additions are prompted by member requests, so please do not hesitate to request new applications (http://www.sbgrid.org/req).
Please continue reading for full details.
Piotr Sliz, Ph.D.
Group Leader, Structural Biology Computing Group, SBGrid
We would like to welcome the following new SBGrid members:
Dr. Mark Mayer from the National Institutes of Health. Dr. Mayer's lab studies "the ligand gated ion channels which mediate excitatory synaptic transmission in the CNS." More details can be found on the lab's website.
Dr. Loren Walensky at the Dana-Farber Cancer Institute and Children’s Hospital Boston. Dr. Walensky's lab studies "chemical biology of deregulated apoptotic and transcriptional pathways in cancer." More details can be found on the Dr. Walensky's webpage.
Dr. Robert Oswald at Cornell University. Dr. Oswald's lab studies "the structure and function of proteins involved in signal transduction". You can read more on his lab's website.
gThumb is a lightweight image organizer with some basic editing capabilities that comes with the Gnome desktop. Gimp, the GNU Image Manipulation Program, is the Photoshop of the Linux world; it rivals Photoshop in both number of features and in complexity, but for complex tasks, the Gimp is a powerful tool. Finally, the Imagemagick suite of tools can do command line manipulation of almost any image format. All three of these applications are available in a full Fedora Core desktop install, but if your machine doesn't have them, they easily installed with yum.
Mac OS X
For Mac OS X, there is of course Preview for simple viewing and exporting to different image formats. Imagemagick is also available at your site for Mac OS X. Lastly, there is a version of Gimp available for Mac OS X. Tips on installing Gimp on your local system can be found on this website.
Fedora 7, the successor to Fedora Core 6, was released on May 31, 2007. Fedora 7 features GNOME 2.18 and KDE 3.5.6. Additionally, it allows for fast user switching, hot plugging of display devices and improved power management. SBGrid has begun testing software titles with Fedora 7, and we hope to fully support our software titles on Fedora 7 by early September.
The following software updates will be available later tonight:
Linux and Mac OS X (PPC and Intel)
Blast will be upgraded to 2.2.16. This version includes performance enhancement for nucleotide searches. It also fixes some object manager leaks, a memory leak, and includes other error fixes. You can use the included script, update_blastdb.pl, to grab the latest databases from NCBI.
PFT3DR will be upgraded to the latest version (20061202). This package is a combination of PFT2, which is used to determine orientations and origins, and EM3DR2, which computes 3-D reconstructions based on the determinations of PFT2. It was originally developed for 3-D cryogenic electron microscopy. Full details on the program can be found on the PFT3DR website.
The MRC Image Processing System will be upgraded to sources released in June 2007. This is mostly a maintenance update on our part to ensure that the programs will work with the latest versions of the Fedora and Macintosh operating systems.
MOLMOL will be upgraded from 2k.1.0 to 2k.2.0. MOLMOL is used for displaying, analyzing, and manipulating macromolecule structures with special emphasis on the structures determined by NMR. Click here for details on the release.
Spider will be upgraded from 13.0 to 15.06 for Linux. It will also be upgraded to 14.18 for Mac OS X (PPC and Intel).
Cara will be upgraded to 1.8.4. This release offers many new features, including labeling explicit support of isotopes and a new repository file format. Due to this new file format, it is important to make a backup of any older CARA file before opening it in this new version as there is a chance that the labeling-scheme will be removed. For full release notes, please visit the CARA website.
Ligplot will be upgraded to 4.5.3. This update improves compatibility with newer Linux distributions, changes bond orders to read in from the CIF-format Het Group Dictionary, and adds additional options in ligplot.prm file for "chemical notation" plots.
Coot will be upgraded to 0.3.3. This version fixes the display frame and the filter button for file selections. Release notes can be found on the Coot website.
Linux and Mac OS X Intel
Xia2 0.2.6.0 is a new system which quickly reduces raw diffraction data. This reduced data can be input into a phasing program to quickly start finding the structure. Full details can be found on the Xia2 website.
Phenix will be upgraded to from 1.26b to 1.3b for both 32-bit and 64-bit machines. This update includes a conversion to the latest version of wxPython, along with revised documentation which can be found on the Phenix website. We plan to introduce the OS X version of Phenix next month.
SGXPro 0.7 is a new program which automates structure determination. It will consecutively execute a series of crystallographic program automatically, including searching for the best programs and parameters automatically. For full details, please read the “sgxpro_readme.doc” file in the sgxpro/0.7/ directory.