December 2007 SBGrid Newsletter
Dear Consortium Members and Affiliates,
We will be pushing a small update tonight which includes new versions of CCP4 Molecular graphics, REFMAC and Rosetta. Have a safe and happy Holidays.
Piotr Sliz, Ph.D.
Structural Biology Grid (SBGrid)
NSF Research Coordination Network The version of X11 shipping with OS X Leopard has been a subject of much discussion on Apple's x11-users mailing list. For heavy users of X11 applications on OS X, the shipped version has been found to be somewhat buggy and lacking in features that were available in the Tiger version of X11.
In response to the many bug reports posted by users and to expedite development of X11 on OS X, the Apple developer responsible for X11 integration into OS X has created a community-oriented development site at MacOS Forge. You can download an updated X11 that includes many bugfixes and some additional features from the download page. This is highly recommended if you are using X11 applications under OS X Leopard. The Apple developers will eventually include this new X11 in an official Software Update, but there is no deadline for that to happen at this time.
The following software updates will be available later tonight:
Linux and Mac OS X (PPC and Intel)
CCP4 Molecular Graphics has been updated to version 1.1 for all supported platforms. New features include a picture wizard that set up standard scenes automatically and offers easier labeling. It also features less automatic superposition to complement the SSM automatic tools, lipid cartoons and an editable picture definition language. The full list of CCP4MG features is available.
Note that CCP4MG has not yet been updated to run on OS X Leopard.
REFMAC5 has been updated to version 5.4.0066 for all supported platforms. Garib Mushudov reports that this version has bug fixes, performance enhancements and additional stability as well as some as yet unannounced new features. This is the new default version in the CCP4i graphical interface.
REFMAC5.5 is an experimental build that has refinement against SAD likelihood function installed for all 3 platforms. The SAD target incorporates the phase information from SAD experiment, gaining it directly from the heavy atom coordinates and F+ and F- differences. The requirements of SAD target are at least one element with number of electrons higher than 8 and known f',f'' formfactors present in the input pdb file and the F+,F-,SIGF+,SIGF- labels. More information is available on the REFMAC website.
You can switch between refmac versions on the command line by specifying a version in your ~/.sbgrid file. More information on customizing your versions is available on our member wiki.
ROSETTA 2.2.0 is a new install for all supported platforms. Rosetta can be used for improving NMR and homology models before they are used in molecular replacement. Please see a recent article from Baker group that was published in Nature for more details. Visit Rosetta Commons for more information.
Mac OS X (Intel)
IMAGIC5 is a new installation for Intel Macs this month. Note that you must have negotiated a separate license for this software. Contact foobarbaz to arrange for access to this software.