Dear Consortium Members and Affiliates,
We are changing our software update procedure! You will have access to new versions of applications on the following morning after the newsletter is distributed.
This month, you will receive updates to Coot, SOLVE/RESOLVE, XPLOR-NIH, PHENIX and CCI Apps, and HKL2MAP. To check that you indeed have access to the latest programs, run ‘sbgrid -v’ and look for ‘20070523’. 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). Last month, in response to your feedback, we made number of corrections to the existing distribution. Bug fixes were applied to BnP, ccp4i (OSX), Amber, and a few other applications.
Please continue reading for details on the software updates, the winner of the best application challenge, Fedora Core 6 tips, and more.
Piotr Sliz, Ph.D.
Structural Biology Computing Group, SBGrid
Coot was chosen by you as the most useful application in the SBGrid tree. Thank you to the numerous members who took the time to respond—your feedback is not only appreciated, but completely necessary in order for us to bring you pertinent and relative information, applications, and events.
Restore Launch Terminal Functionality by Right-Clicking Desktop in Fedora Core 6
Miss the Terminal icon when you right-click on the desktop? There’s a package in Fedora Extras called “nautilus-open-terminal” that brings this functionality back. To install, run as root: 'yum -y install nautilus-open-terminal'. See this and other Fedora Core 6 installation notes on the SBGrid Member Wiki.
Customizing the Menu Bar
Fedora Core 6 also gives you extensive control over the menu bar whose default location is the top of the screen. For example, instead of restoring the right-click terminal functionality, you can actually add it to your menu bar. Simply right-click on the menu bar and select "Add to Panel...". From the list, select Application launcher, click Forward, expand Accessories, click on Terminal, and finally click “Add”.
You can of course use to the Add to Panel command to add other included functions, or to create shortcuts to frequently used applications.
The following software updates will be available on Thursday morning:
Linux (32-bit and 64-bit) and Mac OS X (PPC and Intel)
SOLVE/RESOLVE will be upgraded from to 2.12 to 2.13. This upgrade includes many new features including multi-domain NCS, an automated loop fitting algorithm and automated fitting of flexible ligands to electron density maps in RESOLVE. It also features quicker model building which, according to the release notes on the SOLVE/RESOLVE website, is now three times faster than previous versions.
XPLOR-NIH will be upgraded from 2.16.0 to 2.17.0. XPLOR-NIH, based on XPLOR with additions from NIH, is used by our NMR affiliates. This release includes bug fixes, updates to example scripts, improved handling of PDB entries with chain identifiers, and much more. Please see the XPLOR-NIH website for full release details.
Note: Due to a member request, XPLOR-NIH 2.17.2 will also be included in the distribution. Since this is not the most stable version, the default will still be 2.17.0 for all branches. To switch to 2.17.2, simply modify your .sbgrid file to add the following line: setenv XPLOR-NIH_L 2.17.2.
HKL2MAP 0.2 is now available on Macs. According to the authors, “HKL2MAP is a graphic user interface for macromolecular phasing” and it provides a graphical interface to SHELX and xfit. For full details, visit the HKL2MAP website. Please note that Xfit is not included in the Mac distributions, but you can still use HKL2MAP to find heavy atom sites.
Linux (32-bit) and Mac OS X Intel Only
Coot will be upgraded from version 0.2 to 0.3.1. This release addresses a few crash/bug issues along with added functionality. For example, you can now start with an unphased mtz file and proceed to REFMAC refinement in COOT. Also, the concept of “Active Residue” was added. For full details of many changes, see the release notes.
Linux Only (32-bit and 64-bit)
PHENIX will be upgraded from 1.24.1b to 1.26b. This version includes many changes (documented in the file CHANGES found in the phenix-1.26b folder). These include the integration of Reduce (phenix.reduce), many improved wizards for model building, loop building, omit maps, etc. Phaser, Textal, Resolve ligand identification, phenix.xtriage, phenix.refine, eLBOW, phenix.explore_metric_symmetry, phenix.twin_map_utils, mmtbx.remove_outliers, Phenix GUI, and the installer all have been updated (changes, bug fixes, optimizations, etc.) In response to a user request, we have included the 64-bit version of Phenix for the first time in this release. The SBGrid initialization scripts will detect your environment and select the 32 or 64 bit version automatically.
Included in the PHENIX upgrade is an update to CCI Apps to version 2007_04_26_2350. Changes since the previous version include many bug fixes, new features (ground_anomalous and twin refinment, support for all hydrogens in refinment), integration of phenix.reduce into CCI Apps, and more. See the full changes at the bottom of the CCI Apps webpage.