Dear Consortium Members and Affiliates,
Party time! The monthly update is here! Also the students are back, the campus is crowded and Boston traffic is a mess. The pedagogical cycle begins again.
The update this month includes new versions of CCPNMR, STAMP, REFMAC, PSIPRED, SPIDER, 2dx, NMRView and two new packages: LigPlot+ and R.
Excellent!
New Members
The Hogan Lab at La Jolla Institute for Allergy and Immunology is the newest SBGrid Consortium member. Dr. Hogan is internationally recognized for his work on the calcineurin-NFAT pathway, which regulates gene transcription in many cell types, and for his work on cellular calcium signaling. Welcome!
Software Updates
The following software updates will be available today:
Linux and Mac OS X (PPC and Intel)
STAMP has been updated to version 4.4. This is a tool for the structural alignment of multiple proteins. There is a good STAMP manual. Requested by Van den Berg Lab at Umass Medical.
PSIPRED has been updated to version 3.2. Requested by the Sliz Research Group at HMS.
CCPNMR has been updated to version 2.1.5. The excellent CCPNMR website has tutorials and other documentation. Requested by the Selenko Lab at the Leibniz-Insitut fur Molekulare Pharmakologie.
The mtz2sca and mtz2hkl scripts were updated to the latest version. Requested by the Harrison Lab at HMS.
REFMAC 5.6 is now in the software tree. refmac5 is the version 5.5 binary and refmac now defaults to the version 5.6 binary. The REFMAC home page has documentation on the changes.
OS X Intel and Linux
LigPlot+ is a new version of the venerable LIGPLOT software by Roman Laskowski. It contains some bug fixes and new features, but the notable addition is a new graphical interface for running calculations. The LigPlot+ website has a manual and some additional notes.
R, the statistical plotting and analysis package, is a new software title for us. Version 2.11.1 is installed and in the PATH. Documentation and more is on the R website.
SPIDER has been updated to version 18.15. News and views and SPIDER howtos are on the SPIDER website.
2dx has been updated to version 3.1.2. The 2dx manual and other documentation are available on the new 2dx website. Requested by the Walz Lab at HMS and the Gonen Lab at the University of Washington.
NMRViewJ has been updated to version 8.0rc8. Bruce Johnson, the developer, is working out the final kinks before a full 8.0 release, and we'll update to that version when it becomes available. Documentation is available via the Help menu in the application. Requested by the D'Souza Lab at Harvard University.
Bug Reports
The following bugs have been fixed since the last newsletter:
The Grace plotting tool configuration was incorrect for linux machines. The environment settings were tweaked and Grace was updated to the latest version. Reported by Bryan Lepore, Van den Berg Lab.
Nedit was missing some libraries on some machines. The missing libraries were added to the main software tree. Reported by Wilhelm Weihofen in the Gaudet Lab.
O's ODAT setting was incorrect for users of the new modular configuration system. Reported by Gary Frey in the Harrison-Chen Lab at Children's Hospital Boston.
The PROCHECK task in the CCP4 suite pointed to an incorrect version of bplot. The task module was fixed. Reported by Barry Kreutz in the Eck Lab and Hitoshi Inada in the Gaudet Lab.
The APBS utility in PyMOL was missing some linked libraries on 64-bit linux machines. The binary was rebuilt semi-statically to resolve the issue. Reported by Samuel Stampfer in the Heldwein Lab.
LABELIT was spewing an error when running labelit.version. We reported the bug to Nick Sauter, and it is now fixed in the latest versions of PHENIX. Reported by Bryan Lepore, Van den Berg Lab.