Dear Consortium Members and Affiliates,
Due to an early flu bug laying waste to the SBGrid offices and employees, we missed our September update window, but we have a nice update for October available this evening. Updated packages for this month include Xplor-NIH, Chimera, MrBUMP, NMRPipe, Coot and 2dx, and the new packages include MCCE and Fasta35.
We are pleased to announce that we have negotiated a favorable agreement with Dr. Frank Delaglio of NMRScience to provide NMRPipe 2008 to the entire SBGrid consortium at no additonal charge to our members.
We also have several new software packages in the pipeline that depend on a customized version of Python that has the Numeric and SciPy modules installed.Â We expect to have this special Python build done soon and plan to push out a small update next week for the programs that depend on this customized Python.
We'll send out a brief email with more details at that time. Linux and Mac OS X (PPC and Intel)
MCCE version 2.2 is a new program requested by an SBGrid member at Vanderbilt. Multi-Conformation Continuum Electrostatics is a biophysics simulation program combining continuum electrostatics and molecular mechanics. Protein side chain motions are simulated explicitly while the dielectric effect of solvent and bulk protein material is modeled by continuum electrostatics. MCCE can be used to study protein structural responses to changes in charge, changes in charge state of ionizable residues due to structural changes in the protein and the structural and ionization changes caused by changes in solution pH or Eh. It can also find the location and stoichiometry of proton transfers coupled to electron transfer and make side chain rotomer packing predictions as a function of pH. More details can be found on the MCCE home page including documentation and the FAQ.
UCSF Chimera has been updated to version 1.2540. Detailed documentation, tutorials and related information can be found on the excellent Chimera website.
MrBUMP, the CCP4 group's software for automated molecular replacement, has been updated to version 0.4.4. Along with this update, we have installed the latest FASTA 35 packages as well as the command line Graphviz packages for use with the CCP4i DBviewer. The MrBUMP website has an overview and a tutorial to get you started.
NMRPipe has been updated to version 2008. This is the official NMRPipe package from NMRScience. The NMRPipe reference page has a wealth of information how using and customizing NMRPipe in your environment.
Mac OS X PowerPC Only
2dx has been updated to version 3.0.6. This brings the PowerPC version into parity with the OS X Intel and Linux versions which were updated to version 3 in a previous update.