Dear Consortium Members and Affiliates,
This is the SBGrid summer roll up newsletter.
The July SBGrid Tale featured Anna Pyle, and the August tale is about Zbyszek Otwinowski.
If you missed any of the webinars from our SBGrid Tea Break series, don't despair. We have added a webinar archive posting that includes playback links for previously hosted webinars, so you can listen at your leisure. Not every developer permits us to post these links on our website, so be sure to tune in for the actual event whenever possible.
Our webinar series will resume in October with the following presenters: James Chen of MIT will give a combination seminar/webinar on Thursday, Oct 4th, to describe PARTICLE, a software package for single-particle EM image processing. And don't miss Ronan Keegan's presentation on the new release of CCP4 on November 4th. Complete details can be found in the news section of our website.
With the release of Mac OS X 10.8 Mountain Lion in August, we will be dropping support for OS X 10.5 on Intel Macs this month. Existing software should continue to work, but we will not be testing or deploying applications for 10.5 machines at that point, and we will move to OS X 10.6 as our supported base platform.
The July software update included new versions of CCP4, CCP4mg, Mosflm, iMosflm, NMRPipe, BLAST, PARTICLE, Chimera, XMIPP, CS-Rosetta, Simulaid, MMC and the RCSB PDB Validation tools.
Note that CCP4 6.3.0 is not currently the default version, so in order to use it, you need to use a version override file. Please try it out if you want to see the latest and greatest from the CCP4 group. We will probably make it the default version in late September.
The August update included a recent PHENIX nightly version and updates to XDS, Coot, MAIN, the RCSB PDB validation tools, 2dx, NMR relax, AUTO3DEM, Bsoft, EMAN2 and APBS. The new packages are Dynamo, Specview and PyTOM.
We had three new members join in July, and six new members join in August.
George Phillips has joined our existing members at Rice University in Houston. Oliver Ernst also joined an existing contingent of SBGrid members from the University of Toronto. Finally, Evripidis Gavathiotis is our first member at the Albert Einstein College of Medicine in New York.
Hao Wu is our latest member investigator at the Immune Disease Institute. Nicholas Reiter joins the large existing member group at Vanderbilt University. Gabby Rudenko and Daniel Southworth are our newest members at the University of Michigan. Finally we have two new members at the Okinawa Institute of Technology, Ulf Skoglund and Fadel Samatey.
Welcome to all of our new members!
CCP4 has been updated to the most recent release. CCP4 is now fully integrated with ARP/wARP. ArpNavigator has also been added and supports automatic assignment of secondary structures. SBGrid members using CCP4 software should subscribe to the CCP4 mailing list. We will follow up with an SBGrid webinar on November 1st and SBGrid members are also invited to join the CCP4 study weekend in the UK (January 3-5, further details will follow soon).
We have upgraded Phenix to a recent release. Notable improvements include new bulk-solvent and overall anisotropic scaling procedure, phenix.model_vs_data returns overall molprobity score as well as new commands: phenix.den_refine and phenix.find_peaks_holes.
maxit, a utility developed by PDB, can be used to convert between PDB file formats. Some of the supported options include conversion from PDB to CIF, validation of the PDB format, generation of NCS related strands, deletion and insertion of residues and atoms, insertion of virus matrices and conversion from orthogonal to fractional system. For the full list of 58 options type 'maxit’ in your SBGrid shell.
Data Processing applications: iMosflm and Mosflm were upgraded to the most recent versions. The notable improvements include better handling of Pilatus images and fine-tuning of strategy GUI. XDS was upgraded to the most recent version.
Model Building Applications: Coot was upgraded to the most recent release and we have also installed the most recent version of the application MAIN (developed by Dusan Turk at Jožef Stefan Institute in Slovenia). MAIN supports model building, refinement and structure analysis.
NMR Applications: Dynamo, relax, CcpNmr SpecView, NMRPipe and Chemical-Shift-ROSETTA (CS-ROSETTA) were upgraded to the most recent releases.
BLAST: We have upgraded to version 2.2.26. A notable change includes the addition of the DELTA-BLAST (Domain Enhanced Look-up Time Accelerated BLAST) application. DELTA-BLAST uses the Conserved Domain Database (CDD) to perform initial alignments. You will need to install the CDD database on your local system in /programs/share … directory to use this feature. Installation instructions can be found on the NCBI website. You might also want to review a recent paper about using BLAST to design target-specific primers.
Electron Microscopy: PARTICLEis a new EM application that was written by James Chen. We will continue to provide the application Signature, which was previously developed by James at Brandeis University. Chimera 1.6.2 introduces a new command ‘changechains’ which would allow you to swap chain IDs. EMAN2 has been upgraded to version 2.06. This is the final, stable release before version 2.1, which will be a major upgrade. Notable improvements include a major reworking of the tomography applications and significant performance improvements. AUTO3DEM, an automated image reconstruction system developed by Tim Baker's lab at UCSD, has been upgraded to the most recent release. Version 4.02 includes capsid_generator - a new utility to generate PDB files listing coordinates of the points in an icosahedral lattice. PyTomis an application developed by Friedrich Förster at Max Planck Institute of Biochemistry, Martinsried. PyTom unifies standard tomogram processing steps in a single python-based toolbox.
Simulaid is a new package we have introduced for analysis of molecular simulation, developed by Mihaly Mezei from Mount Sinai School of Medicine. Reference: M. Mezei, Simulaid: a simulation facilitator and analysis program, J. Comp. Chem., 31, 2658-2668 (2010). We have also introduced another program developed in his laboratory for simulation of molecular assemblies (Metropolis Monte Carlo - MMC).