Dear Consortium Members and Affiliates,
Howzya! We are eagerly anticipating the arrival of Ronan Keegan, Charles Ballard and Stuart McNicholas from the CCP4 project who will be in Boston on Friday to host a day-long seminar on various CCP4 tools. We're supposed to have a short break from the wretchedly hot weather Boston has had this year, which will hopefully give them a nice impression of Boston so we can lure them back in the future.
We are now including the ICCB chemical libaries for in-silico screening in the software tree. You can find them in the /programs/share/iccb directory. All compounds included in this library are available at the ICCB Longwood Screening Facility.
We have a large update planned for later today that includes CCP4, Coot, PyMOL, Gnuplot, Jalview, CCP4mg, Xmipp, HKL2000, Chimera, Ultrascan, BEST, HADDOCK and WHATCHECK as well a 3 new packages: Open Babel, FFmpeg and Matt. Oy gevalt! I promise not to wait this long between updates again!
The following software updates will be available tonight or tomorrow:
Linux and Mac OS X (PPC and Intel)
CCP4 has been updated to version 6.1.13. This update includes the latest patches for BUCCANEER as well as the ARP/wARP plugin. Documentation, tutorials, 20 year old newsletters and everything else you can think of is on the CCP4 website. Requested by everyone.
Coot has been updated to version 0.6.2-pre-etc. This equates to Subversion revisions 3011 for OS X and 3064 for linux. The update conttains mostly bugfixes, since Paul Emsley is getting close to an official 0.6.2 release. Requested by everyone.
PyMOL has been updated to version 1.3. The usual plugin suspects, eMovie, APBS, Mole, have all been installed as well. The PyMOL wiki is a nice resource for all things PyMOL. Requested by everyone.
Gnuplot version 4.4.0 has been installed for all branches. The Gnuplot home page has documentation, demos and more. Requested by Pascal Lab at Thomas Jefferson University and Leschziner Lab, Harvard University.
Jalview has been updated to version 2.5.1. This is a bug fix update to the 2.5 release from last month. Documentation is on the website. Requested by Garcia Lab at Stanford.
Open Babel is a new application for the SBGrid collection. It is a utility that allows you to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, and biochemistry and includes support for reading more than 90 file formats. Version 2.2.3 is installed for all branches. More information is on the Open Babel home page.
FFmpeg version 0.6 is another new application for the SBGrid collection. It is a utility for recording, converting and streaming audio and video, and it is used by several of the graphics packages for building movies. If you really want to read it, FFmpeg documentation is on their website. Requested by Sliz Lab, HMS.
Matt is a new application for doing multiple protein structure alignment. It uses local geometry to align segments of two sets of proteins, allowing limited bends in the backbones between the segments. There is a Readme online, but precious little documentation. Requested by Springer Lab, Immune Disease Institute.
HADDOCK has been updated to version 2.1. HADDOCK (High Ambiguity Driven biomolecular DOCKing) makes use of biochemical and/or biophysical interaction data such as chemical shift perturbation data resulting from NMR titration experiments, mutagenesis data or bioinformatic predictions. Details and documentation can be found on the HADDOCK website.
Linux and OS X Intel
CCP4mg has been updated to version 2.4.1, and we are now including a 64-bit version for linux. With the inclusion of FFmpeg, you can now easily make movies in CCP4mg. Rock on! Requested by Sliz Lab at HMS.
XMIPP has been updated to version 2.4. We are also including the MPI linked binaries for running on multi-core machines and clusters. More information is on the Xmipp website. Requested by Leschziner Lab at Harvard University.
Linux
XDSi version 0.92 is a new application for the i386-linux branch. It is a small graphical application for configuring XDS jobs. It looks kind of brittle, with hard-coded paths to various things, and a dependency on some external applications, but it basically seems to work. Someone with a little Tcl-fu could probably make it quite nice for general use. The documentation is on the XDS wiki. Requested by one of our Berkeley Labs.
HKL2000 has been updated to version 0.98.699k2. There is a (possibly ancient) PDF of the HKL2000 manual in the installation directory.
Chimera 1.4.1 for 64-bit linux machines has been added to the linux branch. All things Chimera are on the UCSF Chimera website. Requested by Harrison Lab, HMS.
ULTRASCAN has been updated to version 9.9. This is a tool for analytical ultracentrifugation, so it's a bit of a niche application for most structural biologists. I took a poke at getting the OS X release to run in our environment, but it's not a simple affair. If you anticipate needing to run Ultrascan on your OS X machine, please open a ticket, and I'll see if we can make it work. To run this software, you'll have to request a license key on the Ultrascan website. Requested by one of our labs at the University of Houston.
OS X Intel
BEST 3.2.0 has been added for OS X Intel machines. Here's the BEST manual. Requested by Beese Lab at Duke.
WHATCHECK, the test and error checking routines from the WHATIFF package, has been updated to version 8.0 for OS X Intel. We had an earlier version, but I'm not sure it ever worked, and this one definitely does! Better check that structure before you submit it. Documentation is on the WHATCHECK website. Requested by Heldwein Lab, Tufts University.
The following bugs have been fixed since the last newsletter:
GRACE aliases on OS X Intel and PowerPC were broken. Reported by Ian Stokes-Rees, Sliz Group.
Several small bugs in PHENIX were fixed with patches provided by Nat Echols of the Alber Lab/PHENIX project. Thanks Nat!
ProtSkin, a python application, was pointing to the system python, and not our custom python in the software tree. Reported by John Williams, Williams Lab.
ccp4i, when run from a case-insensitive file system, was occasionally breaking due to an artifact of our software distribution system. Reported by Venkat Dharmarajan, Cosgrove Lab.
Thanks for your bug reports!