Dear Consortium Members and Affiliates,
Hello. Hello? Is this thing on? What's up? This is the SBGrid newsletter.
We have a new SHARP/autoSHARP server set up for Consortium members. As a part of the set up for this new server, we also moved to a unified LDAP accounts system, which means the login credentials for previous SHARP users are no longer valid. When you are ready to use SHARP again, please send an email to email@example.com asking for access to the new SHARP server, and we'll send you a password and instructions on how to access the new server.
The latest Structural Biology tale features Pamela Bjorkman, Max Delbruck Professor of Biology at California Institute of Technology and member of the Consortium since 2006.
We are in the midst of scheduling two SBGrid webinars in June. Clemens Vonrhein will talk about SHARP/autoSHARP on June 19th, and Woody Sherman will give a general presentation on Schrodinger. More details will follow shortly, so stay tuned.
Newsletter fatigue set in, and we didn't send one in April, so here is the combined list of software updates for the last two months. April updates included new versions of PHENIX, PyMOL, Relax, XDS, BEST, NMRPipe, Rcrane, xv and Coot. The new packages for April were RELION, PLOTMTV, Caver, PROMALS and GeFREALIGN.
Updates for May include Coot, MOSFLM and iMosflm, REFMAC and IMOD. The new packages this month are PROSMART, mrprep and the mrprep GUI and xdsme.
SBGrid Affiliate Job Postings
SBGrid Affiliates can now announce new employment opportunities to the SBGrid community. To add your posting to our website and newsletter, email Michelle Ottaviano firstname.lastname@example.org with the position advertisement and/or a link to the position posting. To see a listing of all currently posted positions, check the SBGrid website.
The following software updates will be available later tonight or tomorrow:
Linux 32-bit, Linux 64-bit and Mac OS X Intel
PyMOL was updated to version 22.214.171.124. You can read the change log. This version is much less buggy than the initial 1.5.x releases. We hope. Requested by the Fan Lab at Columbia.
PHENIX nightly version dev-1041 was installed. The PHENIX nightly docs are in their usual place. Requested by everyone.
Coot was updated to 0.7-pre-1-4122 for OS X and 4135 for Linux. You can read the endless Coot change log on its Google Code site. If I'm reading Paul's burn-up chart correctly, the full 0.7 release should be out shortly. Requested by everyone.
IMOD was updated to version 4.5.2. New features and fixed bugs are listed in the change log and there are copious other resources on the IMOD website. Requested by the Leschziner Lab at Harvard University.
XDS was updated to version 20120315. This was a bug fix release.
xdsme is a new package for the software tree that tries to provide a friendlier interface to XDS. There is a tutorial and other documentation on the xdsme website. This packaged was developed by and is in use at the SOLEIL synchrotron. Requested by the Pereira Lab at Universidade do Porto.
MOSFLM and iMosflm were updated to their final releases, 7.0.8 and 1.0.6 respectively. There were a few bug fixes from the betas released with the same version, but no major changes.
REFMAC version 5.7 has been added to the software tree. It has a spiffy new website with docs and the rest. Requested by the Harrison-Chen Lab at Children's Hospital Boston.
PROSMART is a new package from Murshudov Group for the "conformation-independent comparison of protein structures". People on the CCP4bb seem to like it. The website is here. Requested by the Harrison Lab at Rosalind-Franklin.
mrprep is a new package written by Tim Gruene that can "prepare a PDB file for the generation of external restraints and for molecular replacement based on sequence alignment". It's apparently quite useful in conjunction with PROSMART and is also well-regarded on the CCP4bb. There are command line and graphical versions available and more information can be found on the mrprep website.
Caver is a new package this month for the "analysis and visualisation of tunnels and channels in protein structures." This is the standalone version of a tool that was previously only available as a PyMOL plugin. More information is available on the Caver website. Requested by the Kwong Lab at NIH.
Relax, a tool for NMR relaxation analysis, was updated to version 1.3.14. This is a bug fix release for Macs. Version 1.3.15 should be available shortly promising final feature parity between the OS X and linux versions.
NMRPipe was updated to version 20120309. I took the adventurous step of rewriting the NMRPipe initialization files for sh-syntax shells, so if you're a bash/ksh/zsh user and you're feeling brave, feel free to try out NMRPipe in your default shell.
RELION (REgularised LIkelihood OptimisatioN) is a new tool for Maximum A Posteriori (MAP) refinement of (multiple) 3D reconstructions or 2D class averages in cryo-electron microscopy developed in Sjors Scheres lab. The RELION website has documentation and a tutorial to get you started. This version is build with OpenMPI for use on clusters. Requested by the Ohi Lab at Vanderbilt University.
PROMALS is a package for constructing multiple protein sequence alignments using information from database searches and secondary structure prediction. PROMALS documentation is available online. Requested by the Garcia Lab at Stanford.
xv version 3.10a with all the bug fixes and feature patches to support PNG and other image formats was formally added to the distribution.
PLOTMTV version 1.4.1 was added as a requirement for displaying out from BEST (and other tools).
HKL2000 was updated to 0.98.703x. There is no info on the HKL Software website, as usual.
GeFREALIGN is a GPU-enabled build of FREALIGN 8.06. It is somewhat buggy in my testing, but when it works, it's definitely faster than the CPU version. There is a little bit of info on Yifan Cheng's site, but the main difference is that the refinement and reconstruction steps now use separate binaries. Nothing else is supposed to have changed. If you have a fast CUDA-capable GPU, you should try it out.
BEST was updated to version 3.4.4.
There were many bug reports the last two months. When the software developers give you the product of their time and effort for free, you enter a social contract with them that stipulates you will report bugs so they can be fixed for the benefit of all the software users. Thanks for honoring your part of that contract.
Did you really read all the way down here? Good on ya!