Dear Consortium Members and Affiliates,
There's a new release of Mac OS X out... yay! Mac OS X 10.6 Snow Leopard is an officially supported release for the SBGrid Software Suite, so open tickets if you find anything is broken. In my testing, most things run without problems, but I also don't exercise the software the way you all do.
In other OS X news, as of November 1, 2009, I will stop building and testing on Mac OS X Intel 10.4. Building and testing of software for Intel Macs will be done on OS X 10.5 and 10.6 from that point forward. Software for Mac OS X PowerPC will continue to be built and tested on version 10.4 and 10.5.
Mac OS X has generally good forward and backward compatibility, so I suspect people won't have problems with 10.4 Intel Macs for another year or more, but I won't be testing the software on that platform, and bug reports will be low priority. Please plan accordingly.
The update last month was a fairly large one, and we filled a few disks out there. Unfortunately our software distribution system doesn't have a good way to test for available disk space, and it will sometimes blow things up with the disk gets filled. Our official recommendation is to use at least a 250 GB disk for your SBGrid software installation, so please take a moment to check the available disk space for your installation and contact your sysadmin or make plans as necessary to upgrade.
In the queue to get installed or updated is CCP4, APBS, SnB, PyMOL, Frealign and T-Coffee. We also have a handful of not-exactly-crystallography software like R, GNUPlot and GNU Plotutils on the list. And along the lines of the EMBOSS discussion that is happening on the members mailing list, I also have notes to test out UGENE, GENtle and ApE to see if they would be useful additions to the software suite.
If you have an opinion on that matter or anything else related to SBGrid, send us an email at help@sbgrid.org or start a discussion on the members mailing list at members@sbgrid.org.
The following software updates will be available today:
Linux and Mac OS X (PPC and Intel)
PHENIX nightly build version 1.4-153 has been installed. It is now the default version, and I have done away with the 'setenv PHENIX_L nightly' silliness, so please remove it from your ~/.sbgrid file if you were trying it out. If you want to use the "stable" and now quite outdated 1.4-3 version, please use a ~/.sbgrid file to override the default version. Requested by the Springer Lab at the Immune Disease Institute among others.
Coot has been updated to nightly version 0.6-pre-1-r2246 for the OS X branches. On linux, we are running 0.6-pre-1-r2263. The list of changes can be found on the Coot Google Code site.
Bsoft has been updated to version 1.5.7. The change log lists some of the bug fixes and new features. Requested by the Stephen C. Harrison Lab at Harvard Medical School.
PFT3DR has been updated to version 20090717. The two programs, PFT2 and EM3DR2, are user for computing three-dimensional reconstructions from two-dimensional projections of 3D objects. More details are available on the PFT3DR website. This package depends on the Bsoft library, so it has to be updated whenever we update Bsoft.
Perl version 5.10.1 has been installed in the software suite. This was a prerequisite to use some of the web-based features of T-Coffee, which will be appearing in the next few weeks. All things Perlish can be found on the Perl website.
Since I had to install Perl, I went ahead and added BioPerl version 1.6.0 to the installation, so you can get your bioinformatics thang on. The BioPerl website has an FAQ, HowTos and some tutorials to get you started.
I tweaked the HKLDIR setting once again. Here's the final disposition. If you have HKLDIR set in your shell environment before sourcing the labcshrc, it will be honored. If it is unset and /usr/local/hklint exists, then HKLDIR will remain unset. If it is unset and /usr/local/hklint does not exist, then HKLDIR will be set to $HOME/hklint. I think this should satisfy the requirements of every site that I know is using HKL2000. Please open a ticket if I have broken your unique (peculiar) set up.
Pointless and Othercell in CCP4 6.1.1 on OS X Intel and PowerPC were linked against missing libraries. Relinked them against the proper libraries. Reported by Tom Brett, Fremont Lab, Washington University.
Thanks for your bug reports!
Dear Consortium Members and Affiliates,
If you are on the mailing list, you probably saw Ian Stokes-Rees announcement about our upcoming GPU Workshop which will focus on the use of graphics chips for processing scientific data. All the details on how to participate can be found on the GPU workshop page.
We have a small update planned for later today. CCP4, PHENIX, PyMOL, Modeller and ProFit are all being updated to their latest versions. CCP4 updates tend to be a little involved, since there are so many components in the CCP4 suite it's hard to test everything. All the major bits are working, so please open a ticket if you notice any problems.
Is there any interest in seeing a branch of the SBGrid software suite for Microsoft Windows? Email bugs@sbgrid.org if you are interested or post to the mailing list with your thoughts.
Y'all take care now.
The following software updates will be available later today:
Linux and Mac OS X (PPC and Intel)
CCP4 has been updated to version 6.1.2 including all the listed fixes on the problems page. Documentation is available on the CCP4 website. As I mentioned before, everything I tested is working fine, so please open tickets if you notice any problems, and I'll push updates to address them as quickly as possible.
PHENIX nightly build version 1.4-162 has been installed. It is the default version, and we have added a 64-bit build for Linux at the same time. I'm exploring the possibilities for compiling a more heavily optimized version of PHENIX, but for now, these are the binary builds available from the PHENIX project. Note that the documention on the PHENIX website is for version 1.4-3, which is quite old at this point and has diverged in features and keywords from the version in the software tree. The current PHENIX documentation is in the software tree at file:///programs/i386-linux/phenix/1.4-162/phenix-1.4-162/doc/index.html and in both the i386-mac or powermac branches.
PyMOL has been updated to version 1.2r1. For the unhappy few forced to run Windows occasionally, I included the latest PyMOL installer for Windows in the /programs/share/pymol/windows directory. The APBS plugin is included, but I have not installed any other plugins just yet. Let me know if I left your favorite PyMOL plugin out.
Modeller has been updated to version 9v7. This is primarily a bug fix release; details are in the release notes.
ProFit, an application for protein least squares fitting program, has been updated to version 3.1. The ProFit documentation is available on their website.
Spock is broken for OS X. Since it is distributed only as binaries, I have removed it from the software tree. I contacted the author to see if there is an updated version available, but haven't heard back yet. Reported by Yoonsang Cho, Lolis Lab, Yale School of Medicine.
A G5-only version of libgmp.dylib snuck into our last Coot build for OS X PowerPC. I replaced it with a version that runs on G4s. Reported by Jochen Zimmer, Rapoport Lab, Harvard Medical School.
Thanks for your bug reports!
We have a small update planned for later today. CCP4, PHENIX, PyMOL, Modeller and ProFit are all being updated to their latest versions. CCP4 updates tend to be a little involved, since there are so many components in the CCP4 suite it's hard to test everything. All the major bits are working, so please open a ticket if you notice any problems.
Is there any interest in seeing a branch of the SBGrid software suite for Microsoft Windows? Email bugs@sbgrid.org if you are interested or post to the mailing list with your thoughts.
Y'all take care now.