Dear Consortium Members and Affiliates,
We have a small update for you this evening including new versions of XPLOR-NIH, Situs, CCP4mg, IMOD, PHENIX and adxv.
Linux and Mac OS X (PPC and Intel)
XPLOR-NIH has been updated to version 2.23. The change log details the extensive bug fixes and new features.
Situs has been updated to version 2.4.3 for linux and OS X PowerPC and is a new installation on OS X Intel. More information is available on the Situs website.
CCP4mg has been updated to version 1.107.3. This is a bug fix release of the new QT-based CCP4mg. The switch to QT has sped up the interface significantly.
IMOD has been updated to version 3.13.5. This software is a bit tricky to integrate into the SBGrid shell environment. Please let me know if you notice any oddities.
PHENIX version 1.4-78 has been installed. This is a nightly build that includes the new PHENIX graphical interface. Run 'phenix2' from the command line to start the new interface. Note that at the advice of the PHENIX developers, this version has not been set as the default version.
To enable this beta PHENIX version, create a file at ~/.sbgrid with a version override like this:
setenv PHENIX_L 1.4-78
The PHENIX_L shell variable will override the default version setting for the Linux version of PHENIX. To override the default OS X version, use the setting PHENIX_M. More information on overriding default versions for software can be found on our wiki.
I thought we'd try something new in an attempt to keep our members abreast of the changes with the software suite by offering a list of bugs fixed since our last update. This may be more information than most of you want, so let me know if I should leave this out of future newsletters. Without further ado...
NACCESS 2.1.1 was crashing with a bus error on OS X 10.5. Reported by Engin Ozkan, Garcia Lab, Stanford.
BOBSCRIPT 2.6b was linked against incorrect libraries on OS X 10.5. Reporteded by Frederic Metoz, IBS Grenoble.
ARP/wARP's flex_warp expert system was missing some environmental variables needed for use. Reported by Shiven Shandilya, Schiffer Lab, Umass Medical School.
The USF Gerard utilities were missing the aconio program. Reported by Mark Mayer, Mayer Lab, NIH.
adxv 1.9.3 was suffering from an odd bug related to a missing Motif keyboard definitions file that broke the file chooser. Another odd bug: it also couldn't be X-forwarded over SSH to a host operating system newer than Fedora Core 6. Reported by Engin Ozkan, Garcia Lab, Stanford.
REFMAC 5.5.0088 had a bug related to TLS refinement. After a few updates by the developer, Garib Murshudov, we have a working version for linux, 5.5.0093. The Mac branches should receive this updated version soon. Reported by Shiven Shandilya, Schiffer Lab, Umass Medical School.
Thanks for your bug reports!
Dear Consortium Members and Affiliates,
We are pleased to announce a new mailing list for the SBGrid user community, members@sbgrid.org. You can use this list for postings related to the software supported by SBGrid, but postings not directly related to computing are also welcome. As most of us use similar techniques in research, we believe that communication through an SBGrid-wide forum will provide an extra benefit to consortium members. In order to encourage open communication, we have decided to keep the mailing list archives private, so there is no need to fear that conversations will be indexed by search engines.
All registered SBGrid members are initially subscribed to the mailing list. If a member of your lab is not included, PIs can update the list of registered members for their lab by sending an e-mail to accounts@sbgrid.org. If you decide to opt-out, please send email to that same address, and we will remove you immediately.
We pushed a small update overnight that includes Coot, EMAN2 and Xmipp. Most sites should have it by now, but there may be a few final sites that will update this morning.
The following software updates will be available today:
Linux and Mac OS X (PPC and Intel)
Coot has been updated to version 0.6-pre-1-revision-2062 for OS X and 0.6-pre-1-revision-2071 for linux.
EMAN2 has been updated to a nightly build from June 18th, 20090618. This includes all the latest tools and utilities in the EMAN2/Sparx suite.
Xmipp has been updated to version 2.3. The linux installation includes 32 and 64-bit versions and the graphical applications. Unfortunately the graphical applications don't compile under OS X at this point in time, but all the command line utilities are available on OS X Intel and PowerPC.
DYANA 1.5 was crashing on linux. There was also no OS X version available. Linux and OS X Intel versions were built and configured. Reported by Michael Durney, D'Souza Lab, Harvard.
The CCP4 syminfo.lib file is now the standard symmetry file for all platforms. We had previously been using the one that came with SOLVE/RESOLVE.
Thanks for your bug reports!