Dear Consortium Members and Affiliates,
It's that time of the month again. New software, yay!
There was a very small unannounced update in January to provide new XDS binaries, which expired over the Christmas holidays and a new version of CCP4mg, which purported to fix the issue with Zalman 3d LCDs on linux. I still can't get it working here.
The updates available today include Coot, PHENIX, Mosflm and iMosflm, CCP4mg, Chimera, XIA2, APBS, XPLOR-NIH and NMRPipe. More details below the fold.
Y'all take care now.
The following software updates will be available for eligible labs today:
Linux and Mac OS X (PPC and Intel)
Coot has been updated to 0.6.1. There are extensive resources to help you get started with Coot including the manual, FAQ, a couple tutorials and the Coot page on the CCP4 wiki.
PHENIX has been updated to release version 1.6-289. There is updated documentation for this release on the PHENIX website.
Mosflm and the iMosflm graphical interface have been updated to versions 7.0.6 and 1.0.4 respectively. I know we all saw Harry Powell's announcement on the CCP4bb, so I won't rehash it here, but this update contains mostly bug fixes. There is documentation for both Mosflm and iMosflm. That second link contains a nice tutorial to get you started.
CCP4mg has been updated to version 2.1.0. The developers now consider the 2.x branch based on QT to be a full replacement for the old Tcl/Tk-based 1.x branch.
Chimera has been updated to version 1.4.1. The Chimera release notes have details on the changes. There are a ton of resources on the Chimera website to help you get started with the software.
XIA2 has been updated to version 0.3.1.0. Documentation, a tutorial and some other bits are on the XIA2 website.
XPLOR-NIH has been updated to version 2.24. A change log, the documentation and a mailing list are all linked from the XPLOR-NIH web site.
NMRPipe has been updated to the 20091208 release. The Big NMRPipe Reference Page is the best resource for information.
Linux and Mac OS X Intel
XDS has been updated to the 20091228 release. The XDS developers have stopped supporting OS X PowerPC, and since they build expiration dates into their binaries, I have removed XDS from the PowerMac branch.
Linux
APBS has been updated to version 1.2.1. The Mac builds came out a little wonky and will be available in the near future. APBS lives here.
The HADDOCK installation had files with incorrect paths for its data files and to an inappropriate CNS binary. These have all been discovered and fixed thanks to Andrew Ring in the Kuriyan Lab at Berkeley.
Our BUSTER-TNT server had an expired licence. We requested and installed a new licence. Reported by Ben Spiller, Spiller Lab, Vanderbilt.
Our web wrapper for OS X didn't run on OS X 10.5 and 10.6. Initially this was due to Apple breaking 8-bit color support in X11, but with that fixed, we updated the wrapper script to allow web to run on all supported versions of OS X. Note that the 8-bit color map is still a bit glitchy on OS X 10.5 and 10.6, and you may have to minimize-maximize web in order to force a screen refresh.
CCPNMR 2.1.2 was broken due to an errant rsync exclude file leaving out its 'nmr' directory. Reported by Tomas Jacso (and others), Selenko Lab.
CCP4mg 1.114.1 had some issues saving some data files. Fixed by upgrading to the latest version. Reported by my boss, Piotrek Sliz, Sliz Group.
This is not really our bug, but it may bite some of you. tcsh versions prior to 6.16 had a long-standing bug where numbers with leading zeros, which are supposed to be treated as octal values, were treated as decimals. This bug is fixed in the latest version of tcsh, 6.17, and Red Hat helpfully backported the bug fix to their 6.14 tcsh version. We have found a handful of tcsh scripts in the software tree and in use among our labs that used a zero-padded number for naming output files, reading image stacks, etc, and when run with the fixed tcsh, they break. Caveat emptor!