Dear Consortium Members and Affiliates,
My goodness, it's software update time! Boston has had an unusually lovely week of warm weather; the students are breaking, the bulbs are blooming, and the geese are getting broody. Spring approaches!
We have posted a new structural biology tale on our website. Gerard Kleywegt, head of the PDBe, spills the secret of his original "CD" nickname and talks about his efforts to advance structure validation over the years.
We don't have any dates booked yet, but we're working on getting a few new software webinars lined up including presentations from the CCP4 core team about the upcoming 6.3.0 release, a talk on PHASER and all the news from Global Phasing on the latest and greatest version of SHARP/autoSHARP. We'll have more details soon.
This software update includes new versions of PHENIX, PyMOL, VMD, Chimera, CCP4mg, 3DNA, ATSAS, Xia2, XDS, APBS, ProtSkin, Quilt, Ruby, ESCET, and Swiss-PDB Viewer as well as three new packages including VEDA, Nessy and BioXTAS RAW. Fun!
Thanks for reading!
The following software updates should be available now:
Linux and Mac OS X Intel
PHENIX nightly dev-1000 is the latest version in the software tree. It's the usual slew of bug fixes and undocumented new features including PHASER version 2.5. The change log has more details. Please use the built-in PHENIX bug reporting tool for problems with the nightly versions. They incorporated code into PHENIX that lets them know the installation is at an SBGrid member site, and they alert us directly when we need to update.
PyMOL has been updated to version 22.214.171.124. Schrodinger has been releasing point updates in response to your bug reports on the new 1.5 release of PyMOL, so please let us know if you are experiencing any problems with the new version.
VMD has been updated to version 1.9.1. There are a number of new features reported in the release notes including news on the significant performance increases available when running VMD on a modern graphics card. All things VMD including the documentation, tutorials, example data sets and more on available on the VMD home page.
Chimera has been updated to the 1.6.1 release version. This is another major update for a popular model viewing and analysis tool. The long list of features and bug fixes is available in the release notes. Chimera also has excellent documentation, tutorials and example data sets available on the Chimera web site.
CCP4mg has been updated to version 2.5.2. This is mostly a bug fix release. The CCP4mg website has an extensive list of tutorials including examples of how to quickly create simple movies and animations.
3DNA, a package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures, has been updated to version 2.1. Along with this update, there is a new 3DNA website with release notes and a help forum.
Xia2 has been updated to version 0.3.4.0. Along with the update, we have added updated versions of Kevin Cowtan's AIMLESS and POINTLESS tools and their corresponding CCP4 task interfaces. I once heard someone refer to Xia2 as the "civilized interface to XDS". There is documentation and a tutorial with sample data to get you started on the Xia2 website.
XDS has been updated to version 20120305. This is a small update to fix a couple of reported bugs.
APBS has been updated to version 1.3. The APBS website has a wealth of resources for this Adaptive Poisson-Boltzmann Solver including user and developer guides, tutorials, an FAQ and the manual.
ProtSkin has been updated to version 1.82. This is an older tool for looking at protein sequence conservation.
Ruby version 1.9.3 is a new addition to the software tree. Several of the structural biology software tools have recently added support for using ruby in some way, and since it's not widely installed on most workstations, we have added it to the softwar tree to support those packages. Here is the Ruby home page.
ESCET has been updated to version 0.7i. This is Thomas Schneider's tool for comparing three-dimensional protein structures. The ESCET web page has some additional details.
VEDA is a new package for interactively fitting atomic models into 3d EM reconstructions. Version 20110711 is now available in the linux software branches. There is a short VEDA usage guide and a video demonstrating its use on the VEDA home page.
BioXTAS RAW is a new package for high throughtput 2D reduction, manipulation and analysis of SAXS data. Version 0.99.8.3b is now available for linux workstations. The PDF manual and quick start tutorial are available in the software directories (E.g., /programs/i386-linux/raw/0.99.8.3b/doc). The BioXTAS website has a few additional details.
Nessy is a new package for analyzing "NMR relaxation dispersion data of either CPMG or R1p (R1rho) dispersion experiments". Version 12.2.1 is now available on linux. The Nessy website has the manual, tutorials and a mailing list.
Mac OS X Intel
The Swiss-PDB Viewer has been updated to version 4.04. Note that this software is no longer being maintained on linux and won't be receiving updates or bug fixes on that platform. The DeepView website is all new and has the usual resources.
A number of people have reported problems running scripts that use the EMAN2 python modules. The solution is to use the custom e2python wrapper as the script interpreter, which will properly set up the PYTHONPATH and other settings to access the EMAN2 installation. This means you should call your script with 'e2python script.py' or change the shebang line from '#!/usr/bin/python' to '#!/usr/bin/env e2python'.
We also received a slew of bug reports on the latest version of PyMOL 1.5. We are forwarding these on to Schrodinger, and they seem fairly responsive in releasing updates in order to resolve problems, so please keep reporting them to us. If a bug in PyMOL version 1.5 is preventing you from continuing your project, please remember that you can always fall back to the previous 1.4.1 version using a version override.
Xplor-NIH version 2.30 had a library error on OS X Intel systems. Tweaking the xplor wrapper script resolved the problem. Reported by Mukesh Sharma, Chou Lab, HMS.