Newsletter Mar 2008

Newsletter for March, 2008

March 2008 SBGrid Newsletter

Dear Consortium Members and Affiliates,

We have six software packages that will be installed for you tonight. This includes updates to applications Chimera, O and MOLREP. In addition we are installing three new applications: MOLE, Jalview and ESCET. Details of the software updates are included below. The Quo Vadis symposium is approaching soon. Please see the conference news section for information about some minor program changes and information about registration. And finally we are pleased to welcome our new international members from the University of Toronto and from the MRC at Cambridge University.

As we mentioned last month in an effort to better support software users in our member labs, we would like to begin collecting hardware architecture and operating system information from the machines that are using the SBGrid Programs Collection. We plan to do this via a simple shell script that runs when the labcshrc is read by your shell. Information would include the machine hostname, CPU type, operating system version, programs version and operating system compatibility specifics.

This information will allow us to alert you to when your operating system is not fully compatible or not running the latest versions of the programs.  It will also help us to determine where to best to spend our limited resources in supporting operating systems and optimizing software for various hardware architectures. We realize that this could be a privacy concern for some of our members, and we want to implement this sort of statistics gathering in a manner that works for best for all parties. We plan to offer a method for programs users to disable the statistics collection via a setting in their ~/.sbgrid file, but we would appreciate your feedback on this matter.

At this point in time, we would plan to implement basic information reporting with the April update, so please take this opportunity to voice your comments and concerns to We also plan to have a short session at the Quo Vadis summit to talk about this issue, and how SBGrid can work to best support you in your research efforts.

Best regards,

Piotr Sliz, Ph.D.
Structural Biology Grid (SBGrid)
NSF Research Coordination Network Quo Vadis is approaching soon, and the response from the community has been overwhelming. SBGrid members from many remote locations will be attending, including graduate students and postdocs from the University of Washington, Rice University, Yale University and the University of Toronto. Some of the sessions are already full, and we may be forced to close registration for the main structural biology track soon. We have added one more lecture to the program: Leemor Joshua-Tor will talk about her recent discovery that was just published in Science. Her talk is titled "NADP regulates the yeast GAL induction system: A new twist to an old story". To register and see a full schedule of talks and workshops, please visit the conference website for details.

Quo Vadis is a latin phrase that roughly translates to "where are you headed?". This summit is designed to give its attendees an extensive array of opportunities to discuss and learn about the future of structural biology. Throughout this interactive, 2-day symposium, speakers from Harvard University and outside will present their work, plus a multitude of hands-on workshops focused on structural biology computing will be offered.

See you all in May! This month we are pleased to welcome several labs from the University of Toronto. We have also added a number of structural biology groups from the MRC Laboratory of Molecular Biology at Cambridge University. The MRC has been one of the main centers driving development of structural biology applications, and we are particularly pleased to have them on board. The following software updates will be available later tonight:

Linux and Mac OS X (PPC and Intel)

Chimera has been updated to version 1.2470 for all three branches in response to a user request. A complete list of the changes and features in the latest version can be found in the release notes. Several of the experimental features included in previous releases have made it into the main release, and we no longer need separate plugins for features like MorphMap.

MOLE version 1.2 is a new program available this month for all three platforms. MOLE is a universal toolkit for rapid and fully automated location and characterization of channels and pores in molecular structures. Initially offered only as a Linux or Windows binary, the MOLE developers provided us the source code so we could compile a Mac OS X version for one of our Mac-only member labs. More information is available on the MOLE homepage and in the documentation.

O has received a minor version update to fix some bugs. Some of our users have reported problems with the new O version 12.0.0, but it's a simple matter to use the older version by adding 'setenv O_L 11.0.4' to your ~/.sbgrid file. On the Mac platforms, the line should be 'setenv O_M 11.0.4'.

MOLREP has been updated to version 10.2.2 for all 3 branches. This updates both the standalone version and the version included in CCP4i. The MOLREP release notes claim this version is up to two times faster than the 9.x releases. More information can be found on the MOLREP home page.

Jalview is a multiple alignment editor. It is used widely in a variety of web pages, but this version is a standalone general purpose alignment editor. The Jalview home page and documentation contain more information.

Linux Only

ESCET version 0.7g is a program for analyzing and comparing three-dimensinal protein structures.  The developer, Thomas Schneider, kindly allowed us to offer this via our programs collection after a member from Columbia University had requested it. Documentation is on the ESCET home page.

Published March 1, 2008