SBGrid Consortium - News and Events

January Software Updates

Published January 23 2007

All listed applications will be available on Linux and OSX computers (both Intel and PPC) after the Friday evening update.

Pymol will be updated to Release Candidate 6 (RC6) and the APBS plugin installation will be corrected to properly locate electrostatics modules. You can use the APBS plugin to calculate and display electrostatics. Fedora Core Linux installations might require installation of compat-readline43.i386 for compatibility. We have also noticed that structures with B-factors higher than 99 the APBS plugin will not work. To solve this issue, use lx_moleman, LIMIT option (osx_molman on Mac) to limit your high B-factors.

New version of O! We will upgrade to release 11.0. You will now be able to build a structure from a map automatically using the AutoO_build command; the Lsq_proper command …

SBGrid Receives Taplin Funds for Discovery Award for Grid Computing

Published January 23 2007

We are proud to announce that we have just received the Taplin Funds for Discovery award from Harvard Medical School and will soon add another 100 Apple Xeon 64-bit cores to our grid. I am thrilled with this opportunity, and would like to thank Prof. Jim Hogle who applied jointly for the award. The resource will be mostly used for HMS-based research, but as always will be available to all SBGrid members through our general user program. SBGrid System Architect, Ian Levesque, will be in charge of commissioning the system. We will keep you updated as we hope to have it running soon.

SBGrid@NE-CAT

Published January 23 2007

NE-CAT APS members will be soon able to access the SBGrid installation on all beamline computers. Please visit the NE-CAT website for more info about this beamline.

Issue 5

Published January 23 2007

Dear Readers,

Software upgrades and updates are scheduled for Friday night, Jan 26th. Many new exciting applications will be added this month, including new releases of Pymol, O, Chimera, Coot, and EMBOSS.

Please do not hesitate to request new applications (http://www.sbgrid.org/req) or fix existing bugs (http://www.sbgrid.org/bugs). By using SBGrid compiled applications, you have access to programs that are constantly being tested for reliability by us and all SBGrid laboratories.

Kind regards,

Piotr Sliz, Ph.D.
Group Leader
Structural Biology Computing Group, SBGrid

Issue 4

Published December 19 2006

Dear Readers,

Software upgrades and updates are scheduled for Friday night, Dec. 22nd – just in time for your Holiday week structure determinations. Many exciting new programs and updates will be added this month.

As always, we remind our readers that they are welcomed and encouraged to report any software bugs utilizing the SBGrid Bug Tracker (www.sbgrid.org/bugs). We can always correct software bugs in between scheduled software updates. Please note that immediately after software updates you will be using the newest installed versions. If you find problems, you can always switch to an older version of the application. Please use ‘sbgrid –n’ for more info.

Happy Holidays from SBGrid!

Piotr Sliz
Group Leader
Structural Biology Computing Group, SBGrid