Dear Consortium Members and Affiliates,
Software updates will be sent to your site on Friday night, March 23. This month, you will receive several significant upgrades, including a new Java version of NMRView which replaces the previous C versions.
Immediately after receiving the software updates this Friday, you will be using the newest installed versions. If there are any problems, please report them (http://www.sbgrid.org/bugs). You can always switch to an older version of the application while we work on your request—just use ‘sbgrid –n’ for more information. Many of these monthly updates and additions are prompted by member requests, so please do not hesitate to request new applications (http://www.sbgrid.org/req).
Please continue reading for details on the software updates and other news.
Kind regards,
Piotr …
SBGrid - News and Events
Issue 7
Published March 20 2007
March Software Updates
Published March 20 2007
The following software upgrades will be available for all branches after the Friday evening update.
Profit, as described by the author, is a "program for performing least squares fits of two protein structures. It performs a very simple and basic function, but allows as much flexibility as possible in performing this procedure. Thus one can specify subsets of atoms to be considered, specify zones to be fitted by number, sequence, or by sequence alignment." We will be updating from version 2.3 to 2.5.3.1. This is the most recent version and fixes numerous bugs.
To start it up from a shell:
profit reference.pdb mobile.pdb
For full user manual, please see:
http://www.bioinf.org.uk/software/profit/doc/
IMOD, a tomographic image reconstruction program, will be upgraded from 3.7.3 to 3.9.3. The update includes …
Grid News
Published March 20 2007
Our opportunity to join the Open Science Grid is getting closer. We took part in the weekly national conference call last week. Our petition to become an official Virtual Organization in the OSG is now in progress. Also, we would like to remind you that SBGrid provides access to computational resources to all SBGrid affiliates though a general user program: www.sbgrid.org/gup
New Member
Published March 20 2007
Congratulations to Hector Viadu, a former post-doc of Tom Walz. Hector established an independent lab at the Department of Chemistry and Biochemistry at UCSD. Please visit his website; the lab is currently accepting new members.