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 18.104.22.168. 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:
IMOD, a tomographic image reconstruction program, will be upgraded from 3.7.3 to 3.9.3. The update includes number of functional changes as well as bug fixes. The new version will become a default. Please see release notes on the web for full details.
Modeller, Andrej Saliâ€™s program for comparative protein structure modeling, will be updated from version 8v1 to 9v1. The application is now faster, provides a new loop modeling protocol, and improved python functionality. For a full list of changes please see the Modeller release notes.
NMRViewJ 7.05 is a new, actively developed Java version of NMRView which replaces the no longer developed C versions of the program. NMRViewJ allows for the visualization and analysis of NMR datasets, and bills itself as â€œthe leading program for analyzing macromolecular NMR dataâ€. For more information, download the â€œincompleteâ€ book (PDF) on NMRViewJ.
XPLOR-NIH is a structure determination program that builds on the X-PLOR program, including additional tools developed at the NIH. This software will be upgraded from version 2.09 to 2.16.
Ultrascan will be upgraded from version 7.0 to 9.0 for all branches. UltraScan provides a GUI for data editing and analysis related to the â€œhydrodynamic studies of macromolecules and macromolecular assemblies with analytical ultracentrifugation experiments.â€ For more information on version 9.0, please see this announcement from the Ultrascan mailing list.
RAPPER will be updated to the latest build released 12 February 2007. This will only be available for Mac PowerPC and Linux branches. For more information on RAPPER, please visit the website.
Published March 20, 2007