Dear Consortium Members and Affiliates,
This month we are introducing four new programs in response to member requests: LABELIT, QPack, FinchTV and CCPNMR for OS X. We also have updates and bug fixes for Xmipp and MGLTools.
It was great to see many of you last month at Quo Vadis. We hoped you enjoyed the conference as much as we did!
The following software updates will be available today:
Linux and Mac OS X (PPC and Intel)
LABELIT is an auto-indexing program designed to correct three commonly experienced problems: getting the wrong beam center, finding a unit cell that is too large, and improperly identifying the allowed Bravais symmetry. If successful, LABELIT can be operated with minimal user input, and will return its results generally within 30-60seconds. The LABELIT website has the complete manual.
FinchTV is a way to easily view and edit your DNA sequencer chromatogram data. It can display an entire trace in a scalable multi-pane view, and will also display quality values (when available). You can edit your base calls and save your data to a new chromatogram file for later use, select and copy sequence for use in other applications, and print your trace out to paper or a file. You also have the ability to search your sequence data using regular expressions or simple base queries, to view raw data from .ab1 files, and to reverse complement your sequence and traces. An overview is available on the FinchTV website.
QPack performs a "quick" evaluation of steric packing in protein structures. Amino acid side chains are not represented in full atomic detail. Instead, one or more averaged centers of interaction per residue are used. A measure of the quality of side chain packing is determined from the available spherical space available to each residue. Additionally, an empirical pairwise residue contact potential can be used to estimate the correctness of model protein structures. Some additional documentation is availabe on the QPACK web page.
OS X only (Intel and PowerPC)
CCPNMR, introduced for the Linux branch last month, is now available on both OS X branches. CCPNMR Analysis is a new analysis program built on top of the CCP Data Model. The program is inspired partly by the program ANSIG (Per Kraulis) and partly by the program Sparky (T.D.Goddard and D.G.Kneller, UCSF). Documentation and details on the CCPNMR software suite are available on their website.
MGLTools from the Molecular Graphics Laboratory of The Scrips Research Institute has been updated to version 1.5.1. This package includes the AutoDockTools graphical front-end for AutoDock as well as the Python Molecule Viewer and Vision, a program for graphically building computational pipelines. The MGLTools website has extensive documentation.This month we are pleased to welcome Dr. Anna Marie Pyle and the Pyle Lab from Yale University and Dr. Joseph Sodroski from Harvard Medical School and the Dana Farber Cancer Institute.