Two versions installed: for Linux and Iris4d. A paper on 3DNA has been published: "3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures" (Xiang-Jun Lu and Wilma K. Olson, 2003)
SBGrid Consortium - News and Events
New version (1.5) of 3DNA, a versatile package for analyzing and rebuilding 3-dimensional nucleic acid structures installed.
Published June 11 2004
We have installed the newest version, 3.22 of Ribbons for Linux platform.
Published June 8 2004
Main Program updates: Sequence Panel print option gives way to save custom-coloring results.
Sequence Panel scrolling added for very long sequences (eg, ribosomes).
Added Antialiased Lines and Round Dots for polygonal surface display.
Added explicit "Mono" under the Stereo View menu.
To add "SpeedDeamon" global variable to adjust motion speed per platform.
Pirate - Statistical Phase Improvement by by Kevin Cowtan is now installed as part of CCP4 - v5.0 package.
Published June 7 2004
Pirate - unsupported CCP4 module.
pirate performs statistical phase improvement by classifying the electron density map by sparseness/denseness and order/disorder, with the aim of obtaining superior results to conventional solvent mask based methods without requiring knowledge of the solvent content.
The target distributions are generated by a simulation calculation using a known reference structure for which calculated phases are available. The success of the method is dependent on the features of the reference structure matching those of the unsolved, "work" structure. For the common case of a protein of mostly equal atoms (i.e. not a metalloprotein), a standard set of reference structures can be tested, and the one with the best Free residuals used for a full phasing calculation.
User pages of SBGrid website go online! Our webmaster, Krzysztof Satola now works on few remaining components.
Published June 3 2004
News, software, SBGrid manual and contact pages of SBGrid are now fully functional. In addition, the SBGrid administrators can edit site information using a convinient web interface. Within the next few weeks we will complete a software listings to include all the packages which are included in SBGrid software installation.
Chimera 1.1951 added in the newest release of SBGrid sofware (version 040603)
Published June 3 2004
Chimera is becoming increasingly popular for creating images and movies with molecular representation. It can handle surfaces, ribbon representations and electron density maps. If you try it please let us know how it worked for you. The software is free, comes with nice graphical user interface and can handle big assemblies.