SITUS – version 2.2.1 (Linux) - program package for the modeling of atomic resolution structures into low-resolution density maps e.g. from electron microscopy, tomography, or small angle X-ray scattering. Version 2.2.1 provides many significant improvements and added features compared to the previous version (2.1a5). See http://situs.biomachina.org/fnews.html for more information.
Default version after upgrade(Linux): 2.2.1
Other available versions: SITUS_L 2.1a5
COOT – version 0.1.2 (Linux) - The new release includes new functionality, e.g. ‘Least-squares Fit’ and ‘Move Molecule Here’ GUIs and provides many fixes. Tested with older Fedora Core 3 installations, as well as Fedora core 4 and 5 systems. For the full listing, see http://www.ysbl.york.ac.uk/~emsley/coot/.
Default version after upgrade (Linux): 0.1.2
Other available versions: COOT_L 0.1.0 and COOT_L 0.1.1
* You can use other versions …
SBGrid Consortium - News and Events
Software Upgrades
Published October 3 2006
New Software Installations
Published October 3 2006
Buccaneer - Statistical protein chain tracing application
The application developed by Kevin Cowtan from at University of York was recently described in an Acta Cryst. paper (D62, 1002-1011). We have installed it as part of the ccp4, version 6.0.1 distribution. According to Dr Cowtan the application is not strongly sensitive to resolution, but is strongly sensitive to the quality of initial phases. It is therefore complementary to to ARP/wARP, which is more sensitive to the data resolution but could give results with quite poor phases. The method used by Buccaneer appears to be useable at least to the 3.2A low-resolution limit. You are welcome to try it with your data and let us know how it works for you.
NMR applications from Arhtur Palmer Group at Columbia
Installed …
Molecular Visualization Nanocourse: A Case Study of a Clathrin Lattice
Published September 5 2006
This nanocourse has been organized in Boston, MA, and is offered for credit to Harvard graduate students and all SBGrid affiliates. In two workshops we will introduce the SBGrid environment, teach basic UNIX commands, and introduce the RCSB Protein Data Bank file formats. Subsequently, course participants will scrutinize the structure of clathrin coats, 7.7 MDa hexagonal barrel particles, visualize macromolecular properties including side-chain interactions, electrostatic potential, hydrophobicity and solvent accessible area, as well as perform secondary structure identification and structure quality verification. Participants will also learn how to transform coordinates, assemble biological units using symmetry operators, and animate structures. Software tools covered in this course will include ccp4mg, chimera, coot, whatif and procheck. Class will take place in the CMCD computer rooms. Space is limited; please contact Meg …
SBGrid Presentations
Published September 5 2006
Our software architect, David Gohara, spoke about SBGrid, and how we have been integrating labs throughout the country into a standard software environment during the IT State Of the Union at the Apple WWDC conference. Over 900 developers and IT professionals from all over the world attended the talk.
Piotr Sliz highlighted our consortium and the SBGrid computational approaches during a workshop on 2D crystallography at UC Davis, CA (www.2dx.org). His talk focused on adopting 3DX software tools to 2DX structure determination, Aqp-0 in particular. He also discussed the challenges involved in low-resolution refinement.
Web Site Enhancements
Published September 5 2006
We have made two enhancements on the SBGrid web site (www.sbgrid.org). The software page now includes a listing of compiled OSX Intel applications. In addition, after you login to the Member Access pages, application notes contain information about software references. You can use this information when you cite software in your publications. Login/password to access Members’ Pages is affiliate/nanocourse.