SBGrid Consortium - News and Events

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 …

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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 …

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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.

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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.

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We completed the transition of Hogle laboratory (BCMP, HMS) to the core network for Center for Molecular and Cellular Dynamics at HMS. The transition facilitates further integration of structural biology computing at Harvard Medical School and creates a large SBGrid managed network segment. OSX computing infrastructure in Hogle laboratory was initially designed by SBGrid senior software architect, David Gohara, and has been recently highlighted on the Apple web site: http://www.apple.com/science/profiles/harvardmed/

SBGrid welcomes our newest member, Dr. Moonsoo Jin. Dr. Jin obtained his Ph.D. at MIT where he studied cartilage cell and matrix mechanics. He completed his postdoctoral training under Tim Springer at Harvard Medical School. There, he studied cell adhesion molecules like integrin and ICAM-1 (http://www.pnas.org/cgi/content/abstract/103/15/5758). His current research takes place at Cornell University, Department of …

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