We would like to remind you that our 144 CPU computational grid is available to the SBgrid community through the General User Program at no extra charge. Our Research System Architect, Ian Levesque, now maintains the Grid. Proposals are considered through a web-based system for submission, review, and allocation. All members of SBGrid are qualified to apply. Please visit www.sbgrid.org/gup to submit your proposal. This month’s awardees include Josh Campbell for docking calculations (Harrison, Gaudet and Miller laboratories), and Stefan Raunser (Walz laboratory) for EM 3D-classification and angular assignment by maximum-likelihood refinement.
SBGrid Consortium - News and Events
Computing Grid Update (Sept 2006)
Published August 18 2006
Software Updates (Sept 2006)
Published August 18 2006
The new software will be available on your computers on Saturday, September 9th.
The following applications will be updated in the process:
CCP4 to version 6.0.1 – CCP4 version 6.0 is the most recent major release of the CCP4 software suite and was made in February 2006. A current patch release 6.0.1 was made to fix a number bugs, however there were no major changes to functionality.
coot to version 0.1.1. This update in addition to bug fixes adds a nucleotide builder module. See the release notes for full listings.
New software:
Madbend – a program for calculating the curvature of nucleic acids developed by Tamar Schlick’s group at New York University. The manual for the application is available in /programs/arch/madbend directory. …
SBGrid Newsletter - Issue 1
Published August 18 2006
Dear Readers,
Welcome to the first of our monthly newsletters. You are receiving this newsletter because your laboratory or institution subscribes to SBGrid services. It is our hope that through this medium we will provide you with useful and relevant information about SBGrid. In this issue you can learn more about access to SBGrid core computational clusters, a molecular visualization class in Boston, our newest member lab at Cornell University, transition of an HMS laboratory to the SBGrid core infrastructure, enhancements on our website, and finally software upgrades and updates that are scheduled for Friday, September 9th.
Finally, as always, we remind our readers that they are welcome and encouraged to report any software bugs utilizing SBGrid Bug Tracker (www.sbgrid.org/bugs).
Kind regards,
…
Molecular Visualization Nanocourse
Published August 15 2006
Molecular Visualization Nanocourse: A Case Study of a Clathrin Lattice
Want to interpret protein and DNA structures but have no background in structural biology? Need to make publication-quality figures of protein structures and molecular animations for your seminars? This is a hands-on nanocourse for you. We will introduce you to SBGrid Suite – a complete applications environment for structural biology. After learning basic UNIX commands and an introduction to the RCSB Protein Data Bank file formats you will scrutinize the structure of clathrin coats, 7.7 MDa hexagonal barrel particles. We will 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. You will also learn how to transform coordinates, …
Natalia Beglova joins SBGrid
Published May 12 2006
Natalia Beglova, a former instructor in the Stephen Blacklow laboratory received an independent faculty position at the Division of Hemostasis and Thrombosis, BIDMC. She will be using NMR spectroscopy and X-ray crystallography combined with other biophysical and biochemical techniques to gain insights into the function of the ApoE receptor 2 in platelets. Stimulation of platelets controlled by ApoER2 is likely to represent the molecular mechanism of developing thrombosis in antiphospholipid syndrome. She is also responsible for the scheduling and maintenance of the 500 MHz spectrometer owned by the Division of Hemostasis and Thrombosis.