A post-doctoral position is available at The Hospital for Sick Children/University of Toronto to continue our structure-function studies on the polymerization, modification and export of alginate, an exopolysaccharide produced by the opportunistic pathogen Pseudomonas aeruginosa and involved in biofilm formation in the lungs of Cystic Fibrosis patients. While exopolysaccharide biosynthesis and secretion has long been a focus of investigation within the microbiology community, the molecular mechanisms by which multi-protein complexes facilitate export of these polymers are still poorly understood. The position available is ideally suited to a highly motivated and energetic individual who is keen to work in a multi-disciplinary environment involving both microbiology and structural biology research, and has an interest in protein-protein interactions and/or cellular export processes. The successful candidate must have a PhD degree in a relevant field and previous research experience in either protein crystallography, the study of protein-protein interactions and/or microbiology. A strong background in molecular biology and protein chemistry would be an asset.
The position is available May 1, 2009 with funding for a qualified candidate for at least 3 years. Interested candidates should send a CV including a description of research experience(s) and the names of three professional references to: Dr. P. Lynne Howell at firstname.lastname@example.org.
Dear Consortium Members and Affiliates,
The SBGrid Computing School is filling up, so act now if you were thinking of registering. The Python nanocourse is full, but there are still a few spots left in our other courses. One course in particular that was very well received last year is Gael McGill's Molecular Visualization course, where you can learn how Maya and other tools can be used to animate molecular structures. Gaelâ€™s web site Molecular Movies has examples of recent work in this field.
Our software update this month includes updates to the CCI Apps, Coot, LABELIT, ATSAS, EMBOSS, CCP4mg, EMAN and PyMOL. The update started Wednesday evening, so it should already be available for most of our members. While we keep an eye on the major packages used in structural biology, there are so many software applications available that we do rely on our members for requests for new software and updates to existing packages. Please let us know if you have any software requests. Thanks!
The following software updates will be available today:
Linux and Mac OS X (PPC and Intel)
The CCI Apps have been updated to version 2009_02_15_2320. These are the core programs of the PHENIX project and typically receive updates and bug fixes on a more frequent basis than the PHENIX package itself. A list of changes can be found on the CCI Apps download page.
Coot has been updated to version 0.6-pre-1. This new version has a nifty spherical real-space refinement tool you should check out. More details on the Coot website.
LABELIT has been updated to version 1.000rc15. This update provides better compatibility with the latest version of MOSFLM. Usage notes and other documentation can be found on the LABELIT website.
ATSAS, the program suite for small-angle scattering data analysis from biological macromolecules, has been updated to version 2.2. Documentation and usage notes on the various tools are available on the ATSAS home page.
EMBOSS, the The European Molecular Biology Open Software Suite, has been updated to version 6.0.1. Documentation on the many utilities and features of the suite are on the EMBOSS website.
CCP4mg, the CCP4 Molecular Graphics viewer, has been updated to version 1.104. This version uses a new QT-based graphical interface that offers speed and stability improvements over the old Tcl/Tk interface. Documentation, an image gallery and tutorials are available on the CCP4mg website.
EMAN has been updated to version 1.9. This is a bugfix release with only a few minor improvements. Our installation has been updated so that the documentation is now included with the OS X builds. More info can be had on the EMAN website.
PyMOL betas of version 1.2 are now available in the software tree. These are experimental releases are not set as the default versions, but they do offer a few important features for certain use cases. In the linux distribution, we have a 64-bit PyMOL version for the first time, which has support for very large structures (1.2b3-x86_64). On the OS X platforms, we have the traditional MacPyMOL in beta form (1.2b3), but we also have an X11-based PyMOL for OS X that can be used in a true headless mode for use on clusters and on the command line (1.2b0).
To enable these special PyMOL versions, create a file at ~/.sbgrid with a version override like this:
setenv PYMOL_L 1.2b3-x86_64
The PYMOL_L shell variable will override the default version setting for the Linux version of PyMOL. To override the default OS X version, use the setting PYMOL_M. More information on overriding default versions for software can be found on our wiki.