Summer is almost here and Boston is lush with greenery after several rainy days. Now is the time to snatch up that laptop and search for a shady tree and a patch of grass to work, for summer's lease hath all too short a date.
Last week Jan Brezovsky from Loschmidt Laboratories gave us a primer on CAVER 3.0. You can access the recorded version of this presentation from our webinar archive if you missed the original. Before our August break we have one last webinar. On July 11th Jalview developers will join us to demonstrate their JAVA multiple sequence alignment editor.
Our June SBGrid Tale focuses on one of SBGrid's earliest members: Yizhi Tao. Talking about her work with viruses, ongoing at Rice University, Tao reveals that it's the simple thrill of discovering how things work that keeps her motivated.
Renewal invoices went out earlier this month for most of our members. Please contact us at firstname.lastname@example.org with any billing questions, and remember that a discount is applied for each new member that joins from your institute. We can adjust unpaid invoices to reflect the addition of new members until the end of August.
Our May 28th software update included new versions of Bsoft, PyMOL, PHENIX, Chimera, em2em, and SPIDER, as well as one new NMR software application: REDCAT (REsidual Dipolar Coupling Analysis Tool).
Notable Software Changes
We have upgraded PyMOL to version 18.104.22.168 and would like to remind you that SBGrid members have access to a special, incentive version of PyMOL. Some of the special features in this release include access to incentive documentation that comprehensively describes PyMOL's features and updates and includes narrated screencasts and step-by-step tutorials, direct export of QuickTime movies (Mac only), and built-in MTZ map reading. This special documentation is available in the PyMOL Incentive User Area. To access this section, you will need to create a login for the PyMOL documentation site (http://pymol.org/dsc) using the login information in the NOTES file in the PyMOL installation directory in your software installation, e.g. /programs/i386-mac/pymol/NOTES. We also have a recorded webinar highlighting some of these special features that is available in our SBGrid Webinar Archive.
Changes in Bsoft, a collection of programs used in electron microscopy, include a new threading algorithm in the watershed function (bflood application) and fixes to secondary structure parsing and writing routines.
em2em, a program to convert between different formats of 2-D images and 3-D volumes, has been upgraded to the latest April 2013 release. This new version incorporates support for JPEG images and can automatically detect MRC file formats.
The new version of SPIDER can prepare input files for RELION. RELION is a separate program developed as part of the CCP-EM project in the UK and is used for refinement of 3D reconstructions or 2D class averages. We currently have version 1.1 of RELION installed and will upgrade to version 1.2 soon. Please note that RELION should be run in an MPI queue. Contact email@example.com if you have questions about this setup or would like to test it on our shared cluster. Additional changes in SPIDER include a new SYS operation to access UNIX commands (replaces the legacy VM system call), a TF ED function to estimate defocus from the image power spectrum, and CTF ED to estimate defocus from micrographs. A three dimensional reconstruction procedure for single particle specimens using reference projection with defocus has also been established (http://www.wadsworth.org/spider_doc/spider/docs/techs/recon/mr.html).
REDCAT, an RDC analysis tool with a user-friendly graphical-user-interface, requires a molecular structure and assigned RDC data as input. This application can be used to validate a structure, study internal motions, and orient rigid domains with respect to each other. It can also emulate RDC data under static and dynamic conditions.
Our member map now includes Singapore, with the addition of Par Nordlund's lab from Nanyang Technological University. Also new to SBGrid is a second beamline facility - The Molecular Biology Consortium - from the Advanced Light Source Synchrotron.
Welcome to our new members!
Please note that not all software applications are available to every SBGrid member type. If you see an application that you would like to use, but is not included in your software tree, please contact us to find out what options are available for access.