Dear Consortium Members and Affiliates,
2013 arrived in Boston with a crisp, white layer of snow on the ground and temperatures that make the covers all too enticing in the dark morning hours. The new year also ushered in lots of SBGrid news, so please take a moment to read our monthly update.
The organizers for the West Coast Protein Crystallography Workshop, the 21st meeting of its kind spanning over 40 years, would like to invite you to register. SBGrid director Piotr Sliz will speak at the conference, on the topic Molecular Replacement, and would be eager to meet any SBGrid members in attendance. More details about the Workshop can be found at http://www.wcpcw.org.
SBGrid Research Fellow Andrew Morin will be organizing a workshop on "Publishing Reproducible Hybrid-computational Workflows" at the Keystone Symposia on Structural Analysis of Supramolecular Assemblies by Hybrid Methods on March 3rd-7th in Lake Tahoe, CA. The workshop will include a panel discussion by prominent researchers, journal editors, funders, and developers of hybrid-computational methods intended to define a set of best practices for reporting research. More info about the symposia can be found here.
Two SBGrid Tales have been published this month, one featuring SBGrid member Emil Pai from the University of Toronto, the other highlighting software developer Tim Stevens, with some history on his contribution to CCPN and news about where you can find him in the future.
We have several new webinars lined up for the winter and spring seasons. First up will be Stuart McNicholas's presentation on CCP4mg on January 24th, followed by Tom Goddard's February 7th primer on Chimera. Please keep an eye on our homepage and join the SBGrid Google calendar for additional details, dates, and times.
PyMOL developers will be on site at SBGrid on March 7th to give a live seminar to local participants that will be broadcast via WebEx to the rest of the SBGrid community. Following the webinar/seminar, two 90-minute tutorials will be offered to local audiences. Thomas Holder will give an introduction to PyMOL for the novice user or those looking for a refresher, and Jason Vertrees will present an advanced movie-making course. These tutorials will be held simultaneously. Additional details and registration information will follow.
The latest round of software updates was pushed out on January 8th and includes the latest nightly version of PHENIX as well as new versions of MGLTools, CCP4mg, NMRPipe, CAVER, CONCOORD and CCP4 6.3.0 update 12.
Notable Software Changes
CCP4MG (CCP4 Molecular Graphics), an application used to render macromolecular structures, was upgraded to incorporate hardware rendering acceleration. CCP4MG now supports shadows, occlusion lighting, and other rendering effects. Minor changes include better handling of crystallographic symmetry, vibration modes, and automatic figure generations using wizards. Stuart McNicholas from York University will discuss CCP4MG movie making tools and recent rendering improvements during the upcoming webinar on January 24th.
PHENIX was upgraded to the recent release. Several new commands are now available, including phenix.ensemble_refinement, phenix.ligand_pipeline, phenix.sort_hetatms, phenix.cc_star, phenix.pdb_editor, phenix.maximum_entropy_map. A new graphical interface for merging statistics and editing PDB files was also released. Please review a recent paper by Burnley et al., published in eLIFE, to learn more about the new method of incorporating MD in refinement. SBGrid members on the west coast are invited to attend the Phenix Workshop, which is scheduled to take place in Berkeley on March 14th.
MGLTools was upgraded to version 1.5.6. A new documentation website is now available to end-users. Added functionality includes creating 3D animations, beaded ribbons (resembling molscript representation), and a completely redesigned dashboard widget.
We had 8 new members join in the past month. Chao Quan joined as the 4th new user at Biogen Idec and from University of Pennsylvania Gideon Dreyfuss, Kate Ferguson, Siriam Krishnaswamy, Mark Lemmon, Josh Wand, Dewight Williams, and Zhe Lu have all recently signed on.
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.