Introduction
Dear Consortium Members and Affiliates,
As we promised last month, the registration for the Quo Vadis Structural Biology? is now open. Please visit the conference website: www.sbgrid.org/quovadis. In order to give our members preference for workshop selection, the registration is restricted to SBGrid members until November 16th, at which point it will become available to the general public. The registration password is ‘gleevec’. We expect that the event’s workshops will be a major attraction. We will provide three computing rooms with 75 iMacs in total so each attendee will have a personal Macintosh workstation. Workshops will be led by industry veterans including Gael MacGill (animation), David Gohara (Mac programming), Ian Stokes-Rees (Python), Paul Emsley (low resolution model building), Ian Levesque (structural biology system administration) and others. Each computing workshop is limited to 24 participants so please register early.
Please note that due to numerous commencements accommodation in Boston in May can be scarce and expensive. If you are traveling to reach Boston, please make sure to book your hotel early and take advantage of a special SBGrid rate of $179/night at the Inn at Longwood.
As you may know, Apple's OS X Leopard was released today. We have been heavily testing the Leopard beta releases with the SBGrid programs collection, and currently approximately 75% of the applications are supported. Further information about Leopard compatibility are provided below.
I am also pleased to announce that SBGrid signed a memorandum of understanding with the Harvard NeuroDiscovery Center. Through this agreement we will administer and have full access to a 50-CPU opteron cluster at Harvard Medical School. This resource will be available to all members of the consortium through the General User Program.
Our software push is scheduled for tonight. Please take a few minutes after the update to test if your major applications are working well. Our staff will be on call to resolve any urgent issues. This month we have updates for Pymol, MOSFLM and the IMOSFLM graphical interface, APBS, ProFit and Frealign. We are also adding new installations for Haddock, Tensor 2 and Zdock/Rdock.
We would like to thank Warren Delano, the PyMOL developer, for working with us to negotiate a blanket license for all SBGrid member labs to use the sponsored PyMOL incentive build. This license includes access to the official PyMOL documentation available on the Delano Scientific website.
If there are any problems, please report them at http://www.sbgrid.org/bugs. You can always switch to an older version of the application while we work on your request—just use ‘sbgrid –n’ for more information. Many of these monthly updates and additions are prompted by member requests, so please do not hesitate to request new applications at http://www.sbgrid.org/req.
Best regards,
Piotr Sliz, Ph.D.
Director
NSF Research Coordination Network
We are pleased to welcome Anjana Rao and Rao Lab from the Immune Disease Institute (formerly the CBR Institute for Biomedical Research) and Ted Jardetzky from the Stanford School of Medicine.
We have completed testing of the SBGrid Programs Collection for Intel Macs running Leopard and are pleased to report that the core applications of the programs collection are working with Leopard. The notable exception is Coot, which we hope to have working for the November release.
The other applications we know to be experiencing problems on Leopard are 2dx, clustalw, dssp, Emboss, GSL, Imod, the MGLtools, MRC web, naccess, NMRPipe, Quilt, Rasmol, Replace, Ribbons, Sparky, Surfnet and Xplor-NIH.
While we strive to test all applications for compatibility and correctness, our testing can never hope to match the intensive use of the programs by our users, and we rely on your bug reports to help us refine and enhance the programs collection for the entire community. If you are an early adopter of OS X 10.5, please report any problems you encounter with the programs collection. We always welcome your feedback, positive or otherwise.
Linux and Mac OS X (PPC and Intel)
HADDOCK 2.0 is a new install for all three platforms. Haddock relies on an approach that makes use of biochemical and/or biophysical interaction data such as chemical shift perturbation data resulting from NMR titration experiments, mutagenesis data or bioinformatic predictions. More information is available at the Haddock home page.
PYMOL has been upgraded to the sponsored version 1.0r2. The sponsored version of PyMOL includes access to the official PyMOL documentation. . Details about accessing the documentation are available on our website under the PyMOL entry on the software page.
We have integrated the latest version of the APBS electrostatics plugin for Linux and both OS X platforms. To use PyMOL plugins under OS X, you must use the 'pymol' or 'pymol-x11' aliases to run the program. The 'macpymol' and 'macpymol-x11' command aliases run the Aqua PyMOL interface that does not support plugins.
APBS has been updated to version 0.5.1 for all platforms. A list of new features and bug fixses are available in the APBS release notes.
MOSFLM has been upgraded to version 7.0.1 for all three platforms. This is a standalone installation separate from the CCP4 integrated version. The Imosflm graphical interface has also been updated for Linux to version 0.5.3. More details are available on the Imosflm website.
Mac OS X Intel and PowerPC Only
ProFit has been upgraded to version 2.5.3.1 for both OS X platforms. This is primarily a maintenance and bugfix release; details are available on the ProFit website.
TENSOR version 2.0 is a new install for both OS X platforms. Tensor allows the determination of rotational diffusion from three-dimensional structure coordinates and experimental 15N relaxation data, and now, as mentioned below, allows a rigorous model-free analysis of local internal mobility affecting backbone amides, from 15N {R1,R2,nOe} relaxation rates in the presence of an isotropic of anisotropic rotational diffusion tensor. More information can be found in the Tensor documentation.
Linux and Mac OS X Intel Only
ZDOCK/RDOCK, from the Zhiping Lab at Boston University, are two protein docking algorithms, designed to operate in succession. ZDOCK is a rigid-body docking program, and RDOCK is a refinement program. ZDOCK uses a fast Fourier transform to search all possible binding modes for the proteins, evaluating based on shape complementarity, desolvation energy, and electrostatics. The top 2000 predictions from ZDOCK are then given to RDOCK where they are minimized by CHARMM to improve the energies and eliminate clashes, and then the electrostatic and desolvation energies are recomputed by RDOCK.
Linux Only
FREALIGN has been updated to version 7.07, and now includes multiple versions with increasing array sizes for analysis of larger datasets. Note that 'frealign768' requires a 64-bit machine with at least 12 GB of RAM to run.