February 2008 SBGrid Newsletter
Dear Consortium Members and Affiliates,
Quo Vadis is approaching soon and a detailed program description has been posted on our website. The symposium will provide an excellent opportunity to catch up with your computing skills and advance your understanding of computational methods in structural biology. We encourage all members of our consortium to participate. You can review a full list of speakers and a list of offered nanocourses on the latest poster.
Best regards,
Piotr Sliz, Ph.D.
Director
Structural Biology Grid (SBGrid)
NSF Research Coordination Network
January saw an intensive effort to find and fix bugs in the programs collection related to OS X 10.5. The latest version of Coot was installed to support both OS X 10.4 and 10.5, and we currently have a fix for CCP4i on PowerPC Leopard machines in testing.
One thing that became clear this month is that the unofficial builds of Apple's X11 available from MacOS Forge are a significant improvement over the X11 shipped with Leopard, and we recommend that all Leopard users running X11 applications upgrade. You can download the simple to install packages here.
As we rely on your feedback to determine which programs are most important to you, early adopters of Leopard are encouraged to file bug reports on broken programs. As always, software bug reports can be submitted via our website at http://sbgrid.org/bugs.
The following software updates will be available later tonight:
Linux and Mac OS X (PPC and Intel)
Raster3D has been updated to version 2.7d. Additionally, the maximum number of objects has been raised to 500,000 for raster3d for all three platforms. A couple of bugs in the stereo3d and label3d helper scripts have also been fixed for all platforms. Finally, we have added the Ghostscript command line utilities to the programs collection, as they are used by raster3d for labeling features in the generated images.
Maxit version 8.061 is an application for processing and annotating of macromolecular structure data. The Maxit Program Suite was developed by the PDB (Protein Data Bank) and NDB (Nucleic Acid Database) to assist in the processing and curation of macromolecular structure data. A full description of the program's capabilities is available on the Maxit web page.
PDB Validation Suite version 8.061 is another tool for processing and checking PDB structure data. More information is available on the PDB.org website.
Coot has been upgraded to version 0.4.1 for all three branches. This version should run on both OS X 10.4 and 10.5 on both hardware architectures. The OS X builds use the new GTK2 styling for Coot, and all three Coot installations have built-in support for the probe/reduce utilities from Molprobity.
Linux only
Xmipp 2.0.2 is an update for the Linux branch. The "X-windows based microscopy image processing package" (Xmipp) is a specialized suite of image processing programs, primarily aimed at obtaining the 3D reconstruction of biological specimens from large sets of projection images acquired by transmission electron microscopy. Documentation is available on the Xmipp website.
LAFIRE 2.6 is a new install. LAFIRE (Local-correlation-coefficient-based Automatic FItting for REfinement) is an automatic refinement system for protein crystallography. The system starts with an initial model (approximate or partial model) and finishes with the final structure including water molecules. LAFIRE uses the refinement programs CNS or Refmac5. The LAFIRE home page has additional information.
Mac OS X (Intel) only
Molscript 2.1.2 has been rebuilt for OS X Intel to support all output image types.
Mac OS X (PowerPC) only
ctftilt 1.2 and ctffind 3.1 were added to the OS X PowerPC branch. These utilities can be used for finding CTFs of electron micrographs and were written by Nikolaus Grigorieff.
February 2008 SBGrid NewsletterDear Consortium Members and Affiliates,
We have seven software updates for you that will be installed on your computers tonight.
Recent program changes in the Quo Vadis summit include a talk about future of electron microscopy by Joachim Frank, an HHMI investigator from the State University of New York. We hope that the computer programming workshops in particular will allow consortium members to acquire computational skills that are often required to fully utilize SBGrid software. For example, basic Python programming skills will allow you to write simple conversion scripts or to create or refine modules for applications such as Coot or PyMOL. A special workshop by Gael McGill from Digizyme will present participants with tools that are required for the production of high quality molecular movies. That particular workshop has been offered a number of times for graduate students at Harvard but now all SBGrid members have an opportunity to participate in a condensed version of this class.
If you have any questions about workshop selection please do not hesitate to contact the workshop organizers at quovadis@sbgrid.org. If you are planning to participate in the summit, please sign up soon at the Quo Vadis registration site.
In an effort to better support software users in our member labs, we would like to begin collecting hardware architecture and operating system information from the machines that are using the SBGrid Programs Collection. We plan to do this via a simple shell script that runs when the labcshrc is read by your shell. Information would include the machine hostname, CPU type, operating system version, programs version and other operating system compatibility specifics.
This information would allow us to alert you to when your operating system is not fully compatible or not running the latest versions of the programs. It would also help us to determine where to best to spend our limited resources in supporting various operating systems and optimizing software for various hardware architectures.
We realize that this could be a privacy concern for some of our members, and we want to implement this sort of statistics gathering in a manner that works for best for all parties. We plan to offer a method for programs users to disable the statistics collection via a setting in their ~/.sbgrid file.
The statistics collection will not be implemented for several months, so please take this opportunity to voice your comments and concerns to privacy@sbgrid.org. We also plan to have a short session at the Quo Vadis summit to talk about this issue, and how SBGrid can work to best support you in your research efforts.
Best regards,
Piotr Sliz, Ph.D.
Director
Structural Biology Grid (SBGrid)
NSF Research Coordination Network
The following software updates will be available later tonight:
Linux and Mac OS X (PPC and Intel)
O version 12.0.0 has been updated for all three platforms. This is the first release in the 12.0 branch for O, and Alwyn Jones has lifted the requirement for an O access code to use all O features. The A to Z of O has been updated to reflect the features in the new version. Release notes are also available.
Xplor-NIH has been updated to version 2.19 for all three branches. A full change log is on the Xplor-NIH website as is the documentation.
The CCI Apps from the Phenix project have been updated to version 2008_02_08_1610. Documentation for the latest version is on the Phenix website.
Modeller 9v3 is an update for all three branches. This version brings Mac OS X Leopard support and other bugfixes. The Modeller manual has a full list of changes.
XDS has been updated to version 20071206 for all three platforms. Release notes and documentation are available.
The pointless and othercell command line utilities from the CCP4 project have been updated to their latest versions. Additionally, we have included the pointless CCP4i module so it can be used from within CCP4i graphical interface. Documentation on this CCP4 prerelease software is on their FTP site.
Mac OS X (PPC and Intel)
WHAT_CHECK is the protein verification routines from the WHAT IF program, and it is now installed for both Mac OS X platforms. Documentation can be found on the WHAT_CHECK website.
All updates this month were in response to member requests, so if there are known bugs in the version we have installed, or if you have a hankering to try the latest and greatest version of your favorite software package, please let us know.