Dear Consortium Members and Affiliates,
Hey, how's it going? It has been a wet spring in Boston, but we retain our dry sense of humor. Ben has been out on paternity leave the last few weeks, hence the delays on the monthly update. We really wanted to get an update out for April, so we're doing an unusual Friday update. This month is a bit of a hodgepodge with updates for PHENIX, PyMOL, CCP4mg, Bsoft, CCP4mg and Coot and a new package, Electra. Things should be returning to their normal frenetic pace shortly.
We're pleased to report that we've secured competitive pricing on two Linux-compatible workstations from our new preferred hardware vendor, ThinkMate. We're working with ThinkMate because they do a fantastic job with high-quality system builds and because they ensure that each system they build enjoys full Linux compatibility. All systems come with a 3 year warranty and can come pre-installed with CentOS, SBGrid's recommended linux distribution.
The workstation configurations are available at http://thinkmate.com/sbgrid. The SBGrid Standard Workstation comes with a quad-core CPU, 3GB of RAM and an NVIDIA Quadro FX 380 graphics card ($1173). The SBGrid Pro Workstation has a default configuration with two quad-core CPUs, 6GB of RAM and an NVIDIA Quadro FX 580 graphics card ($2123). The Pro Workstation can also serve as a small file server, accommodating up to 8 hot-swap hard drives paired with a 3ware RAID card.
If you have any questions about the configurations, please email us or feel free to contact our ThinkMate sales representative Jon Breen at 800-371-1212 x4249 or via email at jon.breen@thinkmate.com. Please note that we don't receive any sort of compensation from these sales -- we work on these configurations solely for the benefit of our community.
In other news, we're starting up a mailing list for discussion of technical matters related to maintaining and supporting a suite of scientific software. Ben is hoping to strong-arm his favorite sysadmins, power users and software admins into joining the list to discuss best practices for integrating locally-supported and SBGrid-maintained software, thoughts on crowd-sourcing software maintenance via a distributed filesystem (SBGrid AFS cell, anyone?) and other bits of random tech talk. Send email to sympa@cmcd.hms.harvard.edu with the subject "subscribe sbgrid-tech" to join up.
We hope things are going well in your neck of the woods, and Ben promises not to write in 3rd person plural again.
Hasta!
We've had a passel of new members join in the last couple months. We are pleased to welcome Gang Dong from the University of Vienna, Roger Kornberg at Stanford University, Michael Cosgrove at Syracuse University, Jane McGlade at the University of Toronto and four new members at the University of California at Berkeley: Tom Alber, Jamie Cate, Jennifer Doudna and James Berger.
The following software updates will be available some time today:
Linux and Mac OS X (PPC and Intel)
A pre-release version of CNS 1.3 is now available in the software tree. It's not set as the default version, but you can instruct your shell to use it with a ~/.sbgrid file. The CNS website has some details as well as a new wiki.
PyMOL has been updated to the latest incentive versions: 1.2r3s for linux, 1.2r2 for OS X 10.4 and 10.5 and 1.2r3 for 10.6. We have also renewed our subscription to the incentive version of PyMOL through Schrodinger. All SBGrid members can access the PyMOL incentive downloads and documentation at http://pymol.org/dsc using invoice number '5905' and password 'pile5bent'. Note that I keep the PyMOL Windows builds at /programs/share/pymol/windows.
Bsoft has been updated to version 1.6.0 with both 32 and 64-bit versions now included in the software tree. The excellent Bsoft website has documentation, how-tos and helper scripts.
ELECTRA (ELECtron Tomography Resolution Assessment) is a suite of programs written to estimate the resolution of electron density volumes obtained by electron tomography. Basically, two different resolution methods (FSCe/o and NLOO) are implemented, along with some auxiliary tools for preparation of data needed for analysis and postprocessing. There's not a ton of documentation available online, but the README at file:///programs/
Linux and Mac OS X Intel
PHENIX has been updated to the latest release version 1.6.1-357. There are release notes and updated PHENIX documentation to go with the new release. PHENIX no longer offers official OS X PowerPC binaries, and the sources refused to build on our OS X PowerPC machines. I hope to have this version running under PowerPC in a future update.
Linux
Coot has been updated to 0.6.2-pre1-r2940 for 32 and 64-bit linux platforms. I'll be sending bribes to Bill Scott to update the OS X packages shortly. There is also a new Coot home page.
OS X Intel
CCP4mg has been updated to 2.3.0 for Intel Macs. The CCP4mg website has excellent documentation. The linux builds has some odd issues that I need to work out or report as bugs to the developers, and they no longer offer official OS X PowerPC builds. The death knell has been sounded.
The following bugs have been fixed since the last newsletter:
HKL2000 uses a fixed-length buffer for input filenames and when working with datasets that are stored under a very deep directory structure will crash with an inscrutable memory allocation error. I reported this to HKL Software, but didn't get a response. Reported by Sun Hur, Hur Lab at the Immune Disease Institute.
There was a bug in the OS X Intel set up files that picked the wrong Coot version for OS X 10.4 machines. The set up files were changed to choose the correct version. Reported by John Williams, Williams Lab at City of Hope.
XIA2 was still set to use the expired version of XDS on Linux and OS X Intel. The preferred XDS version was changed inside the XIA2 installations. Reported by Terry Lang in the Alber Lab at UC Berkeley.
The VNC-based wrapper scripts for running 8-bit color depth X11 applications on Linux (web-8-wrapper and vnc-8-wrapper) had a bug where they would only run on versions of VNC closely based on the original AT&T version. They have been modified to run on more modern versions of VNC like TightVNC. Reported by Stefan Raunser, Raunser Lab at the Max-Planck-Institute of Molecular Physiology.
2dx for OS X Intel was linked against a missing CCP4 library. The application was re-linked against the proper library. Reported by Rich Hite, Walz Lab, Harvard Medical School.
With the last NMRPipe update, I added support for additional fonts to the NMRPipe set up, and it caused errors in some situations when users tried to tunnel X11 over ssh from a machine that had the software installed to one that didn't have the software installed. The error was harmless, but it has been quashed so as not to be annoying. Reported by Matthias Wolf, Harrison Lab, HMS among several others.
Coot on linux was reporting errors about missing libraries on certain unsupported systems. I added the libraries to the installation in order to hopefully make everyone's life a bit easier.
VMD on OS X was hanging with the infamous beachball. The updated VMD had a slightly different structure to their .app folders and was being read incorrectly by the OS X loader. I moved the files and folders around to match the layout of the older version, and it seems to have resolved the issue. Reported by Fred Metoz, IBS-Grenoble.
Coot 0.6.1 on OS X Intel was barfing a segmentation fault on OS X 10.5 and 10.6. I rebuilt it a half dozen times and finally got a working version. In the interim, we had fallen back to the previous version, but with this update, everyone should be running the same version of Coot. Reported by Yuri Lobsanov, Howell Lab, University of Toronto.Ribbons was crashing with a missing Motif symbol on linux. After a bit futzing around with libraries and package settings, this should be resolved for all our supported linux platforms. Reported by Clinton Heider, Rice University and Michael Durney, D'Souza Lab, Harvard University.
web was crashing due to a bug with input file length limitations. Conversations with Dean Leith at Wadsworth confirm that there is an 80-character limit for input files for web. Reported by Montserrat Samso, Samso Lab, Brigham and Women's Hospital and Berith Isaac, Leschziner Lab, Harvard University.
XPLOR-NIH was not configured for use with OS X 10.6. Editing the platform equivalence files resolved the problem. Reported by Yunsun Nam, Sliz Lab, Harvard Medical School.
Chimera on linux was crashing while trying to save images if the machine was using certain versions of the Nvidia driver. This problem was resolved by updating to the latest version of Chimera and was reported by the inimitable Sabuj Pattanayek at Vanderbilt University.
XDS-Viewer on linux was encountering some sort of library problem resulting in missing symbols errors. The problem was resolved by switching to a static binary. Reported by Andrew Ring, UC Berkeley.
Rosetta was missing some of its helper scripts buried in the source directory. They have been copied from the source tarballs into the software tree to /programs/
Did you really read this far? Good on ya! Thanks for all your bugs reports!
Hey, how's it going? It has been a wet spring in Boston, but we retain our dry sense of humor. Ben has been out on paternity leave the last few weeks, hence the delays on the monthly update. We really wanted to get an update out for April, so we're doing an unusual Friday update. This month is a bit of a hodgepodge with updates for PHENIX, PyMOL, CCP4mg, Bsoft, CCP4mg and Coot and a new package, Electra. Things should be returning to their normal frenetic pace shortly.