Dear Consortium Members and Affiliates,
The monthly update is here... trick or treat?
Frank Delaglio of NMRScience is presenting a WebEx seminar today at 2:00 PM EDT on NMR processing and analysis. The full instructions for joining the seminar are below. We hope you can join us.
This is just the first of a series of WebEx seminars on topics in structural biology that we have planned. If you have a suggestion for a topic, please submit your idea online. Our next speaker will be Mike Campbell of Schrodinger who will present on basic docking techniques on December 2nd. More details coming soon.
We have moved all actively updating software installations to a new software distribution system here at Harvard Medical School. The new system is backed by a beefier server, so we can update remote sites more quickly and also incorporates some new features, such as a bash shell configuration for the software. If you've been dying to use your favorite sh-compatible shell with the SBGrid software, wait no longer. Add 'source /programs/sbgrid.shrc' to your shell start up scripts to test out the new option.
This change is just in time, since the steadily burgeoning PATH length in the shell configuration is once again causing a problem for tcsh users. There are two good options for permanently resolving this problem: update your linux systems to tcsh version 6.17.00, which supports a huge PATH length, or switch to the bash version of the SBGrid shell environment. We'll be making tcsh 6.17.00 RPMs available for CentOS systems in the next week or two.
Updates this month include a recent PHENIX nightly version as well as updates to ATSAS, NMRPipe, Jalview, HKL2000, CNS and the ICCB Chemical Libraries. We also have a few new packages including Ringer, TOPS and Solvate.
We have two new members this month. Satinder Singh is our latest member from the Yale School of Medicine and Marc Kvansakul from La Trobe University in Melbourne, Australia. Marc is our first member PI in Australia, and we're all tickled pink to have him aboard. Welcome!
The following software updates will be available today:
Linux and Mac OS X (PPC and Intel)
Ringer version 1.0 is a new package for the software suite. The Ringer home page has documentation, a tutorial, an FAQ and more. Requested by multiple labs after the announcement on the CCP4bb. A big thanks to Terry Lang in the Alber Lab at UC Berkeley for her assistance in getting us a license.
NMRPipe has been updated to release 20100908. The Big NMRPipe Reference Page has documentation, tutorials and more. Just in time for Big Frank's WebEx seminar.
A PHENIX nightly version, dev-555, has been added to the software tree. This is not the default version, but you can select it in your shell using an overrides file. Requested by the Harrison Lab at HMS.
CNS version 1.3 has been updated to the latest patch set. A shout-out to Axel Brunger for keeping us informed.
Jalview has been updated to version 2.6. The Jalview website has release notes detailing the new features. Requested by the Garcia Lab at Stanford.
OS X Intel and Linux
ATSAS has been updated to version 2.3.2-1. There is a shiny new ATSAS website hosted at EMBL. Requested by the Sondermann Lab at Cornell.
TOPS is a new software package for the software tree. TOPS can be used for "visualization, database searching, comparison and machine learning of protein structural topology." The code is from 1999, but the utility is apparently very useful for certain applications. The TOPS website has some additional detail. Requested by the Williams Lab, City of Hope.
Dowser is another new software package for the software tree. Dowser "surveys a protein molecule's structure to locate internal cavities and assess the hydrophilicity of these cavities in terms of the energy of interaction of a water molecule with the surrounding atoms." There is a manual on the Dowser website. Requested by the D'Souza Lab, Harvard University.
SOLVATE is a final new package for the software tree. SOLVATE is used to "construct an atomic solvent environment model for a given atomic macromolecule model (solute) for use in molecular dynamics simulations." The SOLVATE website has a better description as well as usage notes. Requested by the D'Souza Lab, Harvard University.
HKL2000 has been updated to version 700j. This version is also available in the i386-mac branch, but only runs on 10.6 machines so it is not the default version.
No bug reports this month!
NMRScience WebEx Presentation
To join the online meeting (Now from the Apple iPhone (R) too!)
- Visit this page.
- If requested, enter your name and email address.
- If a password is required, enter the meeting password: nmrpipe
- Click "Join".
To view in other time zones or languages, please click this link.
There is also an audio-only conference. To receive a call back, provide your phone number when you join the meeting, or call the number below and enter the access code.
- Call-in toll-free number (US/Canada): 1-866-699-3239
- Call-in toll number (US/Canada): 1-408-792-6300
- Toll-free dialing restrictions information.
Use access code: 573 097 046
We hope to see you there!