Newsletter

July 2008 SBGrid Newsletter

Dear Consortium Members and Affiliates,

The dog days of summer are upon us, and things are pretty quiet here at Harvard Medical School.  We have a short list of updates for you this month including new versions of CNS, PyMOL, XPLOR-NIH, Modeller and the Swiss-PdbViewer.

Software Updates
The following software updates will be available later tonight:

Linux and Mac OS X (PPC and Intel)

CNS has been updated to version 1.21. This version has been compiled with some additional features courtesy of Kay Diederichs that enable parallel computations for some steps in the refinement process. By default the program will attempt to utilize the maximum number of processors on your system for the portions of the code that are parallelized such as FFTs. In order to reduce the number of processors utilized, you can set the environmental variable OMP_NUM_THREADS to the number of processors you want to use.

PyMOL has been updated to version 1.1r1. These are the official builds from Delano Scientific, and all branches include plugins for APBS, Slerpy, eMovie and MOLE. Note that in order to use plugins under OS X, you must use the X11-based PyMOL run with the 'pymol-x11' command in the shell.  Note that the new Linux version of PyMOL requires Fedora Core 6 or equivalent in order to run.

Modeller has been updated to version 9v4.  This is primarily a bug fix release. The speed of GB/SA calculations has been dramatically increased; the cutoff distance used in the GB/SA calculation can also now be adjusted to balance speed against accuracy (the default cutoff has been decreased from 15.0Å to 8.0Å). More details can be found in the change log and release notes.

XPLOR-NIH has been updated to version 2.20. This version now includes the FX-PLOR package for refinement against fiber diffraction data, as well as changes to the PASD/Marvin automatic NOE assignment facility including many additions, improvements and fixes. There are also new eginput/marvin/cvn example scripts and two new helper scripts: mleFit and domainDecompose. See the change log for complete details.

Mac OS X Intel and PowerPC only

The DeepView Swiss-PdbViewer has been updated to version 4.0. This new version includes support for direct login modelling submissions and result retrieval to/from the SwissModel Workspace, an enhanced Import Menu, an enhanced user interface with taxonomy support, and new sequence alignment features. It also includes a new 3D Motif Searching feature and revised help files accessible from the interface. Linux development seems to have stopped. The DeepView website has more details.