Newsletter Nov 2007

Newsletter for November, 2007

The following software updates will be available later tonight:

Linux and Mac OS X (PPC and Intel)

iPyMOL 0.99 is a new install for all three platforms.  iPyMOL is a command-line oriented version of PyMOL that includes RigiMOL, a morphing application. More information and some examples available in the iPyMOL the 'rigimol' directory of the iPyMOL installation directory.  Note that outside of the RigiMOL functionality, iPyMOL does not contain any additional features over the main PyMOL.  Since new development is occuring in the PyMOL branch, that is the version we will track more closely and will work to ensure we have the latest plugins installed for that version.

Slerpy and eMovie are two new PyMOL plugins that are available as of this update.  They are available under the main PyMOL installation.  Remember that 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. Documentation for Slerpy and eMovie is available.

CCI Apps, the core command-line applications from Phenix, have been updated for Linux and are a new installation on both Mac platforms.  These are typically integrated with the Phenix graphical interface, but are available as a standalone package under the name CCI Applications.  Version 2007_08_18_1856 is available for all platforms.  Visit the Phenix website for documentation and notes on usage.

ATNOS/CANDID is a new install for all three platforms.  The ATNOS/CANDID program bundles together the two algorithms,  ATNOS for automated NOESY peak picking, and CANDID for automated NOE assignment providing a powerful platform for objective and efficient de novo 3D protein structure determination by NMR. A tutorial and other documentation is available on the ATNOS/CANDID website.
Dear Consortium Members and Affiliates,

We will be pushing a small update tonight which includes updates for the CCI Apps from Phenix, some new PyMOL plugins and a new package for NMR labs called ATNOS/CANDID. See below for updates on  Mac OS X Leopard and Fedora 7 compatibility as well as information on the new packages now available. Have a safe and happy Thanksgiving.

Best regards,

Piotr Sliz, Ph.D.
Structural Biology Grid (SBGrid)
NSF Research Coordination Network In addition to the Leopard OS X Intel support mentioned last month, this month we have basic support for the SBGrid Programs Collection for PowerPC Macs running Leopard. Shell initialization should complete successfully, but some applications will have problems. We'll have a more in-depth update on PowerPC compatibility for December. Please feel free to file tickets on any packages that you notice are not running under the new platform.

We are pleased to announce full compatibility of the Linux programs branch with Fedora 7. All applications have been tested and are functional to our knowledge. We have migrated the majority of our supported Linux workstations here at Harvard Medical School to Fedora 7. We will have some updated installation notes for Fedora 7 workstations on the SBGrid Member Wiki in the next few days.

Additionally, we are officially discontinuing support for Fedora Core 3.  While most applications will continue to work without problem on this older Fedora release, we will not test that platform during updates or new installations, and users encountering bugs on FC3 machines will be advised to upgrade. 

Published November 1, 2007