Dear Consortium Members and Affiliates,
This month we have updates for seven existing applications and are adding one new application. Sparky, PHENIX, CCI Apps, 2dx, XDS, HKL200 and MIFit are being updated, and 3D-Dock is our new addition.
Have a pleasant fourth of July holiday.
The following software updates will be available later tonight:
Linux and Mac OS X (PPC and Intel)
Sparky has been updated to the latest version for all three platforms. This is mostly a bugfix update, and it also addresses compatibility issues with the OS X 10.5.
PHENIX has been updated to version 1.3-rc2 for the linux branch and is a new install for both Mac OS X branches.
The CCI Apps that are the core of PHENIX have been updated for all three platforms. This is where the cutting edge PHENIX development happens, so if you're looking for the latest and greatest tools from the PHENIX project, check out the latest CCI Apps.
XDS has been updated for all three main platforms. The change log has a few items: a subroutine to support space group determination was added to the CORRECT step, and automatic assignments are based on a few decision constants that can be modified by the user in XDS.INP. Also a bug was found in calculating reflection boundaries for centered lattices that could lead to inferior results at high resolution in the INTEGRATE step and is now fixed.
Linux and Mac OS X Intel
HKL2000 has been updated to the latest version for both Linux and OS X Intel. HKL Software doesn't post change logs on their website, so you'll just have to try out the software to find out what's new.
2dx has been updated to version 3.0.x. The OS X PowerPC should be available soon as well, since they are currently working on updated packages for OS X. Version 3.0.x includes 2dx_merge, the maximum likelihood code, and an extended version of 2dx_image, which now also allows re-unbending of the images using the merged dataset as reference. They're soliciting feedback on the 3d merging capabilities, so you should check it out if it sounds interesting.
MIFit has been updated to version 7.1. The change log was in their email update: Added ability to control parameters of secondary structure rendering. Changes to OpenGL initialization (only affects some graphics configurations). Fixed alignment of insertion code field in PDB export. Fixed crash when mouseover Solid Surface item in models context menu (only on Linux). Fixed dictionary editor loosing planes when an atom was deleted. Fixed exported bond orders in dictionary editor. Fixed exporting to cif file in dictionary editor. Fixed loading of config.db when MIFit installed on some NFS mounts. Fixed periodic boundary mis-calculation in sphere contouring method. Fixed problem removing hydrogens from a ligand in dictionary editor. Fixed setting of dictionary editor entry name when imported from mol file.
3D-Dock is a new install for Linux. It is comprised of three applications: FTDock, RPScore and MultiDock. FTDock ( Fourier Transform Dock ) performs rigid-body docking on two biomolecules in order to predict their correct binding geometry. FTDock outputs multiple predictions that can be screened using biochemical information. FTDock implements the Fourier correlation algorithm of Katchalski-Katzir and coworkers plus an electrostatics function amenable to Fourier correlation that was developed in this laboratory. RPScore ( Residue level Pair potential Score ) uses a single distance constraint empiricaly derived pair potential to screen the ouptut from FTDock. It has been shown that this can reduce dramatically the list of possible complexes within which can be found a correct solution. This program is fully integrated with the present version of FTDock. A further improvement in the quality of the predictions can be gained by using MultiDock (Multiple copy side-chain refinement Dock ). More information is available on the 3D-Dock website. This month we are pleased to welcome Darst Lab at Rockefeller University. Royer Lab at the University of Massachusetts Medical School has been a member for some time, but we are pleased to add some fellow labs from the medical school: Lambright, Stern and van den Berg are all new members.