Newsletter Sep 2007

Newsletter for September, 2007

Dear Consortium Members and Affiliates,

As we mentioned last month, the first SBGrid structural biology computing conference: ‘Quo Vadis Structural Biology?’ will take place on May 5th and 6th 2008 at Harvard Medical School in Boston. This two-day conference will include lectures and hands-on computing lab sessions. Today I wanted to highlight one of the workshops, "Animating Your Data: Tools from Hollywood”. Gael McGill will teach how Maya and other tools can be used to animate molecular structures. Please visit Gael’s web site to catch a glimpse of recent work in this field. We will have the registration website for the conference in place next month and the registration will be exclusively open to SBGrid members before the event is announced to the general public. Space in all computing workshops will be limited, so if you plan to participate please be ready to register early.

Our software push is scheduled for tonight. Please take a few minutes on Thursday to test if your major applications are working well. Our staff will be on call tomorrow to resolve any urgent issues. This month we have updates for HKL2000, probe and reduce, XDS, Chimera, Ultrascan, MIFit and the Autodock/MGLTools suite.

If there are any problems, please report them at You can always switch to an older version of the application while we work on your request—just use ‘sbgrid –n’ for more information. Many of these monthly updates and additions are prompted by member requests, so please do not hesitate to request new applications




Piotr Sliz, Ph.D.
Structural Biology Grid (SBGrid)
NSF Research Coordination Network


Christopher Garcia at Stanford University

The following software updates will be available later tonight:

Linux and Mac OS X (PPC and Intel)
Probe and Reduce, from the Molprobity suite, have been updated to versions 2.12 and 3.10 respectively. The program Probe allows one to evaluate atomic packing, either within or between molecules. It generates “contact dots” where atoms are in close contact. Probe reads atomic coordinates from protein databank (PDB) format files and writes dot-lists for inclusion in a kinemage file. Alternatively, the packing information can be quantified and displayed in a table listing scores for van der Waals interactions, H-bonds and atomic overlaps.

Reduce is a program for adding hydrogens to a Protein DataBank (PDB) molecular structure file. Hydrogens are added in standardized geometry with optimization of the orientations of OH, SH, NH3+. Please note that Reduce 3.10 supports the new PDB format. If you want to continue to use the older format, please pin Reduce to version 3.03 in your .sbgrid file. Probe and Reduce are also available for use in Coot. Additional details can be found in the Coot documentation.

XDS, a data processing program for X-ray crystallography, has been upgraded on Linux and is a new application for OS X. Version 20070815 is now standard for all platforms. The previous installed version was over 3 years old and the list of new features, bug fixes, and notes is available in the release notes. Please see the note about the HKL2000 update under the OS X Intel section below.

Chimera has been updated to version 1.2422 for all platforms. The latest version finally supports mouse wheels! The lists of changes since the last update is quite large and are available here and here.

Autodock has been upgraded to version 4.0.1. The list of new features is extensive and is available here. Additionally, MGLTools, the graphical interface to the Autodock tool set, has been upgraded as well. This is a minor release containing mostly bugfixes.

Linux Only
Ultrascan has been updated to version 9.3 in response to a user request. This version includes a host of new features for the analysis of velocity data using genetic algorithms and 2-dimensional spectrum analysis methods with a supercomputer backend, a new pseudo-absorbance data processing module, an improved data editor, and updates in the reporting system.

Also available is a new simulator capable of simulating multi-speed profiles with user-selectable acceleration profiles, floatation, and reversible self-association systems with kinetic modulation between instantaneous (diffusion controlled) and non-interacting extremes.

MIFit has been updated to version 4.1. This package includes the MIFit crystallographic model-fitting and display program as well as MIExpert, an application for managing crystallographic structure solution software. MIFit contains a ‘ligand dictionary editor’ for automatically generating, displaying and editing restraints for structure refinement. MIExpert includes a pipeline automation system for rapidly obtaining pre-refined models and maps in repetitive co-crystallography projects with minimal user input.

OS X Intel Only
HKL2000 has been updated to version 698d. This is only the second full release of HKL2000 for OS X, and it brings OS X support to comparable levels with the Linux version.

Published September 1, 2007