From: Willy Wriggers
Sent: Thursday, March 31, 2011 5:12 PM
Subject: New major Situs release: Version 2.6
Dear Situs user:
We have released new versions of Situs, version 2.6, to coincide with our papers in the March 2011 special issue of Journal of Structural Biology on "Combining computational modeling with sparse and low-resolution data". […]
This is the most powerful version of Situs ever released and it includes a number of useful tools and features requested by many of you. The latest version 2.6.1 also includes several bug fixes implemented after community feedback. Also, we completely revised the user guide and the tutorials. New tools and features include:
• Simultaneous multi-fragment refinement with collage. The new refinement tool collage performs a conjugate gradient optimization of the scoring functions known from colores. The main innovation is the simultaneous optimization of multiple rigid fragments that "see" each other and avoid steric clashes. In the new paper we have shown that this approach yields more accurate fits. Also, if all density is accounted for by the fragments, it is no longer necessary to use the Laplacian filter option, even at low resolution. We have created a new tutorial to explain this powerful approach.
• Symmetry now supported. The new collage tool and the existing pdbsymm tool can be combined to impose symmetry constraints on the fragments during multi- fragment docking. Currently we support C, D, and helical symmetry [Note: users are free to replace pdbsymm in our scripts with their own external symmetry program]. This feature should be very useful for many oligomeric assemblies. See the new tutorial for details.
• Map histogram matching with volhist. Computational docking strategies exist for finding the geometric transformations that superimpose structures, but the problem of finding an optimal density transformation, for the purposes of difference calculations or segmentation, has received little attention. In a new paper we show that in certain modeling applications, where densities from different biophysical origins are used, it is important to match the histogram of two registered maps using a linear approach that is parametrized by the surface isovalues and by the centering of the central peak of the trimodal map difference histogram. If you are interested in this approach see the new part II of the classic docking tutorial.
• Point-cloud docking with matchpoint coming of age. The idea of using coarse-grained models of feature points for docking of multi-scale structures is a classic Situs idea that dates back to 1998. We have shown in earlier work that this approach is advantageous at low-resolution > 10Å because the points provide "interior features" (and an encoding of the molecular shape) even in the absence of interior density variations. However, the earlier Situs tools were limited in the number of feature points and in requiring that both point clouds be of equal size. We have recently published a new anchor point registration technique that overcomes these combinatorial limitations and is able to dock smaller point clouds to larger ones. We have now improved the matchpoint tool introduced in version 2.5 to replace all of the functionality of the older Situs tools (qdock and qrange), and we have updated the classic tutorial accordingly. If you are working with lower resolution maps you should have the next-generation matchpoint tool in your arsenal.
• Map averaging with volaver. We have added a new tool, volaver, to perform the real-space averaging of any number of input density maps. These maps can be first registered as described in the new part II of the classic docking tutorial, thereby providing a 3D reconstruction capability for noisy maps or for maps from tomography. Also, the tool can be used to combine (add) segmented parts of maps.
• Tutorial Scripts. To demonstrate the scripting capabilities of Situs tools we have implemented the work flow of all tutorials in executable bash shell scripts named 'run_tutorial.bash'.
Please take a look and thank you for using Situs.