ASSA, a Program for Three-Dimensional Rendering in Solution Scattering from Biopolymers

Abstract

A program for three‐dimensional rendering and interactive model refinement, ASSA, is presented. The program permits the simultaneous display and manipulation of low‐resolution envelope models obtained from solution‐scattering data and the crystallographic or electron microscopic models in the Brookhaven Protein Data Bank format. ASSA is coupled with the shape‐determination program of Svergun, Volkov, Kozin, Stuhrmann, Barberato & Koch [J. Appl. Cryst. (1997). 30, 000–000], thus allowing one to monitor the shape determination process in real time. The program ASSA is written in C using the PHIGS+ standard for the three‐dimensional solid rendering and the XView and XLib libraries for the menu‐driven user interface. The system runs on a Sun SPARC ZX‐20 workstation; a simplified IBM‐PC version is also available.

MASSHA– a graphics system for rigid-body modelling of macromolecular complexes against solution scattering data

“…In contrast to the earlier Unix-based system (Kozin & Svergun, 2000;Kozin et al, 1997), MASSHA runs on a Wintel platform, which makes the rigid-body modelling available for numerous PC users. Furthermore, MASSHA provides enhanced options for interactive modelling and the possibility of an automated re®nement in the vicinity of the current con®guration.…”

“…on contacts between the speci®c residues) can be taken into account by using an interactive search based on visual criteria. An interactive modelling system, running on major Unix platforms (SUN, SGI, DEC), has been developed by us previously (Kozin & Svergun, 2000;Kozin et al, 1997). The three-dimensional graphics program ASSA, coupled with computational modules, permits the manipulation of the subunits as rigid bodies while observing corresponding changes in the ®t to the experimental data.…”

Automated matching of high- and low-resolution structural models

“…(d) Superposition of two models of rat kinesin differing in the length of the coil±coil fragment. All ®gures were prepared on a Silicon Graphics workstation using the program ASSA (Kozin et al, 1997). Table 1 Results of computer simulation tests using SUBCOMB.…”

Investigating Macromolecular Complexes in Solution by Small Angle X-Ray Scattering

“…In this way it can be said that this method provides a very low resolution approximation of the scattering data and usually enables the fitting of only the initial part of the scattering intensity. Program packages that enables the fitting of experimental data are available in the literature (programs ASSA and SASHA, Kozin et al, 1997). An example of this procedure is shown in fig10 where the experimental data for lysozime in solution was adjusted using multipolar expansion by using the program SASHA.…”