RSREF: Interactive real-space refinement with stereochemical restraints for use during model-building

The cristallographic problem: During macromolecular refinement, building the initial model, and subsequent rebuilding (Jones et al., 1991) using interactive computer graphics, are both rate-limiting and quality-determining steps. Optimizing the fit to the electron density map, while retaining good stereochemistry, can be laborious. Method of solution: Real-space refinement is used to least-squares optimize the agreement of electron density calculated from the atomic model with the experimental electron density map. Although map quality can be limiting, Chapman & Blanc (1997) showed that protein models could be improved even when refined against poor multiple isomorphous replacement (MIR) maps. The core of the algorithm was described previously (Chapman, 1995; Chapman & Rossmann, 1996) and differs from prior real-space refinements (Diamond, 1971; Jones & Liljas, 1984) with explicit accounting for the resolution and incorporation of full stereochemical restraints from TNT (Tronrud et al., 1987), both of which lead to significantly improved performance. RSREF release 2.0 facilitates interactive modeling. Refinement options (such as refinement weights, convergence criteria, data files etc.) can now be set within a graphics user interface (GUI) (program edit.pl). The user selects a zone or volume to be refined within the GUI or by picking atoms within O (Jones et al., 1991). At the start of refinement, SelectCoord adds neighboring atoms (including crystallographic and noncrystallographic symmetry equivalents), converts formats (e.g. pdb to tnt), and writes a table of symmetry constraints, according to options selected in the GUI. Refinement cycles include RSREF (Chapman, 1995), Geometry and Shift (Tronrud et al., 1987) with ReExpand enforcing symmetry. Running summary statistics are written to the GUI. Coordinates can be reviewed in O prior to acceptance. Software environment: The GUI is run by a Perl (Wall & Schwartz, 1991) program on a WWW server writing an HTML form (Graham, 1996). Parameters may be initialized from a user file (on the client computer) and are edited using an Internet browser of choice. During the editing, parameters are saved in a temporary server file, with a name chosen to avoid user collisions. Parameters may be saved to a local client file or sent directly to a client Perl program, rsref_client, that: (1) runs the refinement programs; (2) parses the printed output and calculates summary statistics. Other programs are written in C and Fortran. Hardware environment: RSREF programs have been developed on a Silicon Graphics (SG) Indigo II, and should run on any modest Unix workstation. O is supported on various graphics workstations (Jones et al., 1991). Program specification: Performance statistics are given in Table 1. There are 5000 lines in programs, 10000 in subroutine libraries, and 7000 in documentation. The programs have been applied to about a dozen different systems. Documentation: Documentation is written in HTML and can be browsed over the Internet or installed locally. Availability: RSREF is distributed under license over the Internet from http://www.sb.fsu.edu/~rsref. It is distributed without charge to academic users. Users will also need a license for TNT (Tronrud et al., 1987), and O (Jones et al., 1991).