Method for calculating 3-D coordinates from molecular stereograms.

Abstract

The three-dimensional coordinates for the alpha-carbon atoms of crambin and basic pancreatic trypsin inhibitor (BPTI) were determined from the respective alpha-carbon trace stereograms using an improved Simplex algorithm. This algorithm was used in a two-step process to estimate the z-coordinate values. In one approach, an average interatomic distance value, an approximate viewing angle, and a table of digitized values for xleft, yleft and xright, yright are provided in the first step. In the second step, the z-coordinate values are derived by varying z to minimize the bond distance error (Rossmann and Argos, 1980). In another approach, only a reference bond distance table is provided along with the table of xleft, yleft and xright, yright digitized values. In the first step, the viewing angle (phi), a combined scale and viewing distance parameter (q), a rotational angular distortion from digitizing and/or photocopying (z), and translational distortion factors (xerr and yerr) are calculated. In the second step, the z-coordinate values are varied to minimize the bond distance error. RMS difference values of less than 1.5 A were obtained for both crambin and BPTI alpha-carbon atoms.