Method for calculating 3-D coordinates from molecular stereograms
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The three-dimensional coordinates for the α-carbon atoms of crambin and basic pancreatic trypsin inhibitor (BPTI) were determined from the respective α-carbon trace stereograms using an improved Simplex algorithm. This algorithm was used in a two-step process to estimate thez-coordinate values. In one approach, an average interatomic distance value, an approximate viewing angle, and a table of digitized values forxleft,yleft andxright,yright are provided in the first step. In the second step, thez-coordinate values are derived by varyingz 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 ofxleft,yleft andxright,yright digitized values. In the first step, the viewing angle (φ), a combined scale and viewing distance parameter (q), a rotational angular distortion from digitizing and/or photocopying (z), and translational distortion factors (xerr andyerr) are calculated. In the second step, thez-coordinate values are varied to minimize the bond distance error. RMS difference values of less than 1.5 Å were obtained for both crambin and BPTI α-carbon atoms.
KeywordsTrypsin Bioorganic Chemistry Bond Distance Interatomic Distance Argos
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