A Subgroup Algorithm to Identify Cross-Rotation Peaks Consistent with Non-Crystallographic Symmetry
Ryan H. Lilien, Chris Bailey-Kellogg, Amy C. Anderson, and Bruce R. Donald
Acta Crystallographica D, 2004; 60: 1057-67.


The translation-only RMSD (TRMSD) was computed between the model oriented according to each cross-rotation peak and each chain in the crystal structure. We define the TRMSD of two proteins to be the minimum main chain Ca RMSD achievable when the molecules are only allowed to translate relative to one another (i.e., rotations are not allowed). Using this measure we are able to quantify the similarity between models oriented by each cross-rotation peak and each monomer of the crystal structure.

The table displays the TRMSDs measured for a CRANS analysis for the three test systems, 1FQ0, 1CHP, and 1G31. Column 2 lists the PDB chain identifier used in computing the TRMSD for the specified row. The ‘Best Pk.’ column lists the minimum TRMSD observed between the specified chain and all cross-rotation peaks along with its corresponding cross-rotation peak index (in parentheses). Cross-rotation peaks are ordered by sorting them based on the cross-rotation function score where a lower index corresponds to a higher (better) cross-rotation score. The TRMSD and peak index of the peak with the smallest TRMSD among the top 10 cross-rotation function ranked peaks is listed in the ‘Best Pk. in top 10’ column. The TRMSD of the CRANS identified peak of the NCS-consistent rotation set corresponding to the specified chain and its cross-rotation peak index (in parentheses) is listed in column ‘CRANS Pk.’. Peaks computed by CRANS (i.e., those missing in the cross-rotation peak list) are shown in italics with a dash for the peak index.