Evaluating the Effectiveness of Color to Convey Alignment Quality in Macromolecular Structures

We investigated the effectiveness of colormapping as a means to convey uncertainty in sequence-to-structure align- ments for proteins. To this end, we evaluate a color modulation scheme to encode residue conservation by collecting human preference data for a set of structures and alignment qualities. To this end, we conducted a user study on Amazon Mechanical Turk with more than 40 participants expressing a preference in the choice of two images encoding different alignment qualities of the same structure. The results of this study suggest that there is a strong correlation between human preference of an image of a structure and the alignment quality encoded in that image.