The motifs tab allows users to find pre-defined motifs using selection algebra written by Charlie Westin and Brett Hanson. This is done by clicking the drop-down menu of interest and selecting the motif the users believe may be in their protein. The selection algebra is run and the motif is returned represented as sticks on top of the proteins overall structure shown as a cartoon. The resiudes around the active site can also be shown using the adjacent button and the distance slider specifying the amount of angstroms around the motif to display. Since this is solely based on measurements of individual atoms in specified residues to individual atoms in other residues, it is possible to return false positives. False negatives may also be returned, but to accomodate for both of these shortcomings it is possible to slide the precision factor bar to change the multiplier of the default measured values. Moving the slider to the right increases the probability of returns by allowing for residues within a greater distance to be accepted. Moving it to the left makes it much more specific and reduces the allowable distances returned.
Options
Once the motif has been returned and displayed as sticks, the user can then add one of the various options for the active site. A surface can be added enabling the user to find the pocket or surface contact of the motif. The user must look for the colored regions on the white transparent surface to determine these sites. Also residue labels, polar contacts and bound substrates can be shown or hidden. Resources for the protein of interest are at the bottom of the page and include, the Abstract based on input PDB code, FASTA sequence download based on input PDB code, FASTA site link, and a link to the PDB databank. The resources require an internet connection.