Figure 8

Visualization of PyMOL script output. JProfileGrid can write a ".pml" file that will define the following named selections based upon the ProfileGrid information: identical residues (black sidechains); conserved motifs ("mot#") colored from most amino terminal (red) to most carboxyl terminal (green); and connecting variable ("var#") regions (gray). These different selections are mapped on to the E. coli RecA crystal structure [PDB:2REB]. This orientation is defined as the anterior view of the RecA monomer anatomical position. Some of the named selections are indicated by arrows in this PyMOL screen shot.