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.
Roca et al. BMC Bioinformatics 2008 9:554 doi:10.1186/1471-2105-9-554