Shows protein sequences as helices emboss emboss_single_outputfile_wrapper.pl pepwheel -sequence $input1 -graph png -goutfile $out_file1 -squares $squares -diamonds $diamonds -octags $octags -amphipathic $amphipathic -steps $steps -turns $turns -wheel $wheel -auto Sequence Steps, the number of residues plotted per turn is this value divided by the 'turns' value Turns, the number of residues plotted per turn is the 'steps' value divided by this value Residues to mark with squares Residues to mark with diamonds Residues to mark with octagons Plot the wheel Yes No If this is true then the residues ACFGILMVWY are marked as squares and all other residues are unmarked. This overrides any other markup that you may have specified No Yes You can view the original documentation here_. .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/pepwheel.html