From Christoph's Personal Wiki
The input is a protein sequence in FASTA format.
- Number of steps
- The number of residues plotted per turn is this value divided by the 'turns' value.
- Number of turns
- The number of residues plotted per turn is the 'steps' value divided by this value.
- Amphipathic residue marking
- If this is true then the residues
ACFGILMVWYare marked as squares and all other residues are unmarked. This overrides any other markup that you may have specified using the qualifiers '
-diamonds' and '
- Mark as squares
- By default the aliphatic residues
ILVMare marked with squares.
- Mark as diamonds
- By default the residues
DENQSTare marked with diamonds.
- Mark as octagons
- By default the positively charged residues
HKRare marked with octagons.
Format to use for graphics output:
- Portable Network Graphic (png)
- Colour PostScript (cps)
- Black and White Postscript (ps)
- Hewlett-Packard Graphics Language (hpgl)
- Plot data (data)
The following is for the protein sequence of 1fin.
- Input commands:
pepwheel -sequence '1fin.fa' $tmpSFormatOpt -wheel Y -steps 18 -turns 5 \ -amphipathic N -squares 'ilvm' -diamonds 'denqst' -octags 'hkr' \ -graph 'png' -goutfile '1fin.pepwheel.png' -auto
- Graphical output:
- pepwheel man page — on EMBOSS website