
                              EMBOSS: pepwheel
     _________________________________________________________________
   
                               Program pepwheel
                                       
Function

   Shows protein sequences as helices
   
Description

   pepwheel
   displays peptide sequences in a helical representation.
   
   This gives a view of a helix from a protein sequence looking down the
   axis of the helix.
   
   It is useful for highlighting amphipathicity and other properties of
   residues around a helix.
   
Usage

   Here is a sample session with pepwheel.
   
% pepwheel sw:hbb_human -send 30
Shows protein sequences as helices
Graph type [x11]:

   click here for result
   
Command line arguments

   Mandatory qualifiers (* if not always prompted):
  [-sequence]          sequence   Sequence USA
*  -outfile            outfile    Output file name
*  -graph              graph      Graph type

   Optional qualifiers (* if not always prompted):
   -steps              integer    The number of residues plotted per turn is
                                  this value divided by the 'turns' value.
   -turns              integer    The number of residues plotted per turn is
                                  the 'steps' value divided by this value.
*  -squares            string     By default the aliphatic residues ILVM are
                                  marked with squares.
*  -diamonds           string     By default the residues DENQST are marked
                                  with diamonds.
*  -octags             string     By default the positively charged residues
                                  HKR are marked with octagons.

   Advanced qualifiers:
   -[no]wheel          bool       Plot the wheel
   -amphipathic        bool       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
                                  using the qualifiers '-squares', '-diamonds'
                                  and '-octags'.
   -data               bool       Output the match data to a file instead of
                                  plotting it

   General qualifiers:
  -help                bool       report command line options. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   

   Mandatory qualifiers Allowed values Default
   [-sequence]
   (Parameter 1) Sequence USA Readable sequence Required
   -outfile Output file name Output file <sequence>.pepwheel
   -graph Graph type EMBOSS has a list of known devices, including
   postscript, ps, hpgl, hp7470, hp7580, meta, colourps, cps, xwindows,
   x11, tektronics, tekt, tek4107t, tek, none, null, text, data, xterm,
   png EMBOSS_GRAPHICS value, or x11
   Optional qualifiers Allowed values Default
   -steps The number of residues plotted per turn is this value divided
   by the 'turns' value. Integer from 2 to 100 18
   -turns The number of residues plotted per turn is the 'steps' value
   divided by this value. Integer from 1 to 100 5
   -squares By default the aliphatic residues ILVM are marked with
   squares. Any string is accepted ILVM
   -diamonds By default the residues DENQST are marked with diamonds. Any
   string is accepted DENQST
   -octags By default the positively charged residues HKR are marked with
   octagons. Any string is accepted HKR
   Advanced qualifiers Allowed values Default
   -[no]wheel Plot the wheel Yes/No Yes
   -amphipathic 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 using the qualifiers
   '-squares', '-diamonds' and '-octags'. Yes/No No
   -data Output the match data to a file instead of plotting it Yes/No No
   
Input file format

   Any protein sequence USA.
   
Output file format

   An image is output.
   
Data files

   None.
   
Notes

   The default settings for turn (5) and steps (18) apply to alpha
   helices. For other possible secondary structures, see the following
   table:
   
helix       phi   psi  omega  res/turn  transl.  turns  steps
alpha       -57   -47    180       3.6     1.50      5     18
3-10        -49   -26    180       3.0     2.00      1      3
pi          -57   -70    180       4.4     1.15      5     22
PP I        -83   158      0       3.33    1.9       3     10
PP II       -78   149    180       3.0     3.12      1      3
PG II       -80   150    180       3.0     3.1       1      3
anti Beta  -139   135   -178       2.0     3.4       4      9
para Beta  -119   113    180       2.0     3.2       4      9

PP is polyproline
PG II is polyGlycine.

References

    1. Rachamandran and Sasisekharan, Adv. Protein Chem. 23:283-437, 1968
    2. IUPAC-IUB Commission on biochemical nomenclature, Biochemistry
       9:3471-3479, 1970
       
Warnings

   When you specify the number of turns and steps, be aware that you
   should remove common factors from these two numbers. For example, if
   you (for some improbable reason) wished to plot a wheel with 8 turns
   in 18 steps (2.25 residues per turn) you should remove the common
   factor (i.e. 2) and specify 4 turns in 9 steps.
   
Diagnostic Error Messages

   None.
   
Exit status

   0 upon successful completion.
   
Known bugs

   None.
   
See also

   Program name Description
   abiview Reads ABI file and display the trace
   cirdna Draws circular maps of DNA constructs
   garnier Predicts protein secondary structure
   helixturnhelix Report nucleic acid binding motifs
   hmoment Hydrophobic moment calculation
   lindna Draws linear maps of DNA constructs
   pepcoil Predicts coiled coil regions
   pepnet Displays proteins as a helical net
   prettyplot Displays aligned sequences, with colouring and boxing
   prettyseq Output sequence with translated ranges
   remap Display a sequence with restriction cut sites, translation etc
   seealso Finds programs sharing group names
   showalign Displays a multiple sequence alignment
   showdb Displays information on the currently available databases
   showfeat Show features of a sequence
   showseq Display a sequence with features, translation etc
   textsearch Search sequence documentation text. SRS and Entrez are
   faster!
   tmap Displays membrane spanning regions
   
Author(s)

   This application was written by Alan Bleasby (ableasby@hgmp.mrc.ac.uk)
   
History

   Writte (March 1999) - Alan Bleasby
   
Target users

   This program is intended to be used by everyone and everything, from
   naive users to embedded scripts.
   
Comments
