**************************************************************************
                             plot command
                        Leif Laaksonen CSC 2001
**************************************************************************

#
# Plot various things
#

#
# plot an arrow
#

plot  arro$w     Xc1 Yc1 Zc1 Xc2 Yc2 Zc2 Radius Colour appe$nd
                 Xc1 Yc1 Zc1 Xc2 Yc2 Zc2 Radius Colour
     -arro$w

#
# Plot a cut plane through the contour data 
# Choose through which axis the plane goes (x,y or z)
# Give the tag name for the contour
# Give the coordinate on the axis, through which the plane goes
# Give max and min scale (blue -> red)
# Define if the cutplane will be in 2d (flat) or 3d for the respective plane
#

      cutp$lane  x  ContourName Xcoord
                 x  ContourName Xcoord Fmin Fmax
                 x  ContourName Xcoord Fmin Fmax log10/log
                 y  ContourName Ycoord
                 y  ContourName Ycoord Fmin Fmax
                 y  ContourName Ycoord Fmin Fmax log10/log
                 z  ContourName Zcoord
                 z  ContourName Zcoord Fmin Fmax
                 z  ContourName Zcoord Fmin Fmax log10/log
                 2dx
		         3dx
		         2dy
		         3dy
		         2dz
		         3dz
#
# Define (3 possible) arbitrary cutplanes by defining three points and a 
# ScaleMin and ScaleMax values. A plane is calculated from the defined
# 3 points.
#

                 xyz1 ContourName x1 y1 z1 x2 y2 z2 x3 y3 z3 Fmin Fmax
                 xyz2 ContourName x1 y1 z1 x2 y2 z2 x3 y3 z3 Fmin Fmax
                 xyz3 ContourName x1 y1 z1 x2 y2 z2 x3 y3 z3 Fmin Fmax

#
# Show a profile of the grid data in the x-, y- or z-direction
# The data is sampled in Ibins using the Fmin Fmax scaling
# 
                 prof$ile ContourName x Ibins Fmin Fmax
                                      y Ibins Fmin Fmax
                                      z Ibins Fmin Fmax

     -cutp$lane  x
                 y
                 z

#
# Plot a sphere at the defined coordinate
#

      sphe$re    Xc Yc Zc Radius Colour appe$nd
                 Xc Yc Zc Radius Colour
                 Xc Yc Zc Radius Colour Xscale Yscale Zscale
                 Xc Yc Zc Radius Colour Xscale Yscale Zscale appe$nd
     -sph$ere

#
# Plot a cylinder from (x1,y1,z1) to (x2,y2,z2) with radius Radius and colour Colour
# It is also possible to plot a cylinder with a different radius and colour at each ends.
#

      cyli$nder  Xc1 Yc1 Zc1 Xc2 Yc2 Zc2 Radius Colour appe$nd
                 Xc1 Yc1 Zc1 Xc2 Yc2 Zc2 Radius Colour 
                 Xc1 Yc1 Zc1 Xc2 Yc2 Zc2 {Radius1 Radius2} {Colour1 Colour2} 
     -cyl$inder

#
# Plot a line from (x1,y1,z1) to (x2,y2,z2)
#

      line       Xc1 Yc1 Zc1 Xc2 Yc2 Zc2 Colour appe$nd
                 Xc1 Yc1 Zc1 Xc2 Yc2 Zc2 Colour 
     -lin$e

#
# Plot a linear distance plot for the selected atoms
# Put the display state on/off
#

      ldp        atom$s  Seg  Res  Atm
                 on
                 off

#
# Plot a plane through the x,y or z axis at the defined coordinate
# Extend the plane D? in the negative and positive directions
#

      plan$e     x Xcoord Dy Dz Colour
                 y Ycoord Dx Dz Colour
                 z Zcoord Dx Dy Colour
                 x Xcoord Dy Dz Colour append
                 y Ycoord Dx Dz Colour append
                 z Zcoord Dx Dy Colour append

#
# Put cluster display toggle on/off
#

      clus$ter   on
                 off
     -clu$ster

#
# Plot a colour scale with Ilevels from (min) Fmin to (max) Fmax
# Put the display off
#

      csca$le    Ilevels Fmin Fmax
     -csc$ale

#
# Toggle a vector display on/off
# The data has been read by the "import vector" command
# There are two different display methods:
#  1) The force vectors from CHARMM    (import vector charmm)
#  2) Vectors read in from a flat file (import vector flatfile)
#

      vect$or    on
                 off
                 byco$lour                            ;# colouring by the vector norm
                -byc$olour                            ;# turn normal display on
                 rang$e Fmin Fmax                     ;# for vector a display from a file
                 atom$s  Seg  Res  Atm  Radius  Scale ;# this is only for CHARMM force vectors

#
# Toggle the cell display between on/off
#

      cell       on
                 off

#
# A very simple way to plot text
#
# Plot text (static) in Colour at x,y (0.0 - 1.0) with string
# TextString
# 
# Plot text (fixed in the x,y,z space) in Colour at x,y,z with
# TextString
#

      text       Colour Xcoord Ycoord TextString
      text3      Colour Xcoord Ycoord Zcoord TextString
     -tex$t      

#
# Plot the local coordinate system at selected atoms (Segment Residue Atom)
#
# Turn the plot off

      axis  Segment Residue Atom
      axis  Segment Residue Atom XaxisLength YaxisLength ZaxisLength

     -axi$s

**************************************************************************
LUL/2001
**************************************************************************