**************************************************************************
                         define command
                        Leif Laaksonen CSC 1996
                        Eero Häkkinen  CSC 2002
                        Timm Uhlmann       2003
**************************************************************************

#
# define background colour by defining a colour name or
# integer or float triplet (rgb) values
#

defi$ne    bgco$lour    Colour.Name
                        "Fred Fgreen Fblue"

#
# define bond display style options:
#   smooth (atom colour changes smoothly along the bond)
#   half or default (half of the bond is in the colour of the connected atom)  
#

           bondst$yle   smoo$th
                        half
		                defa$ult

#
# define cell dimensions, line width and colour 
#

            cell       dime$nsions  Fa Fb Fc
                       angl$es      Falpha Fbeta Fgamma
                       line$width   Ivalue
                       colour       ColourName
                                    "Fred Fgreen Fblue"

#
# define colour mapping for values between 0.0 ... 1.0
# the scale goes from (0.0) blue to (1.0) red through green at (0.5)
#

            colorm$apping     texture
                              rainbow

#
# define the display "colour" type. choose between colour and grayscale
# if you choose grayscale the display will switch to grayscale.
#

            colort$ype        colo$r
                              gray$scale

#
# define the length of the cross used for atom display
#

            cros$s            Fvalue

#
# Put the global usage of display lists on/off
#

            disp$laylists     on
                              off

#
# Sets the type specific usage of display lists on/off
# Global setting "off" will overwrite this.
#

            disp$laylists     on  defa$ult
                              off defa$ult
            disp$laylists     on  TypeName
                              off TypeName

#
# define the draw buffer (default is back)
#

            drawb$uffer back
                        fron$t

#
# define the near plane distance and step values
#

            near$plane  step   Fvalue
                        valu$e Fvalue

#
# define the far plane distance and step values
#

            farp$lane   step   Fvalue
                        valu$e Fvalue

#
# define viewing angle for perspective projection
#

            viewa$ngle         Fvalue

#
# define material specular (0.0 - > 128.0)
#

            mate$rial   spec$ular Fvalue

#
# molecule line width in pixels
#

            mlin$ewidth Ivalue

#
# not in use
#

            node        Node.Name

#
# contour line width in pixels
#

            clin$ewidth Ivalue

#
# define licorice sphere and cylinder for the molecule display
# good for the ball and stick display
# the Ivalue defines the structure number
# to apply for all structures use the character "*" or word "all"
#

            licos$phere   Fvalue Ivalue
            licos$phere   Fvalue *
            licoc$ylinder Fvalue Ivalue
            licoc$ylinder Fvalue *

#
# define the cylinder and sphere quality
#

            cyli$nderquality Ivalue # any number > 0 (default 10)
            sphe$requality Ivalue # any number > 0 (default 10)

#
# not in use
#

            hurl           URL.Address
            webb$rowser    WebBrowser.Name

#
# define default coordinate file type and extension
#

            defa$ult       coor$dinate type ambe$r
                                            char$mm
                                            gaus$sian
                                            hype$rchem
                                            insi$ght
                                            mol2
                                            mumo$d
                                            open$mol
                                            pdb
                                            xmol
                                            xyz
                                            yasp
                            exte$nsion      ambe$r String
                                            char$mm String
                                            gaus$sian String
                                            hype$rchem String
                                            insi$ght String
                                            mol2 String
                                            mumo$d String
                                            open$mol String
                                            pdb String
                                            xmol String
                                            xyz String
                                            yasp String

#
# define default trajectory file type and extension
#

                            traj$ectory     type           ambe$r
                                                           ceri$us2
                                                           char$mm
                                                           disc$over
                                                           grom$os
                                                           hype$rchem
                                                           mumo$d
                                                           xmol
                                                           xplor
                                                           yasp
                                            exte$nsion     ambe$r String
                                                           ceri$us2 String
                                                           char$mm String
                                                           disc$over String
                                                           grom$os String
                                                           hype$rchem String
                                                           mumo$d String
                                                           xmol String
                                                           xplo$r String
                                                           yasp String

#
# Gromos96 uses a constant with which the coordinates will be
# multiplied (default = 10.0).
#

             gromos96        coorda$mplifier Fvalue 

#
# toggle rotations state between on/off
#

              rota$tion   stat$e on
                                 off

#
# toggle translation state between on/off
#

              tran$slation stat$e on
                                  off

#
# activate or deavtivate the state for picking atoms
#

              iden$ntify on
                         off


#
# recalculate automatically atom reconnectivity
#

              reco$nnectivity on
                              off

# recalculate automatically atom hydrogen bonds
#

              hbre$connectivity on
                                off

#
# defines whether the system is translated around origo or not
# this is active both at reading a new structure or when there
# already are structures read 
#

             syst$em     tran$slation    on
                                         off

#
# define the projection method orthographic/perspective
#

             proj$ection       orth$ographic
                               pers$pective

#
# define window actions
# single/multi windowing
# update is automatic/manual
#

             wind$owing        sing$le
                               multi
                               upda$te      auto$matic
                                            manu$al

#
# put the trajectory frame number display on/off
#

             traj$ectory       fid           on
	                                     off

#
# define the cutplane 3d magnitude. Constant with which the magnitude is
# multiplied with. The range is between 0.0 and 1.0.
#

              cutp$lane         damp$ing   Fvalue

#
# define scaling mode. It is possible to scale in "global" mode that
# scales all objects equally  or in an "local" mode when only
# one or some of the objects are scaled. Using this mode ruins of
# course the chemistry/physics of teh system. It can only be use
# for display purposes. The objects are selected from the main window.
#

               scal$ing          glob$al
                                 loca$l

#
# put the stereo pair display mode on/off
# define the distance between the objects in the stereo pair mode
# define the "tilt" angle for the objects (+-)
#

               spai$r            on
                                 off
                                 distance Fvalue
                                 angle    Fvalue

#
# put the harware stereo (stereo in a window mode on/off
# define the "tilt" angle for the objects (+-)
#
                                            
              quad$stereo       on
                                off
                                angl$e    Fvalue


#
# be careful with these commands ... do not use them!
#
# Reconnectivity defines if the atom connection table
# is recalculated between the frames or not.
# Hbreconnectivity defines if the atom hydrogen bond
# connection table is recalculated between the frames or not.
# Maxconnectivity is the max number of connections (bonds)
# an atom can have
# Covar radius is used while calculating connections.
#

               atom         coor$dinates Fx Fy Fy IAindex ISindex
                            char$ge      Fvalue   IAindex ISindex
                            labe$l       Name     IAindex ISindex
                            resn$umber   Ivalue   IAindex ISindex
                            vdw          Fvalue   IAindex ISindex
                            iden$ntify   on
                                         off
                            reco$nnectivity    on
                                               off
                            hbre$connectivity  on
                                               off
                            maxc$onnectivity
                            cova$r       AtomSymbol    Fradius
                                         ElementNumber Fradius

               resi$due     labe$l       Name  IAindex ISindex
               segm$ent     labe$l       Name  IAindex ISindex
               stru$cture   StrucName  Iatoms   new
                                                appe$nd

#
# define atom neighbour search window (in atoms)
#

               atom         wind$ow    Inumber


#
#
#	define global text string
#

       gtext "string"


#
#	Define light position
#	       light diffuse color	
#

         ligh$t        posi$tion
		               		c
					nw
					ne
					n
					w
					e
					sw
					se
					s
			diff$use
					red	fval
					gree$n	fval
					blue	fval


#
#
#	Sets redisplay mode to fast or slow
#

       redi$splay        fast
	                 slow


#
#
#	Sets transformation mode
#

      transf$ormation        global
	                     local
	   		     user
		              

**************************************************************************
LUL/2002
**************************************************************************