This file contains a list of PREPIPS keywords.  Keywords are divided
into catagories:

	GENERAL KEYWORDS
	DISPLAY AREA AND BACKGROUNDS
	DATA INPUT KEYWORDS
	DATA TRANSFORMATION KEYWORDS
	SECONDARY STRUCTURE DISPLAY KEYWORDS
	LIST OF PREPIPS COLOURS



GENERAL KEYWORDS
________________

BACKPLANE -0.4 0.0 1.0	! Shadow Plane. Do NOT use - not working yet properly.



BOND  RADIUS r  SIDES n  COLOUR c  SHADE  STRIPE  TAPER t  NOINTERCHAIN
			! This defines the default parameters for all bonds.
			! A solid bond is essentially a cylinder. Increasing "n" 
			! (number of faces defining the cylinder) makes the
			! bond surface much smoother - but output file sizes
			! become larger. SHADE gives the bond a 3D feel if the
			! n is greater than 2. STRIPE puts strips along bond. Cool
			! but cant remember why I wanted this ! TAPER applies
			! perspective as the bond goes away from the viewer.
			! t should be 0.0 to 1.0. Typically t is 0.5. NOINTERCHAIN
			! will not draw bonds (if any) between chain segments.
			! Examples of Use
			! BOND  RADIUS 0.1  SIDES 2  COLOUR white
			! BOND  RADIUS 0.25  SIDES 12  SHADE COLOUR white TAPER 0.5

BOND			! This keyword can also be used for the following options:
  COLOURBYnnn o		! This tells the program how to colour the object "o".
			! "o" can be one of the following:
			!	CALPHA
			!	MAINCHAIN
			!	SIDECHAIN
			!	HETATM
			! Please see section X for full explanation. Exampels of use
			! BOND  COLOURBYCHAIN CALPHA
			! BOND  COLOURBYATOMTYPE SIDECHAIN



BACKPLANE -0.4 0.0 1.0	! Shadow Plane. Do NOT use - not working yet properly.



BOND  RADIUS r  SIDES n  COLOUR c  SHADE  STRIPE  TAPER t  NOINTERCHAIN
			! This defines the default parameters for all bonds.
			! A solid bond is essentially a cylinder. Increasing "n" 
			! (number of faces defining the cylinder) makes the
			! bond surface much smoother - but output file sizes
			! become larger. SHADE gives the bond a 3D feel if the
			! n is greater than 2. STRIPE puts strips along bond. Cool
			! but cant remember why I wanted this ! TAPER applies
			! perspective as the bond goes away from the viewer.
			! t should be 0.0 to 1.0. Typically t is 0.5. NOINTERCHAIN
			! will not draw bonds (if any) between chain segments.
			! Examples of Use
			! BOND  RADIUS 0.1  SIDES 2  COLOUR white
			! BOND  RADIUS 0.25  SIDES 12  SHADE COLOUR white TAPER 0.5

BOND			! This keyword can also be used for the following options:
  COLOURBYnnn o		! This tells the program how to colour the object "o".
			! "o" can be one of the following:
			!	CALPHA
			!	MAINCHAIN
			!	SIDECHAIN
			!	HETATM
			! Please see section X for full explanation. Exampels of use
			! BOND  COLOURBYCHAIN CALPHA
			! BOND  COLOURBYATOMTYPE SIDECHAIN



BORDER n		! Border from edges of window to draw data. Units
			! can be INCH,CM,MM,PIXEL. Examples of use
			! BORDER 0.5 CM
			! BORDER 72 PIXEL


CACABOND  n		! A bond between 2 c-alpha atoms is defined if distance
			! less than or equal to n. Defalut value of n is 4.9A

 
CHAIN n			! This defines a chain label for subsequent data definition.



COIL			! This keyword can also be used for the following options:
  SHADE			! Apply shading. Gives coil a 3D feel. Exmaple of use
			! COIL SHADE
  SMOOTH n		! This defines the spline smoothing. N will take the range
			! 1 to 5. Typically use 3. Larger n means smoother coil
			! but larger file sizes. Exmaple of use
			! COIL SMOOTH 3
  ADDARROWHEAD		! Adds an arrow head to the c-terminus of the coil.
  TAPERRES n		! Increase the coil radii by a factor of n for selected
			! residues.
  COLOURBYnnn		! This tells the program how to colour. Please see section
			! X for full explanation.
  n COLOUR c ON/OFF     ! This lets you set colours, turn on or off from display
			! individual coil regions. When PREPIPS runs it will list
			! (numerically) the coil regions as it processes them.
			! If you wish to apply this option, then it may be best
			! to run the program & note down the numerical order in
			! which the coil regions are processed. Note the numbers.
			! For example if you did not want to display the 5th coil
			! segment and also colour the 2nd coil region specifically
			! magenta then the following would be used
			! COIL  2 COLOUR magenta on
			! COIL  5 COLOUR bluebright offHELIX  RADIUS r SIDES n  COLOUR c
			! This defines the default parameters for helices
			! DRAWN AS CYLINDERS. Increasing "n" (number of faces
			! defining the cylinder) makes the helix surface
			! much smoother - but output file sizes become larger.
			! Example of Use
			! HELIX  RADIUS 2.0  SIDES 18  COLOUR bluebright


BORDER n		! Border from edges of window to draw data. Units
			! can be INCH,CM,MM,PIXEL. Examples of use
			! BORDER 0.5 CM
			! BORDER 72 PIXEL


CHAIN n			! This defines a chain label for subsequent data definition.



CHAINCOL n colour	! Define a default colour for chain number n
			! (n is the nth chain read from your data).
			! Example of use
			! CHAINCOL 1 red          



COIL			! This keyword can also be used for the following options:
  SHADE			! Apply shading. Gives coil a 3D feel. Exmaple of use
			! COIL SHADE
  SMOOTH n		! This defines the spline smoothing. N will take the range
			! 1 to 5. Typically use 3. Larger n means smoother coil
			! but larger file sizes. Exmaple of use
			! COIL SMOOTH 3
  ADDARROWHEAD		! Adds an arrow head to the c-terminus of the coil.
  TAPERRES n		! Increase the coil radii by a factor of n for selected
			! residues.
  COLOURBYnnn		! This tells the program how to colour. Please see section
			! X for full explanation.
  n COLOUR c ON/OFF     ! This lets you set colours, turn on or off from display
			! individual coil regions. When PREPIPS runs it will list
			! (numerically) the coil regions as it processes them.
			! If you wish to apply this option, then it may be best
			! to run the program & note down the numerical order in
			! which the coil regions are processed. Note the numbers.
			! For example if you did not want to display the 5th coil
			! segment and also colour the 2nd coil region specifically
			! magenta then the following would be used
			! COIL  2 COLOUR magenta on
			! COIL  5 COLOUR bluebright offHELIX  RADIUS r SIDES n  COLOUR c
			! This defines the default parameters for helices
			! DRAWN AS CYLINDERS. Increasing "n" (number of faces
			! defining the cylinder) makes the helix surface
			! much smoother - but output file sizes become larger.
			! Example of Use
			! HELIX  RADIUS 2.0  SIDES 18  COLOUR bluebright


COLOURBYnnn		! This keyword is used after object keywords (e.g. bond,
			! helx, sheet) to select a colouring scheme. nnn can be
			! the folowing:
			! DEFAULT, CHAIN, SPECIFICS, RESTYP, BVALUE, BVALCOLOUR,RESIDUE
			! Example of use
			! HELIX COLOURBYCHAIN
			! HELIX COLOURBYRESIDUE



DEFINE COLOUR c r g b	! Define user colour called c with red, green and
			! blue components r,g & b respectively. r,g & b
			! are in therange of 0 - 255. Example of use
			! DEFINE COLOUR magenta 255 0 255



DEPTHCUE  [n]  [TOWHITE] [TYPE1]
			! Apply Depthcue with following options:
			! n - This is the minimum allowed intensity.
			! Id it is 0.0 then the furthest object from user
			! will be totally black (or white when using
			! the TOWHITE keyword). n should be between 0.0-1.0.
			! The default is 0.2.
			! TOWHITE - Normally objects get darker as they get
			! further away (i.e. Z -> -infinity). However with
			! a WHITE BACKGROUND, it is sometimes more effective
			! to fade the objects away (become totally white).
			! TYPE1 - By default intensity drops off in a linear
			! manner with distance. TYPE1 causes it to fall
			! of exponentially. Examples of use
			! GLOBAL DEPTHCUE 0.2
			! GLOBAL DEPTHCUE 0.2 TOWHITE



ELEMTYPE  atom_symbol colour vdw_radii ball_radii
			! Define colour & ball radii for an element. The
			! ball_radii is used when drawing ball & stick
			! models. Example of use
			! ELEMTYPE  FE  RED  1.000   0.250        



ELLIPSOID		! This keyword is used with the following options to draw
			! a wire frame inertial ellipsoid for given residues:
  DRAW AXIS		! Draws axis.
  3D			! This draws a 3D ellipsoid. Default is 2D.
  VOLUME		! Percentage volume to draw. This controls the size
			! size of the inertial ellipsoid.
  CHAIN c		! Draw for chain label C.
  RESIDUE m TO n	! Draw for residue range m to n.




GLOBAL			! This keyword allow the user to turn objects on & off from
			! display without having to remove object keywords from
			! the input file
  BLACKANDWHITE		! Draw in black and white only.
  BONDCAOFF		! Do not display c-alphas. 
  BONDMAOFF		! Do not display main-chain. 
  BONDSIOFF		! Do not display side-chain.
  COILOFF		! Do not display coil.
  HELIXOFF		! Do not display helices.
  SPHEREOFF		! Do not display spheres.
  STRANDOFF		! Do not display strands.
  TEXTOFF		! Do not display text.


NOINTERCHAIN		! Program will not attempt to bond atoms between
			! chains (e.g. disulphide bridges)



ORTHO  minimum_X maximum_X  minimum_Y maximum_Y  minimum_Z maximum_Z [ABSOLUTE] 
			! Apply clipping to data. Data will only be plotted
			! if it is on or within the box defined by the
			! minimum and maximum x,y,z.  Examples of use
			! ORTHO  -10.0 10.0 -10.0 -10.0 -10.0 -10.0
			! In the above example a 10 Angstrom (or what ever
			! unit your coordinates are in) box about the centre of
			! origin will limit display of data.
			! The box if defined RELATIVE to the center of
			! of the data. If the ABSOLUTE keyword is given then
			! this box is defined in absolute data coordinates.
			! Note ORTHO keyword is identical to the CLIP keyword.
ORTHO  box    n [ABSOLUTE]
			! Not in Use
ORTHO  sphere n [ABSOLUTE] 
			! Not in Use
ORTHO  circle n [ABSOLUTE] 
			! Not in Use


PERSPECTIVE		! Apply perspective - Not in Use



PLOT			! Plot data. This is default when the end of an input file
			! is reached. It is usually placed within a file when
			! different datasets are plotted on the same page.



RESIDUE   m TO n   COLOUR c 
			! Defines colours for residues m to n. Example of use
			! RESIDUE  21 to 45  COLOUR magenta

RESIDUE	  m TO n	! This keyword can also be used for the following options:
  BONDCALPHA		! This tells the program draw c-alpha chain
  BONDMAIN		! This tells the program draw main-chain
  BONDSIDE		! This tells the program draw side-chain
  SPHERE		! Draw van der Waal's spheres
  LINE n		! If this keyword is present then the specified range
			! of residues will be DRAWN AS LINES (as opposed to solid
			! cylinders) of thickness n pixels (Postscript units).
			! Typically n is 1 - 10. Deflat for c-alpha is 2 & side-chains
			! is 1. Examples of use
			! BOND  1 TO 35  BONDCALPHA  LINE 5  COL magenta
			! BOND  1 TO 35  BONDSIDE    LINE 2  COL green
  LINEDASHED n		! Same as LINE except line is drawn in dashed form.
  RAD r			! Draw bonds as cylinders of radius r angstroms. If the
			! LINE keyword is present in the same LINE then this is
			! ignored.




DISPLAY AREA AND BACKGROUNDS
____________________________

PICTURE FRAME COLOUR c THICKNESS n FILL COLOUR cb
			! This puts a nice solid frame colour "c" and thickness
			! "n" around the drawing. If the FILL option is
			! provided then the frame is given a solid background
			! of colour cb. Examples of use
			! PICTURE FRAME COLOUR black THICKNESS 2
			! PICTURE FRAME COLOUR black THICKNESS 2 FILL COLOUR blue

SHADOW 1. 1. 1.		! Cast Shadows. Do NOT use - not working yet properly.


WINDOW  xb xt  yb yt	! Define a display area on an A4 page by defining
			! the x range (i.e. xb to xt) & y range (i.e. yb to yt)
			! Example : a Full postscript A4 page (72 points per inch)
			! WINDOW   0.0 612.0   0.0 792.0
			! Example : a Full postscript A4 page with 1 inch border
			! WINDOW  72 540  72 722
			! Example : Bottom Left 1/4 of Page
			! WINDOW   0.0 306.0   0.0 396.0 ! BOTTOM LEFT
			! Example : Top Left 1/4 of Page
			! WINDOW   0.0 306.0 396.0 792.0 ! TOP LEFT
			! Example : Bottom Right 1/4 of Page
			! WINDOW 306.0 612.0   0.0 396.0 ! BOTTOM RIGHT
			! Example : top Right 1/4 of Page
			! WINDOW 306.0 612.0 396.0 792.0 ! TOP RIGHT



DATA INPUT KEYWORDS
___________________

PDBFILE file		! Name of the input PDB format datafile



READ CHAIN label	! Only read the chain labelled "label" from
			! the input data file. Example of use
			! READ CHAIN A



READ CHAIN # n		! Only read the chain number "n" from
			! the input data file. Useful if more than one
			! chain has the same label within a data file.
			! Example of use
			! READ CHAIN # 2



NOATOMHYDROGENS		! Do not read ATOM hydrogen atoms
NOHETHYDROGENS		! Do not read HETATM hydrogen atoms
NOWATER			! Do not read Water (HOH,DOD,H2O) atoms
NOHETATM		! Do not read any HETATM data
READCALPONLY		! Read C-alpha data only
READMAINONLY		! Read Main-chain data only



DATA TRANSFORMATION KEYWORDS
____________________________

ROT X n
ROT Y n
ROT Z n			! Rotate around the respective axis by n degrees.
			! This is used to select a view.


SETORIGIN		! Not in Use


MATRIX			! Not in Use


VIEWNAME  n		! Not used (written by PREPI for completeness)

VIEWDATA  1   r11  r12  r13  r14   r21  r22  r23  r24
VIEWDATA  1   r31  r32  r33  r34   r41  r42  r43  r44
			! This written by PREPI and is a transformation
			! matrix. There MUST be two lines containing the matrix
			! such that
			! x' = x*r11 + y*r12 + z*r13 + r14
			! y' = x*r21 + y*r22 + z*r23 + r24
			! z' = x*r31 + y*r32 + z*r33 + r34

VIEWSCAL  m n		! Not used (written by PREPI for completeness)


SECONDARY STRUCTURE DISPLAY KEYWORDS
____________________________________

COIL  RADIUS r SIDES n  COLOUR c
			! This defines the default parameters for the coil
			! (i.e. regions not defined as helix or sheet). A
			! coil is essentially a cylinder. Increasing "n" 
			! (number of faces defining the cylinder) makes the
			! coil surface much smoother - but output file sizes
			! become larger.  Examples of Use
			! COIL  RADIUS 0.2  SIDES 2  COLOUR bluebright
			! COIL  RADIUS 0.5  SIDES 12  COLOUR bluebright


HELIX RIBBON WIDTH w THICKNESS t SMOOTH n 
			! This defines the default parameters for helices
			! DRAWN AS RIBBONS. Increasing "n" makes the helix
			! surface much smoother - but output file sizes larger.
			! Typically n is 1 - 5. Example of Use
			! HELIX RIBBON WIDTH 2.0 THICKNESS 0.3 SMOOTH 3 

HELIX			! This keyword can also be used for the following options:
  SHADE			! Apply shading to helices. Usually a selected option.
  INSIDE n		! If helices are drawn as RIBBONS (as opossed to a cylinders)
			! this option allows you to darken the interior for better
			! contrast. n should be 0.0 - 1.0. Typically n is 0.7.
			! colour c. Examples of use
			! HELIX SHADE
			! HELIX INSIDE 0.7
  NTERM COLOUR c	! For CYLINDERICAL representation colour the n-terminus 
			! colour c. Example of use
			! HELIX NTERM COLOUR cyan
  CTERM COLOUR c	! For CYLINDERICAL representation colour the c-terminus 
			! colour c. Example of use
			! HELIX CTERM COLOUR red
  STRIPE		! Puts strips along helix cylinder. Cant remember why I
			! wanted this !
  COLOURBYnnn		! This tells the program how to colour. Please see section
			! X for full explanation.
  n COLOUR c ON/OFF     ! This lets you set colours, turn on or off from display
			! individual helices. For example if you did not want
			! to display the 5th helix (as read in from the PDB file)
			! and also colour the 2 helix specifically magenta then
			! the following would be used
			! HELIX  2 COLOUR magenta on
			! HELIX  5 COLOUR bluebright off



STRAND WIDTH w THICKNESS t COLOUR c 
			! This defines the default parameters for strands.
			! STRAND WIDTH 1.0 THICKNESS 0.35 COLOUR magenta 

STRAND			! This keyword can also be used for the following options:
  EDGE COLOUR c		! Colour stand edges with colour c. Example of use
			! STRAND EDGE COLOUR yellow
  USECO			! Use the carbonyl C to O vector to guide the plane of
			! strand. If this is commented out then the C-alpha atoms
			! are used. The latter produces more smooth strands.
  COLOURBYnnn		! This tells the program how to colour. Please see section
			! X for full explanation.
  n COLOUR c ON/OFF     ! This lets you set colours, turn on or off from display
			! individual strands. For example if you did not want
			! to display the 5th strand (as read in from the PDB file)
			! and also colour the 2 strand specifically magenta then
			! the following would be used
			! STRAND  2 COLOUR magenta on
			! STRAND  5 COLOUR bluebright off


SSEX 1D			! Will draw a secondary structure profile at bottom of
			! page.



LIST OF PREPIPS COLOURS
_______________________

RED        GREEN      BLUE       WHITE      YELLOW
ORANGE     CYAN       MAGENTA    MAUVE      BLACK
BRIGHTBLUE NAVYBLUE   GOLD       VIOLET     DARKVIOLET
BROWN      LIME       KHAKI      GREY10*    GREY20
GREY30     GREY40     GREY50     GREY55     GREY60
GREY65     GREY70     GREY75     GREY80     GREY85
GREY90     GREY95**   UserColour UserColour UserColour
UserColour UserColour UserColour UserColour UserColour
*  Nearly White
** Nearly Black

Program will recognise GREY or GRAY. UserColour's are colours defined by use
of the "DEFINE COLOUR name r g b" command.
