Using the graphics (GRAFIC)

• Introduction.
• Interaction via the mouse
  • The pickable bar at the right of the screen
    • WAIT
    • NOID
    • INIT
    • NEIM
    • YES
    • NO
    • CONT
    • LINE
    • FBRT
    • DIST
    • ANGL
    • TANG
    • NAYB
    • MOVE
    • REFI
    • TORS
    • M1 - M4
    • ROCK
    • STER
    • SHEL
    • CHAT
    • RSET
    • (arrow buttons)
    • MOV+
    • MOV-
    • <>VEL
    • <>ANG
    • SLAB
    • SPHR
    • CHAR
    • HELP
  • The pick buttons in the bottom bar
  • Pulldown menus
  • The privat menu
  • Manipulating the pulldown menus
• The graphics menus
• Graphics configuration
  • X11 configuration: explanation of environment variables
    • Initial size of the X11 WHAT IF window "WIFSIZE"
    • Graphics mode for X11 WHAT IF
      • Graphics mode MODEF
      • Set graphics mode on X11 systems MODES
      • Set graphics mode on X11 systems MODEC
      • Set graphics mode on X11 systems MODEP
  • Configuring GL based machines
    • Background colour
• Direct action mode (DIRECT)
• Controlling the graphics screen in WHAT IF
  • Pass control to the graphics screen with GO
  • Remove all objects (INIGRA)
  • Remove one object (INIOBJ)
• Displaying atoms, residues, molecules
  • Displaying protons
    • Display hydrogens (HYDON)
    • Dont display hydrogens (HYDOFF)
  • Showing the whole soup (SHOTOT)
  • Showing all residues (SHOALL)
  • Displaying multiple zones (ZONES)
  • Showing alpha carbons (GRACA)
  • Showing the back bone (GRABB)
  • Showing sidechains (GRASCH)
  • Draw alpha carbons plus sidechains (CASCH)
  • Drawing a sphere (SPHERE)
  • Drawing a sphere in a zone (SPHZON)
  • Creating a cylinder and arrow plot (SPLINE)
  • Showing the accessible surface (GRAACC)
  • Showing a vanderdot surface (GRAVDD)
  • Showing potential water positions (POTH2O)
  • Showing one cluster (GRACLU)
  • Showing salt bridges (GRASBR)
• Manipulating viewing parameters
  • Centering the display (ACON)
  • Centering the display (CENTER)
  • View optimalisation (OPTVIE)
  • Dictating the view parameters (SETVIE)
  • Requesting view parameters (SHOVIE)
  • Set side by side stereo mode (CROSS)
• Other options
  • Drawing double bonds (DBLBND)
  • Drawing dashed residues (DSHBND)
  • Removing the working model (NOMODL)
  • Remove from direct mode (UNDISP)
  • Plotting options
  • Flipping back and forth between MOL-objects (TOGGL2)
  • Changing the linewidth (LINEWI)
  • Changing the viewing angle (ROTY+6)
  • Changing the viewing angle (ROTY-6)
  • Restricting the rotation directions (XONLY)
  • Restricting the rotation directions (YONLY)
  • Restricting the rotation directions (ZONLY)
  • Undoing XONLY or YONLY (NOONLY)
  • Setting the X display (DISPLA)
  • Demonstration modus (DEMO10)
• Activating more commands (MORE)
• Options kept for compatibility, or to meet frequent typos
  • (ALLGRA)
  • (GRAALL)
  • (GRATOT)
  • (TOTGRA)
  • (GRASS)
  • (SS)
  • (GRAPHI)
  • (GRAPOT)
  • (ROTY6)
  • (ZONE)
  • (INIT)
  • (VIEWOP)