General options (GENERAL)

• Introduction.
• Obtaining coordinates
  • Reading coordinates from a PDB file (GETMOL)
  • Reading a set of PDB files (GETMLS)
  • Reading coordinates from a GROMOS file GETGRO
  • Reading a demo file (START)
• Demonstration of WHAT IF options (DEMOS)
• Listing coordinates or sequences
  • Looking at sequence in the soup (LISTR)
  • Looking at the sequence in the soup (LISTRR)
  • Looking at atomic coordinates (LISTA)
  • Looking at atomic coordinates (LISTAA)
  • Looking for sequence patterns (SHOPAT)
• Information and help related options
  • Documentation in hypertext format (APROPO)
  • Starting a command script creation AUTOON
  • Terminating automatic script file creation AUTOOF
  • Starting a log file DOLOG
  • Terminating a log file NOLOG
  • History logging HISTOR
  • Spawning a DOS/UNIX sub process (SHELL)
  • Very extensive help (INFO)
  • Normal help (HELP)
  • Short help (SHORT)
  • Short help (MAN-K)
  • Finding options (FIND)
  • Short help for main menu options (SHORTT)
  • Automatic help for every option (NOVICE)
  • Direct execution of DOS/UNIX commands (DOLLAR)
  • Executing commands in other menus (%)
  • Changing what if version level (NEWMOD)
  • Changing what if version level (OLDMOD)
  • Continue in Dutch (DUTCH)
  • Continue in English (ENGLIS)
  • Continue in French (FRENCH)
  • Continue in French (SPANIS)
• Program parameters
  • (Re)-setting program parameters (SETPAR)
    • (LINCOL)
    • (LINMOD)
    • (AA1OR3)
    • (INSFLG)
    • (VDWOVR)
    • (DFBFAC)
    • (CYSCYS)
    • (NEICON)
  • (Re)-setting program parameters (PARAMS)
  • (Re)-setting program parameters (SETWIF)
  • Displaying internal program parameters (SHOWIF)
• Modifying proteins (or nucleic acids)
  • Mutating a residue (MUTATE)
  • Mutating a range of residues (MUTZON)
  • Mutating residues back to themself (MUTSLF)
  • Suggesting mutations (SUGMUT)
  • Protein re-packing (TRYMUT)
  • Removing bumps (DEBUMP)
  • Removing bumps (DEBHBO)
  • Removing bumps (DEBALL)
  • Removing bumps (DEBTRS)
• Program flow
  • Automatic regular SOUP backups (IUKKEL)
  • Renaming commands. (<)
  • Repeating commands (!)
  • Repeating commands (.)
  • Renaming commands. (>)
  • Getting some modelling files for the tutorial (MAKSCR)
  • Script files SCRIPT
  • Repeat script files over multiple molecules LSCRIP
  • Running teaching scripts with TEACH
  • Go back to previous menu (END)
  • Go back to previous menu (QUIT)
  • Terminating what if (FULLST)
  • Using your own menu (MYMENU)
  • Activating more commands (MORE)
  • Deactivating commands (LESS)
  • Pass control to the graphics (GO)
  • Editing files (EDT)
  • Restarting WHAT IF (INIALL)
• Other options
  • Inter atomic angle (ANGLE3)
  • Inter atomic distance (DIST)
  • Direct action mode DIRECT
  • Inter atomic distance (DSTOFF)
  • Determining extremes of a molecule (MINMAX)
  • Listing cell dimensions (SHOCEL)
• Hidden commands
  • Centering the graphics (CENXYZ)
  • A chess program (CHESS)
  • Selecting a range for multiple options (CHOOSE)
  • Time and date (FOOOOD)
  • Time and date (TIME)
  • (Re-)set default editor (SETEDT)
  • Set graphics mode on X11 systems (MODEF)
  • Set graphics MODES on X11 systems (MODES)
  • Set graphics MODEC on X11 systems (MODEC)
  • Set graphics MODEP on X11 systems (MODEP)
  • De-activating pre-selected residue ranges (NEWRNG)
  • Renumbering residues (RENUMB)
  • Automatic setting of MOL-object and item names SIMPLE
  • Manual transformations (TRAROT)
  • Status of the screen buttons (SHOBUT)
  • Status ob the screen buttons (SHOIRF)
  • Toggling the graphics flags (TOGGLI)
  • Show type ahead buffer (STYPEA)
  • List open FORTRAN units (LSTOPN)
  • Verifying the soup (MOL200)
• The SPCIAL menu
  • (ANNEU)
  • (CACADI)
  • (HNDTST)
  • (VICTOR)
  • (VICTR2)
  • (DHELS)
  • (ATMAT2)
  • (FLIPER)
  • (SWODAK)
  • (CONECT)
  • (CUTRES)
  • (HELNOE)
  • (ROBALI)
  • (KLEBE)
  • (TSTAOK)
  • (GRAPH)
  • (AVEQUA)
  • (HSTCON)
  • (HSTCN2)
  • (OPTALL)
  • (TRIAAC)
  • (PIETER)
  • (TRILST)
  • (EWBANK)
  • (ALFONS)
  • (ALFON2)
  • (TOCACB)
  • (DAVID1)
  • (SPHMAX)
  • (MAK5DM)
  • (GRA5DM)
  • (GRTKON)
  • (GRTKOF)
  • (ROST)
  • (ROTNOR)
  • (SPHCPK)
  • (3DPLOT)
  • (VINCEN)
  • (ANNALI)
  • (DGEOM3)
  • (DGEOM2)
  • (ALFON3)
  • (ALFON4)
  • (ALFON5)
  • (DGRQUA)
  • (SYMCNT)
  • (ALIOUT)
  • (DGEOM)
  • (NARDY)
  • (CRONET)
  • (RBUILD)
  • (DISIJA)
  • (DBDIS2)
  • (DBDIS3)
  • (TRSFRC)
  • (VOLUME)
  • (VOLUM2)
  • (DBVOL1)
  • (VOLUM3)
  • (HELHEL)
  • (READIN)
  • (NOBBBB)
  • (NOBBSC)
  • (NOSCSC)
• Alternative names for often mistyped options
  • (SPECIA)
  • (RESET)
  • (QUALIT)
  • (GRFAIC)