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)
  • Reading coordinates from dssp file (GETDSP)
• Demonstration of WHAT IF options (DEMOS)
• Listing coordinates or sequence
  • Looking at sequence in the soup (LISTR)
  • Looking at the sequence in the soup (LISTRR)
  • Looking at atomic coordinates (LISTA)
  • 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)
• Program parameters
  • (Re)-setting program parameters (SETPAR)
  • (Re)-setting program parameters (PARAMS)
  • (Re)-setting program parameters (SETWIF)
  • Displaying internal program parameters (SHOWIF)
• Looking at secondary structure
  • Determine secondary structure (SHOHST)
  • Re-calculate secondary structure (NEWHST)
  • Hidden command (ALLHEL)
  • Hidden command (EDTHST)
• Modifying the structure
  • Mutating a residue (MUTATE)
  • Mutating a range of residues (MUTZON)
  • Removing bumps (DEBUMP)
  • Removing bumps (DEBHBO)
  • Removing bumps (DEBALL)
  • Removing bumps (DEBTRS)
• Program flow
  • Renaming commands. (<)
  • Repeating commands (!)
  • Repeating commands (.)
  • Renaming commands. (>)
  • Script files (SCRIPT)
  • Repeat script files over multiple molecules (LSCRIP)
  • Go back to previous menu (END)
  • Terminating what if (FULLST)
  • Using your own menu (MYMENU)
  • Activating more options (MORE)
  • Deactivating commands (LESS)
  • Pass control to the graphics (GO)
• Other menus
  • Multiple structural superposition 3SSP
  • Molecular dynamics trajectory analysis ANATRA
  • Accessibility calculations ACCESS
  • Atomic contact analysis ANACON
  • Ab initio model building BUILD
  • Cell angle operations (CELADM)
    • Look at cell dimensions (SHOCEL)
  • Checking PDB files CHECK
  • Torsion angles CHIANG
  • Inspecting H,K,L,F files CHKMDF
  • Clusters and families CLUFAM
  • Coloring atoms, residues and molecules COLOUR
  • Interface to Connolly software CONOLY
  • Loop searches DGLOOP
  • Drug design options DRUG
  • Protein folding prediction EXTRA
  • Essential dynamics ESSDYN
  • The GROMOS menu GROMOS
  • Graphical commands GRAFIC
  • Extra graphics commands GRAEXT
  • Two dimensional graphics GRATWO
  • The grin / grid interface GRID
  • Hydrogen bond operations HBONDS
  • Property moment calculations HYDMOM
  • The HSSP file menu HSSP
  • The item administration menu ITMADM
  • Labeling atoms LABEL
  • The working model MODEL
  • Manipulations on (electron density) maps MAP
  • Electron density map manipulations MASMAP
  • Envelope editor MAPEDT
  • The neural network menu NEURAL
  • The notebook menu NOTES
  • The plot file generation menu PLOTIT
  • Real fancy graphics PORNO
  • The NMR menu NMR
  • Sequence menus PIRPSQ
  • Protein packing quality control QUALTY
  • Regularisation REFINE
  • Superposition of proteins SUPPOS
  • Van der Waals radius menu SETVDW
  • The relational database menu SCAN3D
  • Parameter correlation searches SEARCH
  • Selecting proteins to use in SCAN3D SELECT
  • Creation of the database SEQ3D
  • Manipulations of the soup SOUP
  • The special menu SPCIAL
  • Symmetry operations SYMTRY
  • Spread sheet TABLES
  • Sequence operations WALIGN
  • Manipulating water atoms WATER
  • The X-ray menu XRAY
• Other options
  • Inter atomic distance (DIST)
  • Direct action mode (DIRECT)
  • Charges for protein atoms (CHARGE).
  • Determining extremes of a molecule (MINMAX)
  • Listing transformation matrices etc (TRNSFM)
• Hidden commands
  • Centering the graphics (CENXYZ)
  • A chess program (CHESS)
  • Selecting a range for multiple options (CHOOSE)
  • Set graphics mode on X11 systems (MODEF)
  • Set graphics mode on X11 systems (MODES)
  • Set graphics mode on X11 systems (MODEC)
  • Set graphics mode on X11 systems (MODEP)
  • De-activating pre-selected residue ranges (NEWRNG)
  • Renumbering residues (RENUMB)
  • Changing internal program parameters (SETWIF)
  • Changing configuration file parameters (SETICO)
  • Automatic setting of MOL-object and item names (SIMPLE)
  • Show type ahead buffer (STYPEA)
  • Manual transformations (TRAROT)