# Command List

`AddAco` - add angle constraints
`AddAngle` - add dihedral angle
`AddAtom` - add new atom
`AddBond` - add bond between two atoms
`AddCircles` - add circles around atoms
`AddCylinder` - add cylinder for schematic drawing
`AddDipole` - add arrow showing dipolar moment
`AddDist` - add distance between two atoms
`AddDrawobj` - add line, rectangle or circle
`AddHbond` - add H-bond between two atoms
`AddIsosurface` - add isosurface of potential
`AddLol` - add lower limit between two atoms
`AddPlates` - add plates for rings
`AddPseudo` - add new pseudo atom
`AddRes` - add residue to molecule
`AddRibbon` - add ribbons (schematic drawing)
`AddSheet` - add sheet for schematic drawing
`AddSolid` - add solid for schematic drawing
`AddSurface` - add surface
`AddText` - add 3D text annotation
`AddTitle` - add 2D text annotation
`AddTrajec` - add trajectories
`AddUpl` - add upper limit between two atoms
`AttrAtom` - list attributes of atoms
`AttrBond` - list attributes of bonds
`AttrDist` - list attributes of distances
`AttrInit` - list initial attributes
`AttrPrim` - list attributes of primitives
`AutoScale` - scale/translate molecules to window size
`BackColor` - change background color
`BondMode` - choose bond display mode
`CalcAngle` - calculate angular order parameters
`CalcAtom` - calculate missing atom coordinates
`CalcAxis` - calculate lengths of principal axes
`CalcBond` - calculate bonds between close atoms
`CalcCluster` - reduce number of structures
`CalcDist` - find short distances between atoms
`CalcHbond` - find H-bonds
`CalcHelix` - calculate angles between helix axes
`CalcMatch` - calculate best matching structure parts
`CalcPot` - calculate electrostatic potential
`CalcRmsd` - calculate RMSDs and displacements
`CalcSecondary` - calculate secondary structure
`CalcShift` - calculate ring current shifts
`CalcSurface` - calculate solvent accessible surface
`CalcVdw` - find Van der Waals violations
`Center` - change rotation center
`ChangeRes` - change residue type
`CheckAco` - check angle constraints
`CheckBond` - check number of bonds
`CheckLol` - check lower limits
`CheckUpl` - check upper limits
`ClipPos` - set position of clipping planes
`ClipSize` - set distance of clipping planes
`ColorAtom` - set color of atoms
`ColorBond` - set color of bonds
`ColorDist` - set color of distances
`ColorInit` - set initial color
`ColorPrim` - change color of primitives
`DefPropAngle` - define angle property
`DefPropAtom` - define atom property
`DefPropBond` - define bond property
`DefPropDist` - define distance property
`DefPropMol` - define molecule property
`DefPropPrim` - define primitive property
`DefPropRes` - define residue property
`DialColor` - switch color dialog on and off
`DialMeasure` - switch measurement dialog on and off
`DialMol` - switch molecule dialog on and off
`DialRmsd` - switch RMSD dialog on and off
`DialSelect` - switch selection dialog on and off
`DialStyle` - switch style dialog on and off
`DrawDelay` - set drawing delay
`DrawPrec` - set drawing precision
`DrawSize` - set size of drawing area
`EditText` - edit text annotation
`FigAngles` - show angle distribution bars
`FigCircles` - show angle distribution circles
`FigContact` - show contact map
`FigDist` - show distance vs. structure number
`FigLimit` - show map of distance constraints
`FigOff` - switch from figure to normal display
`FigRamach` - Ramachandran plot
`FirstMol` - move molecules to front of molecule list
`Fit` - calculate structure superpositions
`FlipAtom` - flip atoms for better superposition
`Fog` - setup of fog (depth cueing)
`Fullscreen` - switch fullscreen display on and off
`Group` - define molecule groups
`HelpAbout` - show program version and copyright
`HelpApropos` - locate commands by keyword
`HelpButton` - show definition of buttons
`HelpCmd` - get help on command
`HelpIndex` - show HTML command index
`HelpManual` - show manual in web browser
`HelpMouse` - show help text about using the mouse
`HelpProp` - show definition of standard properties
`HelpTip` - show "Tip of the Day"
`HelpTutorial` - show tutorial in web browser
`HelpViewer` - set viewer for help files
`InitAll` - delete and initialize everything
`LabelAtom` - set format of atom label
`LabelDist` - choose label of distances
`LabelInit` - set initial format of labels
`LengthBond` - set length of bonds for display
`LengthPrim` - set length of primitives
`Light` - setup of light source
`LineAtom` - set style and width of atom lines
`LineBond` - set style and width of bond lines
`LineDist` - set style and width of distance lines
`LineInit` - set initial style and width of lines
`LinePrim` - set style and width of primitive lines
`ListPropAngle` - list all angle properties
`ListPropAtom` - list all atom properties
`ListPropBond` - list all bond properties
`ListPropDist` - list all distance properties
`ListPropMol` - list all molecule properties
`ListPropPrim` - list all primitive properties
`ListPropRes` - list all residue properties
`ListSelectedAngle` - list selected angles
`ListSelectedAtom` - list selected atoms
`ListSelectedBond` - list selected bonds
`ListSelectedDist` - list selected distances
`ListSelectedMol` - list selected molecules
`ListSelectedRes` - list selected residues
`MaterialAtom` - set material properties of atoms
`MaterialBond` - set material properties of bonds
`MaterialDist` - set material properties of distances
`MaterialInit` - set initial material properties
`MaterialPrim` - set material properties of primitives
`MeanMol` - create mean molecule
`MoveDrawobj` - move draw object
`MoveInit` - undo all translations
`MovePrim` - move primitive
`MoveX` - move molecule in X direction
`MoveY` - move molecule in Y direction
`MoveZ` - move molecule in Z direction
`NameMol` - change molecule name
`NearPrim` - set near clipping plane of primitives
`NewMol` - create new molecule
`PaintRibbon` - set coloring style of ribbons
`PaintSurface` - set coloring style of surfaces
`PathNames` - set path names
`PlotBmp` - make a BMP (Windows bitmap) plot
`PlotFm3` - make a FrameMaker 3 plot
`PlotFm4` - make a FrameMaker 4 plot
`PlotJpeg` - make a JPEG plot
`PlotMeta` - make a Windows enhanced metafile plot
`PlotMpov` - make a MegaPov plot
`PlotPar` - set plot parameters
`PlotPng` - make a PNG plot
`PlotPov` - make a POV-Ray plot
`PlotPs` - make a PostScript plot
`PlotRib` - make a RenderMan plot
`PlotTiff` - make a TIFF plot
`PlotUnit` - set unit of plot parameters
`PlotVrml1` - make a VRML 1.0 plot
`PlotVrml2` - make a VRML 2.0 (VRML97) plot
`Projection` - choose projection
`Quit` - quit the program
`RadiusAtom` - set radius of atoms
`RadiusBond` - set radius of bonds
`RadiusDist` - set radius of distances
`RadiusInit` - set initial radius
`RadiusPrim` - set radius of primitives
`ReadAco` - read file with angle constraints
`ReadAng` - read DIANA dihedral angle file
`ReadDg` - read DG file
`ReadDump` - read dump file
`ReadLib` - read and error check residue library
`ReadListAng` - read list of DIANA dihedral angle files
`ReadListDg` - read list of DG files
`ReadListPdb` - read list of PDB files
`ReadLol` - read file with lower limits
`ReadOmap` - read O electron density map
`ReadPdb` - read PDB file
`ReadPot` - read potentials for surface coloring
`ReadSeq` - read sequence
`ReadShift` - read file with chemical shifts
`ReadSybyl` - read SYBYL Mol2 file
`ReadUpl` - read file with upper limits
`ReadXyz` - read XYZ file
`RecordMac` - open macro recorder
`Register` - register as MOLMOL user
`RemoveAco` - remove angle constraints
`RemoveAngle` - remove angles
`RemoveAtom` - remove atoms
`RemoveBond` - remove bonds
`RemoveDist` - remove distances
`RemoveMol` - remove molecules
`RemovePrim` - remove primitive
`RemoveRes` - remove residues
`Rendering` - set rendering options
`ReplaceDg` - replace with DG file
`ReplaceListDg` - replace with list of DG files
`ReplaceListPdb` - replace with list of PDB files
`ReplacePdb` - replace with PDB file
`RotateAngle` - rotate dihedral angles
`RotateInit` - undo all rotations
`RotateX` - rotate molecule around X axis
`RotateY` - rotate molecule around Y axis
`RotateZ` - rotate molecule around Z axis
`SelectAngle` - select angles
`SelectAtom` - select atoms
`SelectBond` - select bonds
`SelectDist` - select distances
`SelectMol` - select molecules
`SelectPrim` - select primitives
`SelectRes` - select residues
`SetAngle` - rotate dihedral angles
`SetNeigh` - set sheet neighbours of residues
`SetRef` - set reference atoms
`SetUndo` - set the number of possible undos
`ShadeAtom` - set shading of atoms
`ShadeBond` - set shading of bonds
`ShadeDist` - set shading of distances
`ShadePrim` - set shading of primitives
`SizePlate` - set sizes of plates
`SizeRibbon` - set sizes of ribbons
`SizeText` - resize text
`SplitRibbon` - split ribbons
`StartAnim` - start animation
`StartRock` - start rock
`Stereo` - set stereo mode
`StopAnim` - stop animation
`StopRock` - stop rock
`StyleAtom` - set display style of atoms
`StyleBond` - set display style of bonds
`StyleCylinder` - set display style of cylinders
`StyleDist` - set display style of distances
`StyleDrawobj` - set display style of draw objects
`StyleInit` - set initial display styles
`StyleMap` - set display style of density map
`StyleRibbon` - set display style of ribbons
`StyleTrajec` - set display style of trajectories
`System` - execute operating system command
`TextureAtom` - set texture of atoms
`TextureBond` - set texture of bonds
`TextureDist` - set texture of distances
`TextureInit` - set initial texture
`TexturePrim` - set texture of primitives
`TintDist` - set secondary color of distances
`TintInit` - set initial secondary color
`TintPrim` - change secondary color of primitives
`TrimSurface` - cut away part of a surface
`TypeRibbon` - set type of ribbons
`UndefProp` - undefine property
`Undo` - undo effect of last command
`UserInterface` - switch elements of user interface
`ViewAngle` - set view angle
`WriteAng` - write DIANA dihedral angle file
`WriteDg` - write DG file
`WriteDump` - write dump file
`WriteLib` - write entries for residue library
`WriteLol` - write file with lower limits
`WritePdb` - write PDB file
`WriteSecondary` - write macro with secondary structure
`WriteSeq` - write sequence
`WriteTransform` - write current transformation
`WriteUpl` - write file with upper limits
`XMacStand` - execute standard macro
`XMacUser` - execute user macro
`ZoomAbs` - zoom absolute
`ZoomRel` - zoom relative