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
AttrPrim - list attributes of primitives
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
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
HelpMouse - show help text about using the mouse
HelpProp - show definition of standard properties
HelpViewer - set viewer for help files
InitAll - delete and initialize everything
LabelAtom - set format of atom label
LabelDist - choose label of distances
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
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
MaterialAtom - set material properties of atoms
MaterialBond - set material properties of bonds
MaterialDist - set material properties of distances
MaterialPrim - set material properties of primitives
MeanMol - create mean molecule
MoveDrawobj - move draw object
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
PlotPar - set plot parameters
PlotPng - make a PNG plot
PlotPov - make a POV-Ray plot
PlotPs - make a PostScript plot
PlotTiff - make a TIFF plot
PlotUnit - set unit of plot parameters
PlotVrml - make a VRML plot
Projection - choose projection
Quit - quit the program
RadiusAtom - set radius of atoms
RadiusBond - set radius of bonds
RadiusDist - set radius of distances
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
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
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
TexturePrim - set texture of primitives
TintDist - set secondary color of distances
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
WriteRotation - write current rotation
WriteSecondary - write macro with secondary structure
WriteSeq - write sequence
WriteUpl - write file with upper limits
XMacStand - execute standard macro
XMacUser - execute user macro
ZoomAbs - zoom absolute
ZoomRel - zoom relative

Reto Koradi, kor@mol.biol.ethz.ch