• Add<Obj|All> - Add objects to the soup
• AddBond - Add covalent bonds
• AddCap<Obj|All> - Add N/C-terminal capping groups
• AddEnv<Atom|Res|Mol|Obj|All> - Add to environment for surface calculations
• AddHyd<Atom|Res|Mol|Obj|All> - Add missing hydrogens
• AddPos<Atom|Res|Mol> - Sum atom positions to calculate average and standard deviation
• AddRes - Add terminal residue
• AddSpring - Link atoms with a spring
• AddTer<Obj|All> - Add C-terminal oxygens
• AlignObj - Align objects
• Angle - Set/get angle between atoms
• AnimateImage - Animate appearance and disappearance of images
• AnimateWin - Animate Windows
• AnnealSteps - Set simulated annealing steps
• Antialias - Switch antialiasing on/off
• AtomPlasma - Switch plasma inside atoms on/off
• AtomSize - Set size of atoms
• AtomSymbol - Switch element symbol inside atoms on/off
• AtomTexture - Set texture style of atoms
• AutoMove<Obj|All> - Move objects or scene automatically
• AutoMoveImage - Move images automatically
• AutoMoveTo<Obj|All> - Move objects or scene automatically to a certain location
• AutoRotate<Obj|All> - Rotate objects or scene automatically
• AutoRotateTo<Obj|All> - Rotate objects or scene automatically to a certain orientation
• AveragePos<Atom|Res|Mol> - Average atom positions
• BFactor<Atom|Res|Mol|Obj|All> - Set/get the B-factor
• Ball<Atom|Res|Mol|Obj|All> - Style atoms as balls
• BallRadius - Set ball radius in balls&sticks
• BallStick<Atom|Res|Mol|Obj|All> - Style atoms as balls&sticks
• BindEnergyObj - Calculate binding energies
• Boundary - Set cell boundary
• BuildAtom - Build single atom
• BuildLoop - Build central or terminal loop
• BuildLoopDB - Build loop data base
• BuildMol - Build peptide chain
• BuildRes - Build single residue
• CD - Change working directory
• Cell - Set/get simulation cell dimensions
• Center<Atom|Res|Mol|Obj|All> - Center atoms
• Charge<Atom|Res|Mol|Obj|All> - Set/get the summed up charge
• Check<Atom|Res|Obj|All> - Check structure quality
• Clean<Obj|All> - Clean objects for molecular dynamics simulation
• Clear - Clear scene
• Color<Atom|Res|Mol|Obj|All> - Set/get atom colors
• ColorBG - Color background
• ColorBonds - Color bonds
• ColorFog - Color fog
• ColorHBo - Color hydrogen bonds
• ColorPar - Set default color parameters
• ColorSurf<Obj|All> - Color surface
• Compare<Atom|Res> - Compare selections
• Console - Switch console on/off
• ConsolePar - Set console parameters
• CoordSys - Set coordinate system
• CorrectCis - Correct cis-peptide bonds during simulation
• CorrectConv - Correct naming conventions during simulation
• CorrectIso - Correct wrong isomeres during simulation
• Count<Atom|Res|Mol|Obj> - Count selected units
• Crystallize<Obj|All> - Crystallize objects to fill the unit cell
• Cutoff - Set force cutoff distance
• Del<Atom|Res|Mol|Obj|All> - Delete atoms
• DelBond - Delete covalent bonds
• DelFile - Delete file on disk
• DelHyd<Obj|All> - Delete all hydrogens
• DelImage - Delete images
• DelRest<Obj|All> - Delete restraints
• DelTab - Delete tables
• DelWater<Obj|All> - Delete all water molecules
• Dihedral - Set/get dihedral angle between atoms
• Dipole<Atom|Res|Mol|Obj> - Calculate electric dipole moments
• Distance - Set/get distance between atoms
• Duplicate<Obj|All> - Duplicate objects
• Energy<Atom|Res|Mol|Obj|All> - Calculate force field energies
• EnergyUnit - Set energy unit
• Exit - Exit YASARA
• Experiment - Choose and control experiments
• FileSize - Get file size
• FillCellObj - Fill simulation cell with object
• FillCellWater - Fill simulation cell with water
• FirstSurf<Atom|Res> - Get first surface atom(s) or residue(s) and area(s)
• Fix<Atom|Res|Mol|Obj|All> - Fix atoms during simulation
• FlipTab - Flip table axes
• Fog - Set fog density
• Font - Set font for 3D letters
• FontFog - Switch font fog on/off
• Force<Atom|Res|Mol|Obj|All> - Set/get force on atoms
• ForceField - Set force field
• FormEnergy<Atom|Res|Mol|Obj|All> - Calculate formation energies
• FormatRes - Format residue output
• FramesPerSec - Set screen update frequency
• Free<Atom|Res|Mol|Obj|All> - Free atoms during simulation
• FullScreen - Switch fullscreen mode on/off
• Go - Go to another position in the macro
• Grab<Obj|All> - Grab object or scene for mouse movement
• GrabNext - Grab next object for mouse movement
• GrabPrev - Grab previous object for mouse movement
• GroupAngle - Get angle between two atom groups
• GroupDihedral - Get dihedral angle between two atom groups
• GroupDistance - Get distance between two atom groups
• HUD - Switch head up display
• Hide<Atom|Res|Mol|Obj|All> - Hide atoms
• HideArrow<Atom|Res|Mol|Obj|All> - Hide arrows
• HideHBo<Atom|Res|Mol|Obj|All> - Hide hydrogen bonds
• HideImage - Hide images
• HideMessage - Hide text message at the bottom
• HideRest<Atom|Res|Mol|Obj|All> - Hide restraints
• HideSecStr<Res|Mol|Obj|All> - Hide secondary structure
• HideSurf<Atom|Res|Mol|Obj|All> - Hide surface
• HideTrace - Hide trace through atoms
• ImageFog - Switch image fog on/off
• Install - Install accessory program
• Interactions - Set force field terms
• Join<Atom|Res|Mol> - Delete split points
• JoinObj - Join objects to one final object
• KekulizeBond - Remove fractional bond orders
• Label<Atom|Res|Seg|Mol|Obj|All> - Add labels
• LabelDis - Label atom distances
• LabelPar - Set label parameters
• LightSource - Configure the light source
• Link<Atom|Res|Mol|Obj|All> - Find bonds automatically
• List<Atom|Res|Mol|Obj> - List selection
• ListCon<Atom|Res|Mol|Obj> - List contacts
• ListFloat<Obj|All> - List floating assignments
• ListHBo<Atom|Res|Mol|Obj> - List hydrogen bonds
• ListRest<Atom|Res|Mol|Obj|All> - List restraints and energies
• Load* - Import file with OpenBabel
• LoadBMP - Load image from BMP file
• LoadPDB - Load Protein Data Bank file
• LoadPNG - Load image from PNG file
• LoadSce - Load complete scene
• LoadSim - Load simulation snapshot in sim format
• LoadTab - Load formatted table
• LoadTbl - Load XPLOR distance and dihedral angle restraints
• LoadXTC<Obj|All> - Load simulation snapshot in XTC format
• LoadYOb - Load YASARA object
• LogAs - Log output of next command
• Longrange - Set long range interactions
• MacroTarget - Set macro target
• MakeImageObj - Make object with attached image
• MakeTab - Make a table
• MakeTextObj - Make text object to print 3D letters
• MarkAtom - Mark atom with fireflies
• Mass<Atom|Res|Mol|Obj|All> - Calculate mass
• Menu - Switch menu on/off
• MinStep - Set energy minimization step
• MouseWheel - Assign command to mouse wheel
• Move<Atom|Res|Mol|Obj|All> - Move atoms, objects or scene
• MoveMesh - Move polygon mesh
• Name<Atom|Res|Seg|Mol|Obj> - Set/get names of objects, segments, molecules, residues and atoms
• NiceOri<Obj|All> - Orient objects nicely
• Occup<Atom|Res|Mol|Obj|All> - Set/get the occupancy
• Oligomerize<Obj|All> - Oligomerize objects to generate the biologically active form
• OnError - Set error action
• OptHyd<Obj|All> - Optimize hydrogen bonding network
• Optimize<Res|Mol|Obj|All> - Optimize molecular geometry
• Ori<Obj|All> - Set/get object or scene orientation
• P5 - Set state of p5 data glove
• PWD - Print working directory
• PlayMacro - Play back macro
• PlayMovie - Play back macro as a movie
• PointPar - Set point and line radius and plasticity in wire frames
• PointerStyle - Set style of mouse pointer
• Pos<Atom|Res|Mol> - Set/get atom positions
• Pos<Obj|All> - Set/get object or scene position
• PosText - Position and justify text
• PressureCtrl - Set pressure control
• Print - Print text
• PrintCon - Print to console
• PrintHUD - Print to head up display
• PrintObj - Print to text object
• Processors - Set/get number of processors to use
• Projection - Set perspective or parallel projection
• Prop<Atom|Res|Mol|Obj|All> - Set/get the property value
• QuantumMechanics - Set quantum mechanics method
• RMSD<Atom|Res|Mol|Obj> - Calculate RMSDs
• RMSF<Atom|Res|Mol> - Calculate root mean square fluctuations
• Radius<Atom|Res|Mol|Obj|All> - Calculate the VdW radius
• RaiseError - Display error message
• RayTrace - Create raytraced screenshot using POVRay
• RecordLog - Record all console output in a log file
• RecordMacro - Record all following commands in a macro
• Redo - Redo changes
• Regularize<Obj|All> - Regularize covalent geometry
• Remove<Obj|All> - Remove objects from the soup
• RemoveEnv<Atom|Res|Mol|Obj|All> - Remove from environment for surface calculations
• Renumber<Obj|All> - Renumber objects
• RenumberRes - Renumber residues
• RequireVersion - Require a minimum YASARA version
• Reset - Reset YASARA to startup state
• ResonateBond - Introduce fractional bond orders
• RestEnergy<Obj|All> - Calculate restraint energies
• RestViol<Obj|All> - Get restraint violation statistics
• RestrainDih - Restrain dihedral angle
• RestrainDis - Restrain distance
• RestrainPar - Set/get restraining parameters
• RestrainPot - Set/get restraining potential function
• Rotate<Obj|All> - Rotate objects or scene
• RunPlugin - Run Python plugin
• SampleDih - Sample dihedral angles
• SampleLoop - Sample central or terminal loop
• Save* - Export file with OpenBabel
• SaveBMP - Save screenshot as Windows bitmap
• SaveMPG - Save MPEG video
• SaveMacro - Save a macro to restore the current state
• SavePDB - Save Protein Data Bank file
• SavePLI<Atom|Res|Mol|Obj> - Save plugin input file
• SavePOV - Save POVRay scene description
• SaveSce - Save complete scene
• SaveSim - Save simulation snapshots in sim format
• SaveTab - Save formatted table
• SaveTbl - Save XPLOR distance and dihedral angle restraints
• SaveXTC - Save simulation snapshots in XTC format
• SaveYOb - Save YASARA object
• ScaleForce - Set/get force scaling factors
• ScaleRest<Atom|Res|Mol|Obj|All> - Scale restraints
• Screen - Fix YASARA window on a certain screen
• ScreenSize - Set/get window and fullscreen size
• SearchDoc - Search documentation
• SecStr<Res|Mol|Obj|All> - Set/get secondary structure
• SecStrPar - Set secondary structure display parameters
• SelectTab - Select table to add cells
• SeqSelector - Switch sequence selector on/off
• Shell - Execute shell command
• Show<Atom|Res|Mol|Obj|All> - Show atoms
• ShowArrow - Show arrows between atoms or points
• ShowBox - Show a rectangular box
• ShowButton - Show clickable button
• ShowCom - Show command description
• ShowCone - Show a cone, cylinder, pyramid or prism
• ShowDoc - Show documentation
• ShowESP - Show electrostatic potential
• ShowHBo<Atom|Res|Mol|Obj|All> - Show hydrogen bonds
• ShowImage - Show images
• ShowMessage - Show text message at the bottom
• ShowRest<Atom|Res|Mol|Obj|All> - Show restraints
• ShowRota<Res|Mol|Obj|All> - Show side-chain rotamers
• ShowSecStr<Res|Mol|Obj|All> - Show secondary structure
• ShowSimGrid - Show simulation grid
• ShowSphere - Show a sphere or ellipsoid
• ShowSurf<Atom|Res|Mol|Obj|All> - Show surface
• ShowTab - Show table data as 3D object
• ShowTorus - Show a torus
• ShowTrace - Show trace through atoms
• Sim - Control simulation
• SimSpeed - Set simulation speed
• SimSteps - Set number of simulation steps per screen update
• SolvDensity - Get solvent density in simulation cell
• SolvEnergy - Calculate solvation energy
• SpaceballButton - Assign command to Spaceball button
• SpaceballPar - Set Spaceball parameters
• Span<Atom|Res|Obj> - Determine first and last unit spanning a selection
• SpeedUp - Speed up movements when graphics are slow
• Split<Obj|All> - Split objects at split points
• Split<Atom|Res|Mol> - Introduce split points
• Stereo - Set stereo mode
• StereoPar - Set stereo parameters
• Stick<Atom|Res|Mol|Obj|All> - Style atoms as sticks
• StickRadius - Set stick radius
• StopLog - Stop log recorder
• StopMacro - Stop macro playback or recording
• StopPlugin - Stop running plugin
• Style - Set general display style
• StyleWin - Style Windows
• Sup<Atom|Res|Mol|Obj> - Superpose objects
• Surf<Atom|Res|Mol|Obj|All> - Calculate surface areas
• SurfPar - Set/get surface parameters
• SwapAtom - Swap chemical element of atoms
• SwapBond - Swap order of covalent bonds
• SwapHyd<Obj|All> - Swap hydrogen ordering in residues
• SwapImage - Swap images
• SwapObj - Swap two objects in the list
• SwapPosAtom - Swap atom positions
• SwapRes - Swap residue side-chains
• Switch<Obj|All> - Switch objects on/off
• Tab - Set/get table cells
• Tabulate - Add cells to table
• Temp - Set/get simulation temperature
• TempCtrl - Set temperature control
• Time - Set/get simulation time
• TimeStep - Set simulation time step
• Transfer<Obj|All> - Transfer objects into another coordinate system
• Transform<Obj|All> - Transform objects
• TypeAtom - Get the atom type
• TypeBond - Assign bond orders automatically
• Undo - Undo changes
• UndoLevels - Set number of undo levels
• Unlabel<Atom|Res|Seg|Mol|Obj|All> - Delete labels
• UnlabelDis - Delete distances labels
• UnrestImage - Let animated image disappear
• UserInput - Set user input
• Volume<Atom|Res|Mol|Obj|All> - Calculate volumes
• Wait - Wait for certain time period or condition
• WarnIsError - Treat warnings as errors
• WinFont - Set window font
• WinTexture - Set window background texture
• Zoom<Atom|Res|Mol|Obj|All> - Zoom in on atoms
• pH - Set/get default pH
• pKaRes - Set/get residue pKa