°  File - Load and save the scene or parts of it °  New scene - Start again Clear all objects and bitmaps for a fresh start or reset YASARA entirely, including simulation parameters and undo-history. °  Clear - Clear scene °  Reset - Reset YASARA to startup state °  PDB files - Load and save objects in plain PDB format Load PDB files and save them again in standard PDB or X-Plor format. °  LoadPDB - Load Protein Data Bank file °  SavePDB - Save Protein Data Bank file °  YASARA objects - Load and save complete objects Load single objects in YASARA's own format, including styles and items and save them to disk. °  LoadYOb - Load YASARA object °  SaveYOb - Save YASARA object °  YASARA scenes - Load and save the entire scene Load all objects together and save them including styles,items and the view. °  LoadSce - Load complete scene °  SaveSce - Save complete scene °  Sequences - Load and save sequence files Save parts of the soup as a sequence in FASTA format, or build proteins and nucleic acids from FASTA files. °  SaveSeq<Res|Mol|Obj> - Save residue sequence °  OpenBabel - Import and export molecules using OpenBabel When working with more exotic file formats, import and export structures with OpenBabel. °  Load* - Import file with OpenBabel °  Save* - Export file with OpenBabel °  Screenshots - Save plain or ray-traced screenshots Save simple screenshots compressed or uncompressed (optionally including the menu), save scene descriptions for POVRay or run it immediately to create photorealistic images including shadows. °  RayTrace - Create raytraced screenshot using POVRay °  SaveBmp - Save screenshot as uncompressed Windows bitmap °  SavePNG - Save screenshot as compressed PNG bitmap °  SavePOV - Save POVRay scene description °  MPEG movies - Encode plain or ray-traced animations Save MPEG movies (optionally including the menu). °  SaveMPG - Save MPEG video °  Simulation snapshots - Load and save simulation states Load simulation snapshots to restore atom positions and velocities at a certain time or save them in periodic time intervals. Atom positions without velocities can also be saved and restored in XTC format, which minimizes the required storage space. Atom types and point charges can be saved as AMBER Prep topologies, they are however ignored when Prep topologies are loaded. °  LoadPrep - Load AMBER Prep topology °  LoadSim - Load simulation snapshot in sim format °  LoadXTC<Obj|All> - Load simulation snapshot in XTC format °  SavePrep<Res|Mol|Obj|All> - Save AMBER Prep topology °  SaveSim - Save simulation snapshots in sim format °  SaveXTC - Save simulation snapshots in XTC format °  Exit - Quit YASARA Exit YASARA immediately. °  Exit - Exit YASARA °  Edit - Change content and properties of the soup °  History - Undo and redo changes Undo and redo a number of changes up to the maximum undo-level. °  Redo - Redo changes °  Undo - Undo changes °  UndoLevels - Set number of undo levels °  Objects - Center, transform, transfer, remove, add and delete Center objects for more intuitive mouse rotations, transfer them on top of another object, transform the atom coordinates, remove them temporarily from the soup (e.g. to exclude them from simulations), bring them back and delete them partly or entirely. °  Add<Obj|All> - Add objects to the soup °  Center<Atom|Res|Mol|Obj|All> - Center atoms or polygon meshes °  Del<Atom|Res|Mol|Obj|All> - Delete atoms °  Remove<Obj|All> - Remove objects from the soup °  Transfer<Obj|All> - Transfer objects into another coordinate system °  Transform<Obj|All> - Transform objects °  Split points - Edit split points, split and join entire objects Split points correspond to 'TER' entries in PDB files. Add or delete them, or split entire objects into multiple child objects, joining them again later. °  JoinObj - Join objects to one final object °  Join<Atom|Res|Mol> - Delete split points °  Split<Obj|All> - Split objects at split points °  Split<Atom|Res|Mol> - Introduce split points °  Bonds - Add, type and delete bonds Add bonds between certain atoms, change the order of existing bonds, find bonds automatically, assign the bond orders automatically, change bond orders to the Kekule or resonance form, and delete them again. °  AddBond - Add covalent bonds °  ColorBonds - Color bonds °  DelBond - Delete covalent bonds °  KekulizeBond - Remove fractional bond orders °  Link<Atom|Res|Mol|Obj|All> - Find bonds automatically °  ResonateBond - Introduce fractional bond orders °  SwapBond - Swap order of covalent bonds °  TypeBond - Assign bond orders automatically °  Building - Build atoms to molecules, oligomers, crystals and loops Swap chemical elements, atom positions, residue side-chains and entire objects. Create individual atoms, or residues, build loops or entire proteins, extending them at the C-terminus, possibly adding missing oxygens and protection caps. To prepare a molecular dynamics simulation, clean the structures. When looking at oligomers, duplicate objects, use the BIOMT transformations in the PDB file to create the biological oligomeric state or add the crystal symmetry related copies. °  AddCap<Obj|All> - Add N/C-terminal capping groups °  AddRes - Add terminal residue °  AddTer<Obj|All> - Add C-terminal oxygens °  BuildAtom - Build single atom °  BuildLoop - Build central or terminal loop °  BuildMol - Build peptide or nucleic acid chain °  BuildRes - Build single residue °  Clean<Obj|All> - Clean objects for molecular dynamics simulation °  Crystallize<Obj|All> - Crystallize objects to fill the unit cell °  Duplicate<Obj|All> - Duplicate objects °  Oligomerize<Obj|All> - Oligomerize objects to generate the biologically active form °  SwapAtom - Swap chemical element of atoms °  SwapObj - Swap two objects in the list °  SwapPosAtom - Swap atom positions °  SwapRes - Swap residue side-chains °  Geometry manipulation - Set or correct distances, angles and dihedrals The quickest way of setting distances, angles and dihedrals is to mark up to four atoms with the mouse and click on Geometry in the atom context menu. It is always the last atom (marked with red fireflies) that moves. In the Twinset, you can also regularize the covalent geometry. °  Angle - Set/get angle between atoms °  Dihedral - Set/get dihedral angle between atoms °  Distance - Set/get distance between atoms °  Regularize<Obj|All> - Regularize covalent geometry °  Geometry optimization - Optimize small molecules, side-chains and loops The geometry of small molecules up to 120 atoms can be optimized using semi-empirical quantum chemistry, side-chains can be optimized using a rotamer library and dead-end elimination, and loops can be tuned considering known conformations from the PDB and force field energies. °  OptimizeLoop - Optimize central or terminal loop °  Optimize<Res|Mol|Obj|All> - Optimize molecular geometry °  Sampling - Search conformational space Possible side-chain rotamers or domain movements can be analyzed by sampling dihedral angles (internal coordinates), while protein flexibility is best looked at in cartesian space by sampling loops or using Bert de Groot's CONCOORD plugin (currently Linux only). Apply CONCOORD only to energy-minimized structures without bumps, otherwise you may run into convergence problems. °  SampleDih - Sample dihedral angles °  SampleLoop - Sample central or terminal loop °  Surface environments - Define the context of surface analysis To show or calculate partial surfaces, add or remove atoms to/from the surface environment. °  AddEnv<Atom|Res|Mol|Obj|All> - Add to environment for surface calculations °  RemoveEnv<Atom|Res|Mol|Obj|All> - Remove from environment for surface calculations °  Hydrogens - Add, swap, delete and optimize hydrogen bonding networks Add missing hydrogens at default positions, change their order within the residue and delete them when needed. In YASARA Structure or the Twinset, you can also optimize the hydrogen bonding network. °  AddHyd<Atom|Res|Mol|Obj|All> - Add missing hydrogens °  DelHyd<Obj|All> - Delete all hydrogens °  OptHyd<Obj|All> - Optimize hydrogen bonding network °  SwapHyd<Obj|All> - Swap hydrogen ordering in residues °  Water - Delete all waters Quickly delete all water molecules in an object. °  DelWater<Obj|All> - Delete all water molecules °  Names and numbers - Set or get properties of atoms to objects Change or retrieve names of atoms, residues, molecules, segments and objects, reorder objects in the scene and change the residue numbers, including insertion codes. You can also change the Occupancy and B-factor of individual atoms. °  BFactor<Atom|Res|Mol|Obj|All> - Set/get the B-factor °  Name<Atom|Res|Seg|Mol|Obj> - Set/get names of objects, segments, molecules, residues and atoms °  Occup<Atom|Res|Mol|Obj|All> - Set/get the occupancy °  Prop<Atom|Res|Mol|Obj|All> - Set/get the property value °  Renumber<Obj|All> - Renumber objects °  RenumberRes - Renumber residues °  Seg<Atom|Res|Mol|Obj|All> - Set/get the segment name °  Simulation - Simulate the soup °  Preparing a simulation - Define and fill the cell First define a simulation cell with true walls or periodic boundaries, then fill it with objects and water. A more sophisticated way of filling the cell includes pKa prediction, counter ion placement and a simulation of the solvent to arrive at the right density. °  Boundary - Set cell boundary °  Cell - Set/get simulation cell dimensions °  FillCellObj - Fill simulation cell with object °  FillCellWater - Fill simulation cell with water °  Force fields - Get the recipe Choose the force field and the force cutoff for non-bonded interactions, calculate electrostatic forces without a cutoff using PME for accurate results. In special cases, you may want to scale or exclude some force field components. The force field and AM1BCC atom types can also be retrieved to visualize YASARA's assignments. °  Cutoff - Set force cutoff distance °  ForceField - Set force field °  Interactions - Set force field terms °  Longrange - Set long range interactions °  ScaleForce - Set/get force scaling factors °  ShowSimGrid - Show simulation grid °  SimSpeed - Set simulation speed °  TypeAtom - Get the atom type °  Simulation parameters - Choose your favorite ingredients Switch between normal molecular dynamics at a given temperature, simulated annealing with a certain cooling level and energy minimization with a maximum step size. Control the pressure in the cell, set the simulation time, the time step and the number of screen updates per simulation step. °  AnnealSteps - Set simulated annealing steps °  MinStep - Set energy minimization step °  PressureCtrl - Set pressure control °  SimSteps - Set number of simulation steps per screen update °  Temp - Set/get simulation temperature °  TempCtrl - Set temperature control °  Time - Set/get simulation time °  TimeStep - Set simulation time step °  Constraints - Remove translational and vibrational degrees of freedom Fix atoms to prevent them from moving, and free them again later. Constraining bond lengths and bond angles permits larger timesteps and thus enables faster simulations. These temporarily frozen degrees of freedom can be brought back to life, exhibiting bond and bond angle vibrations during the simulation. °  FixBond - Constrain bond length during simulation °  FixAngle - Constrain bond angle during simulation °  Fix<Atom|Res|Mol|Obj|All> - Fix atoms during simulation °  FreeBond - Remove bond length constraint during simulation °  FreeAngle - Free bond angle during simulation °  Free<Atom|Res|Mol|Obj|All> - Free atoms during simulation °  Restraints - Enforce distances and dihedral angles In addition to simply linking atoms with a spring, you can determine NMR structures using the same functions as XPLOR to restrain distances and dihedral angles individually or all together via a restraint file. The violation energies and statistics can be obtained using various potential functions and parameters like distance averaging. The restraints can be listed, selectively shown (satisfied restraints in green, violated ones in red), styled, hidden or deleted. Floating assignments can also be analyzed. °  AddSpring - Link atoms with a spring °  DelRest<Obj|All> - Delete restraints °  HideRest<Atom|Res|Mol|Obj|All> - Hide restraints °  LoadTbl - Load XPLOR distance and dihedral angle restraints °  ListFloat<Obj|All> - List floating assignments °  ListRest<Atom|Res|Mol|Obj|All> - List restraints and energies °  RestEnergy<Obj|All> - Calculate restraint energies °  RestViol<Obj|All> - Get restraint violation statistics °  RestrainDis - Restrain distance °  RestrainDih - Restrain dihedral angle °  RestrainPar - Set/get restraining parameters °  RestrainPot - Set/get restraining potential function °  SaveTbl - Save XPLOR distance and dihedral angle restraints °  ScaleRest<Atom|Res|Mol|Obj|All> - Scale restraints °  ShowRest<Atom|Res|Mol|Obj|All> - Show restraints °  Running a simulation - Keep the soup from boiling When everything is ready, start the simulation. Note the possibility to save and restore simulation snapshots in the File menu. When running a non-realistic simulation (like high temperature NMR structure generation or some modeling tasks), you can correct cis-peptide bonds and wrong isomers on the fly, reporting these errors when needed. MD simulations can be steered by modifying forces, accelerations and velocities. A translational motion of the solute can be removed to keep it from crossing periodic boundaries. °  Accel<Atom|Res|Mol|Obj|All> - Set/get acceleration of atoms °  CorrectCis - Correct cis-peptide bonds during a simulation °  CorrectConv - Correct naming conventions during a simulation °  CorrectDrift - Correct solute drift during a simulation °  CorrectIso - Correct wrong isomers during a simulation °  Force<Atom|Res|Mol|Obj|All> - Set/get force on atoms °  Sim - Control simulation °  Speed<Atom|Res|Mol|Obj|All> - Set/get speed and velocity of atoms °  WarnIsError - Treat warnings as errors °  Analyze - Analyze the soup °  Atom position - Calculate average positions, RMSFs and RDFs Get or set the position of selected atoms, sum up positions to calculate averages and root mean square fluctuations, and sort distances into bins to calculate the radial distribution function. °  AddPos<Atom|Res|Mol> - Sum atom positions to calculate average and standard deviation °  AveragePos<Atom|Res|Mol> - Average atom positions °  BinDistance - Sort distances into bins to calculate the radial distribution function °  Pos<Atom|Res|Mol> - Set/get atom positions °  RDF - Calculate radial distribution function °  RMSF<Atom|Res|Mol> - Calculate root mean square fluctuations and B-factors °  Superposition - Superpose atoms and calculate RMSDs Superpose objects based on a selected set of atoms individually, possibly ordered or all together and calculate the resulting RMSDs or CASP global distance test. The actual coordinate transformation can also be accessed. °  GDT<Atom|Res|Mol|Obj> - Calculate global distance test °  RMSD<Atom|Res|Mol|Obj> - Calculate RMSDs °  SupMulti<Atom|Res|Mol|Obj> - Superpose multiple objects °  SupOrdered<Atom|Res|Mol> - Superpose objects on ordered units °  Sup<Atom|Res|Mol|Obj> - Superpose objects °  Transformation - Get previously applied transformations °  Alignment - Align objects and find related sequences and structures Protein structures can be aligned automatically in pairs or all together based on either their structure or sequence with certain parameters. The actual coordinate transformation can also be accessed. Alignments can be saved in various formats. Similar sequences can be retrieved from the PDB, SwissProt and TrEMBL with a built-in BLAST. Similar structures in the PDB can be located thanks to an all-against-all comparison carried out at the RCSB. °  AlignMulti<Obj|All> - Align multiple objects °  AlignPar - Set/get alignment parameters °  AlignPDBMol - Align similar proteins from the PDB °  Align<Mol|Obj> - Align objects and molecules °  BLAST<Res|Mol|Obj|All> - Blast protein sequence °  SaveAli - Save alignment between objects °  Energy - Calculate energies Analyze the potential energy including individual terms, kinetic energies, binding energies, solvation energies (with adjustable parameters) or formation energies (i.e. heats of formation). °  BindEnergyObj - Calculate binding energies °  Energy<Atom|Res|Mol|Obj|All> - Calculate force field energies °  FormEnergy<Atom|Res|Mol|Obj|All> - Calculate formation energies °  KinEnergy<Atom|Res|Mol|Obj|All> - Calculate kinetic energy °  SolvEnergy - Calculate solvation energy °  SolvPar - Set/get solvation parameters °  Electrostatics - Calculate charges, dipole moments and potentials Sum up the charges in a selection of atoms or calculate the resulting dipole moment. In combination with surface analysis, calculate the electrostatic surface potential. °  Charge<Atom|Res|Mol|Obj|All> - Set/get the summed up charge °  Dipole<Atom|Res|Mol|Obj> - Calculate electric dipole moments °  SurfESP<Atom|Res|Mol|Obj|All> - Calculate electrostatic surface potentials °  Geometry analysis - Measure distances, angles, dihedrals and show KBPs For quick measurements, click on an atom, then hold down <Ctrl> and click on up to three more atoms. When analyzing a molecular dynamics simulation, distances (also from surfaces), angles, dihedrals and radii can also be measured from within a macro. The same holds for distances between geometric centers, angles between regression lines and dihedrals between planes fit to groups of atoms. Lines and planes can also be fit to groups of atoms directly. Of course the geometric centers or centers of mass can also be calculated. The preferred distances and dihedrals can be shown as a knowledge-based potentials. °  Angle - Set/get angle between atoms °  Dihedral - Set/get dihedral angle between atoms °  Distance - Set/get distance between atoms °  GroupAngle - Calculate angle between two atom groups °  GroupBox - Calculate bounding box around atom group °  GroupCenter - Calculate geometric center or center of mass °  GroupDihedral - Calculate dihedral angle between two atom groups °  GroupDistance - Calculate distance between two atom groups °  GroupLine - Calculate optimal line through atom group °  GroupPlane - Calculate optimal plane through atom group °  Radius<Atom|Res|Mol|Obj|All> - Calculate the radius °  ShowKBP - Show knowledge-based potential °  Rotamers - Show rotamer distributions Show the backbone-dependent rotamer distribution for selected residues, or put it directly in the soup. °  ShowRota<Res|Mol|Obj|All> - Show side-chain rotamers °  Scene content - List, count and compare units, get sequences and bounds List the properties of atoms to objects, including names, numbers and secondary structure, count how many units or covalent bonds are contained in a selection, find differences between selected atoms, residues or bonds, extract the sequence, determine the first and last atom or object spanning a selection and sum up atom masses. °  CompareBond - Compare bonds °  Compare<Atom|Res> - Compare atoms and residues °  CountBond - Count bonds °  Count<Atom|Res|Mol|Obj> - Count selected units °  ElementAtom - Get chemical element °  List<Atom|Res|Mol|Obj> - List selection °  Mass<Atom|Res|Mol|Obj|All> - Calculate mass °  Sequence<Res|Mol|Obj|All> - Get residue sequence °  Span<Atom|Res|Obj> - Determine first and last unit spanning a selection °  Contact analysis - List contacts and hydrogen bonds Search for contacts and hydrogen bonds between two selections. °  ListCon<Atom|Res|Mol|Obj> - List contacts °  ListHBo<Atom|Res|Mol|Obj> - List hydrogen bonds °  Secondary structure analysis - Assign and predict secondary structure List the assigned secondary structure per residue and the overall secondary structure content or predict secondary structure using the DSC method. °  PredSecStr<Res|Mol|Obj|All> - Predict secondary structure °  SecStr<Res|Mol|Obj|All> - Set/get secondary structure °  Surface analysis - Calculate surface areas, distances and potentials Calculations of surface areas and electrostatic surface potentials are influenced by the current surface environment and the resolution of the surface grid. If a protein has cavities, they can be treated separately. °  FirstSurf<Atom|Res> - Get first atom or residue facing each surface and the surface area °  SurfPar - Set/get surface parameters °  SurfDis<Atom|Res|Mol|Obj> - Calculate distance from surface °  SurfESP<Atom|Res|Mol|Obj|All> - Calculate electrostatic surface potentials °  Surf<Atom|Res|Mol|Obj|All> - Calculate surface areas °  Cavity analysis - Find empty space inside macromolecules Locate cavities inside macromolecules and get the first atom or residue facing them and their volume, which can also be calculated separately. °  CaviVol<Atom|Res|Mol|Obj|All> - Calculate cavity volumes °  FirstCavi<Atom|Res> - Get first atom or residue facing each cavity and the cavity volume °  Volumes - Calculate VdW, molecular and solvent accessible volumes Calculations of volumes are influenced by the resolution of the surface grid. °  Volume<Atom|Res|Mol|Obj|All> - Calculate volumes °  Checks - Search for errors Check objects for cis-peptide bonds, wrong isomers and deviations from naming conventions. In YASARA Dynamics, you can additionally check for incorrectly placed water molecules and unsual force field energies and calculate the current solvent density. In YASARA Structure 1D and 3D packing interactions can also be checked. In the Twinset, WHAT IF contributes 22 additional checks. °  Check<Atom|Res|Obj|All> - Check structure quality °  SolvDensity - Get solvent density in simulation cell °  View - Change the appearance of the soup °  Colors - Add a fourth dimension to your figures In addition to coloring atoms, you can also change the background color gradient and the default colors for chemical elements, secondary structure, B-factors etc. . Other commands to color covalent bonds, hydrogen bonds, surfaces and the fog are listed in the section they belong to. °  ColorBG - Color background °  ColorPar - Set default color parameters °  Color<Atom|Res|Mol|Obj|All> - Set/get atom colors °  Visibility - Show and hide, switch on and off Show and hide atoms, switch entire objects on and off. Look in the essentials section for details. °  Hide<Atom|Res|Mol|Obj|All> - Hide atoms °  Show<Atom|Res|Mol|Obj|All> - Show atoms °  Switch<Obj|All> - Switch objects on/off °  Style - Display atoms as balls, balls&sticks, sticks and traces Display atoms as space filling balls (CPK), balls of a certain radius connected with sticks or just plain sticks of a given radius. Show and hide a trace through a selection of atoms (e.g. Calpha atoms). When showing a trace, it may help to additionally hide atoms that are not traced. °  BallStickRadius - Set ball and stick radii in balls&sticks °  BallStick<Atom|Res|Mol|Obj|All> - Style atoms as balls&sticks °  Ball<Atom|Res|Mol|Obj|All> - Style atoms as balls °  HideTrace - Hide trace through atoms °  PointPar - Set point and line radius and plasticity in wire frames °  ShowTrace - Show trace through atoms °  StickRadius - Set stick radius °  Stick<Atom|Res|Mol|Obj|All> - Style atoms as sticks °  Style - Set general display style °  Secondary structure visualization - Show tubes, ribbons and cartoons Indicate the secondary structure by showing a plain tube, ribbons, and cartoons with cylindric helices. Change the radius, width and height of the secondary structure elements and hide them again later. It is also possible to override YASARA's secondary structure assignment. °  HideSecStr<Res|Mol|Obj|All> - Hide secondary structure °  SecStrPar - Set secondary structure display parameters °  ShowSecStr<Res|Mol|Obj|All> - Show secondary structure °  Surface visualization - Show VdW, molecular and accessible surfaces Show or hide three kinds of surfaces at various resolutions, color them afterwards or extract fragments by defining a surface environment. °  ColorSurf<Obj|All> - Color surface °  HideSurf<Atom|Res|Mol|Obj|All> - Hide surface °  ShowSurf<Atom|Res|Mol|Obj|All> - Show surface °  SurfPar - Set/get surface parameters °  Cavity visualization - Show empty space inside macromolecules Visualize cavities faced by selected atoms. °  ShowCavi<Atom|Res|Mol|Obj|All> - Show cavities °  Contact visualization - Show contacts and hydrogen bonds Visualize contacts, from bad bumps to favorable interactions, Show or hide all hydrogen bonds made by selected atoms and choose their color and transparency level. °  ColorHBo - Color hydrogen bonds °  HideHBo<Atom|Res|Mol|Obj|All> - Hide hydrogen bonds °  ShowCon<Atom|Res|Mol|Obj> - Show contacts °  ShowHBo<Atom|Res|Mol|Obj|All> - Show hydrogen bonds °  Ions and electrostatic potentials - Show ion binding sites and ESPs Use valence scanning to predict and show ion binding sites or display the electrostatic potential inside the cell. °  ShowESP - Show electrostatic potential °  ShowIonSites<Obj|All> - Show ion binding sites °  Atoms - Choose atom styles Set the overall atom size, attach various textures to the atoms, and toggle the display of the chemical element symbol or a whobbling plasma inside those atoms that are cut open by the viewplane. °  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 °  Cut-planes - Look inside Create cut-plane objects to look into other objects. °  Cut<Obj|All> - Cut objects open °  Projection - Switch the perspective Switch between perspective and parallel projection. °  Projection - Set perspective or parallel projection °  Lighting - Light the scene Configure the lightsource including shadows and ambient influence, and add fog of a certain color to the scene. °  ColorFog - Color fog °  Fog - Set fog density °  LightSource - Configure the light source °  Effects - Change and animate the scene °  Position - Place and move objects, detect collisions Choose object positions on an absolute or relative scale (including polygon meshes), grab either one, the next or the previous object for movement with mouse and 3DConnexion controller, or let them move automatically in a certain direction or to a certain spot. Collisions between objects can also be detected. °  AutoMoveTo<Obj|All> - Move objects or scene automatically to a certain location °  AutoMove<Obj|All> - Move objects or scene automatically °  GrabNext - Grab next object for mouse movement °  GrabPrev - Grab previous object for mouse movement °  Grab<Obj|All> - Grab object or scene for mouse movement °  IntersectObj - Perform collision detection to find intersecting objects °  MoveMesh - Move polygon mesh °  Move<Atom|Res|Mol|Obj|All> - Move atoms, objects or the scene °  PosOri<Obj|All> - Set/get object or scene position and orientation °  Pos<Obj|All> - Set/get object or scene position °  Orientation - Orient and rotate objects Orient or rotate objects, continuously, until a certain orientation is reached or to a nice view. Rotations about an arbitrary axis are also possible. The orientation angles corresponding to certain direction vectors can also be calculated. °  AutoRotateTo<Obj|All> - Rotate objects or scene automatically to a certain orientation °  AutoRotate<Obj|All> - Rotate objects or scene automatically °  NiceOri<Obj|All> - Orient objects nicely °  OriVec - Get vector orientation °  Ori<Obj|All> - Set/get object or scene orientation °  Rotate<Atom|Res|Mol|Obj|All> - Rotate atoms, objects or the scene °  RotAxis<Atom|Res|Mol|Obj|All> - Rotate atoms about a specified axis °  Size - Scale objects Change the size of objects by scaling the atom coordinates or the vertices of a polygon mesh. °  Scale<Atom|Res|Mol|Obj|All> - Scale atom positions and polygon meshes °  Labels - Display text labels Label anything from atoms to the entire scene and distances, change the label style including font, color or perspective, finally delete atom- and distance labels again. °  LabelDis - Label atom distances °  LabelPar - Set label parameters °  Label<Atom|Res|Seg|Mol|Obj|All> - Add labels °  UnlabelDis - Delete distances labels °  Unlabel<Atom|Res|Seg|Mol|Obj|All> - Delete labels °  Marks and zooms - Mark atoms with fireflies and zoom in Mark one atom and display its properties in the head up display, then zoom in closely on one or more atoms. °  MarkAtom - Set/get atoms marked with fireflies °  Zoom<Atom|Res|Mol|Obj|All> - Zoom in on atoms °  Arrows - Show arrows connecting atoms or points Show arrows and hide those connecting atoms or delete those connecting points. °  HideArrow<Atom|Res|Mol|Obj|All> - Hide arrows °  ShowArrow - Show arrows between atoms or points °  Polygons - Show polygons connecting atoms or points Show polygons (possibly inside rings) and hide those connecting atoms or delete those connecting points. °  HidePolygon<Atom|Res|Mol|Obj|All> - Hide polygons °  ShowPolygon - Show polygon between atoms or points °  ShowRing<Atom|Res|Mol|Obj|All> - Show polygon inside ring °  Solids - Show spheres, boxes, pyramids, cylinders, tori and others Show solid spheres & ellipsoids, boxes & cubes, cones, cylinders, pyramids & prisms, or a torus. °  ShowBox - Show a rectangular box °  ShowCone - Show a cone, cylinder, pyramid or prism °  ShowSphere - Show a sphere or ellipsoid °  ShowTorus - Show a torus °  Images - Show and animate bitmaps Load a bitmap in Windows BMP- or PNG-format, show it on screen, move it around or do more complicated animations and let the image disappear again. You can also swap images, attach them to objects, toggle fogging, hide them and finally delete them. °  AnimateImage - Animate appearance and disappearance of images °  AutoMoveImage - Move images automatically °  DelImage - Delete images °  HideImage - Hide images °  ImageFog - Switch image fog on/off °  LoadBmp - Load image from BMP file °  LoadJPG - Load image from jpg file °  LoadPNG - Load image from PNG file °  MakeImageObj - Make object with attached image °  ShowImage - Show images °  SwapImage - Swap images °  UnrestImage - Let animated image disappear °  Text - Print text, possibly in 3D letters By default, printing is done to the console. To get fancier text output, create a text object and redirect printing. Choose a font, possibly with fog, position the cursor, then print three-dimensional characters. You can also print to the top right head up display. °  Font - Set font for 3D letters °  FontFog - Switch font fog on/off °  MakeTextObj - Make text object to print 3D letters °  PosText - Position and justify text °  Print - Print text °  PrintCon - Print to console °  PrintHUD - Print to head up display °  PrintObj - Print to text object °  Wire frames - Display selected polygon meshes as wire frames All polygon meshes can be shown as a wire frame, where only the edges connecting the mesh vertices are visible. This is a common visualization style for X-ray density. °  ShowWire<Obj|All> - Show polygon mesh as wire frame °  Options - Other commands °  Experiments - Let YASARA cook for you Some things are non-trivial. Nevertheless, YASARA delivers the answer at the touch of the 'Experiment' button. During an experiment, YASARA takes over control and uses its 'artificial intelligence' to do various things in the right order. A message at the bottom will keep you informed. Some experiments accept additional parameters, look at the example macros to see how it works. °  Experiment - Choose and control experiments °  Macros - Watch YASARA do the work for you Save YASARA's current state in a macro or record your input as a macro (excluding mouse movements), play back your own macros or those made by others with a higher stage of YASARA, stopping whenever you want. You can use the back/forward icons in the top right corner to jump around in the macro. Macros can wait for certain events before they continue, raise errors if something goes wrong, take a certain action if an error occurs, disallow user input, speedup animations if the graphics get slow, require a minimum YASARA version, and be applied to a certain target. You can save a lot of time by running macros in text console mode (start YASARA with command line parameter -con). °  Go - Go to another position in the macro °  MacroTarget - Set macro target °  OnError - Set error action °  PlayMacro - Play back macro °  PlayMovie - Play back macro as a movie °  RaiseError - Display error message °  RecordMacro - Record all following commands in a macro °  RequireVersion - Require a minimum YASARA version °  SaveMacro - Save a macro to restore the current state °  SpeedUp - Speed up movements when graphics are slow °  StopMacro - Stop macro playback or recording °  UserInput - Set user input °  Wait - Wait for certain time period or condition °  Tables - Collect, visualize and export data When analyzing data, you often want to visualize it. This is achieved by creating a one-, two- or three-dimensional table, selecting it for data collection, tabulating the results and showing a graphical representation of the data. Tables can also be listed and manipulated on the column, row and page level, flipped, deleted entirely, imported and exported for use with other programs like Excel and XMGrace. °  Tabulate - Add cells to table °  DelTab - Delete tables °  FlipTab - Flip table axes °  LoadTab - Load formatted table °  MakeTab - Make a table °  SaveTab - Save formatted table °  SelectTab - Select table to add cells °  ShowTab - Show table data as 3D object °  Tab - Set/get table cells °  Formats - Choose the residue output format Many commands output a list of residues. Change the format for residue names if you log this output. °  FormatRes - Format residue output °  Logs - Redirect output to a file Many YASARA commands, especially those in the Analyze section, write their output to the console. You can log all output or just the result of the next command to a file and stop logging at a later point. °  LogAs - Log output of next command °  RecordLog - Record all console output in a log file °  StopLog - Stop log recorder °  Plugins - Run plugins from a macro Normally plugins are run by clicking on the options they add to the menus. In some rare cases, it may help to create a plugin input file and then run a plugin directly. If there is a bug in the plugin and it crashes, you must additionally stop it before it can be run again. °  RunPlugin - Run Python plugin °  SavePLI<Atom|Res|Mol|Obj> - Save plugin input file °  StopPlugin - Stop running plugin °  Default pH - Set the H+ ion concentration and residue pKas YASARA normally assigns bond orders and protonation patterns according to pH 7.0. Here you can change this value and also assign pKas to certain residues, overriding YASARA's predictions made during the neutralization experiment. °  pH - Set/get default pH °  pKaRes - Set/get residue pKa °  Quantum mechanics - Configure YAPAC YASARA provides semi-empirical quantum chemistry based on YAPAC, a derivative of James Stewart's MOPAC. Choose one of the MNDO, AM1 or PM3 methods, optimize geometries (possibly in water) and calculate formation energies. °  QuantumMechanics - Set quantum mechanics method °  Coordinate system - Live in a left or right handed world YASARA's default is a left-handed coordinate system, feel free to live in a right-handed world. °  CoordSys - Set coordinate system °  Units - Choose your favorite units By default, YASARA displays energies in kJ/mol. Here you can switch to kcal/mol. °  EnergyUnit - Set energy unit °  Parallel computations - Configure multi CPU core usage Today's CPUs contain more than one core to speed up calculations. Here you can change the number of CPUs YASARA should use. °  Processors - Set/get number of processors to use °  Input devices - Configure the interaction with YASARA Choose between three different pointer styles, change the function of the mouse wheel or the keyboard repeat rate, activate the P5 data glove or configure the 3DConnexion controller and its buttons. °  MouseWheel - Assign command to mouse wheel °  P5 - Set state of p5 data glove °  PointerStyle - Set style of mouse pointer °  RepeatKey - Set/get keyboard repeat rate °  SpaceballButton - Assign command to Spaceball button °  SpaceballPar - Set Spaceball parameters °  Shell - Execute shell commands Change or print your current working directory, delete files, get their size or run any other shell command. °  CD - Change working directory °  DelFile - Delete file °  FileSize - Get file size °  PWD - Print working directory °  Shell - Execute shell command °  Window - Change the display properties °  Location - Place the YASARA window The YASARA window can be resized, cover the entire screen and be fixed on one of multiple connected screens. °  FullScreen - Switch fullscreen mode on/off °  Screen - Fix YASARA window on a certain screen °  ScreenSize - Set/get window and fullscreen size °  Menus - Change the appearance of menus and the head-up display Adapt the style to match your operating system, animate windows in various ways, choose your favorite background texture and font, or hide all menus, including the sequence selector at the bottom and the head up display. The latter can be configured by showing or hiding selected units. °  AnimateWin - Animate Windows °  HideHUD<Atom|Res|Mol> - Hide in head-up display °  HUD - Switch head up display °  Menu - Switch menu on/off °  SeqSelector - Switch sequence selector on/off °  ShowHUD<Atom|Res|Mol> - Show in head-up display °  StyleWin - Style Windows °  WinFont - Set window font °  WinTexture - Set window background texture °  Messages and buttons - Communicate with the users of your macro When writing a plugin or macro, it sometimes helps to show a text message at the bottom and hide it afterwards or show a button to click. °  HideMessage - Hide text message at the bottom °  ShowButton - Show clickable button °  ShowMessage - Show text message at the bottom °  Console - Configure the console YASARA's command console can be extensively configured and hidden to speed up calculations and movies. Several console functions like copy/paste are explained here. °  Console - Switch console on/off °  ConsolePar - Set console parameters °  Antialiasing - Smooth is better Toggle YASARA's built in antialiasing and note that it only affects atom balls. Activate fullscreen antialiasing separately in your OpenGL settings. °  Antialias - Switch antialiasing on/off °  Frequency - Change the frames per second and save battery power Depending on the power of your computer, you can let YASARA update the screen more often or enter a special power saving mode when running on a notebook. °  FramesPerSec - Set screen update frequency °  Stereo - Time to touch your molecules Choose a stereo mode and adjust the stereo parameters to let molecules fly out of the screen. °  Stereo - Set stereo mode °  StereoPar - Set stereo parameters °  Help - Access the documentation and solve problems °  Manual - Browse the HTML documentation Enter the manual at the top level, jump directly to a certain command or search for individual keywords. The preferred web browser can also be changed. °  Browser - Set web browser °  SearchDoc - Search documentation °  ShowCom - Show command description °  ShowDoc - Show documentation °  Installation - Download missing programs YASARA uses other programs to perform additional tasks, here you can install them. °  Install - Install accessory program °  Index - All commands in alphabetic order Accel<Atom|Res|Mol|Obj|All> - Set/get acceleration of atoms 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 Align<Mol|Obj> - Align objects and molecules AlignMulti<Obj|All> - Align multiple objects AlignPDBMol - Align similar proteins from the PDB AlignPar - Set/get alignment parameters 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 BLAST<Res|Mol|Obj|All> - Blast protein sequence Ball<Atom|Res|Mol|Obj|All> - Style atoms as balls BallStick<Atom|Res|Mol|Obj|All> - Style atoms as balls&sticks BallStickRadius - Set ball and stick radii in balls&sticks BinDistance - Sort distances into bins to calculate the radial distribution function BindEnergyObj - Calculate binding energies Boundary - Set cell boundary Browser - Set web browser BuildAtom - Build single atom BuildLoop - Build central or terminal loop BuildMol - Build peptide or nucleic acid chain BuildRes - Build single residue CD - Change working directory CaviVol<Atom|Res|Mol|Obj|All> - Calculate cavity volumes Cell - Set/get simulation cell dimensions Center<Atom|Res|Mol|Obj|All> - Center atoms or polygon meshes 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 atoms and residues CompareBond - Compare bonds Console - Switch console on/off ConsolePar - Set console parameters CoordSys - Set coordinate system CorrectCis - Correct cis-peptide bonds during a simulation CorrectConv - Correct naming conventions during a simulation CorrectDrift - Correct solute drift during a simulation CorrectIso - Correct wrong isomers during a simulation Count<Atom|Res|Mol|Obj> - Count selected units CountBond - Count bonds Crystallize<Obj|All> - Crystallize objects to fill the unit cell Cut<Obj|All> - Cut objects open Cutoff - Set force cutoff distance Del<Atom|Res|Mol|Obj|All> - Delete atoms DelBond - Delete covalent bonds DelFile - Delete file 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 ElementAtom - Get chemical element 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 FirstCavi<Atom|Res> - Get first atom or residue facing each cavity and the cavity volume FirstSurf<Atom|Res> - Get first atom or residue facing each surface and the surface area Fix<Atom|Res|Mol|Obj|All> - Fix atoms during simulation FixAngle - Constrain bond angle during simulation FixBond - Constrain bond length 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 FreeAngle - Free bond angle during simulation FreeBond - Remove bond length constraint during simulation FullScreen - Switch fullscreen mode on/off GDT<Atom|Res|Mol|Obj> - Calculate global distance test 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 - Calculate angle between two atom groups GroupBox - Calculate bounding box around atom group GroupCenter - Calculate geometric center or center of mass GroupDihedral - Calculate dihedral angle between two atom groups GroupDistance - Calculate distance between two atom groups GroupLine - Calculate optimal line through atom group GroupPlane - Calculate optimal plane through atom group 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 HideHUD<Atom|Res|Mol> - Hide in head-up display HideImage - Hide images HideMessage - Hide text message at the bottom HidePolygon<Atom|Res|Mol|Obj|All> - Hide polygons 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 IntersectObj - Perform collision detection to find intersecting objects Join<Atom|Res|Mol> - Delete split points JoinObj - Join objects to one final object KekulizeBond - Remove fractional bond orders KinEnergy<Atom|Res|Mol|Obj|All> - Calculate kinetic energy 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 LoadJPG - Load image from jpg file LoadPDB - Load Protein Data Bank file LoadPNG - Load image from PNG file LoadPrep - Load AMBER Prep topology 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 - Set/get atoms marked 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 the 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 OptimizeLoop - Optimize central or terminal loop Ori<Obj|All> - Set/get object or scene orientation OriVec - Get vector 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 PosOri<Obj|All> - Set/get object or scene position and orientation PosText - Position and justify text PredSecStr<Res|Mol|Obj|All> - Predict secondary structure 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 RDF - Calculate radial distribution function RMSD<Atom|Res|Mol|Obj> - Calculate RMSDs RMSF<Atom|Res|Mol> - Calculate root mean square fluctuations and B-factors Radius<Atom|Res|Mol|Obj|All> - Calculate the 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 RepeatKey - Set/get keyboard repeat rate 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 RotAxis<Atom|Res|Mol|Obj|All> - Rotate atoms about a specified axis Rotate<Atom|Res|Mol|Obj|All> - Rotate atoms, objects or the scene RunPlugin - Run Python plugin SampleDih - Sample dihedral angles SampleLoop - Sample central or terminal loop Save* - Export file with OpenBabel SaveAli - Save alignment between objects SaveBmp - Save screenshot as uncompressed 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 SavePNG - Save screenshot as compressed PNG bitmap SavePOV - Save POVRay scene description SavePrep<Res|Mol|Obj|All> - Save AMBER Prep topology SaveSce - Save complete scene SaveSeq<Res|Mol|Obj> - Save residue sequence 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 Scale<Atom|Res|Mol|Obj|All> - Scale atom positions and polygon meshes 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 Seg<Atom|Res|Mol|Obj|All> - Set/get the segment name SelectTab - Select table to add cells SeqSelector - Switch sequence selector on/off Sequence<Res|Mol|Obj|All> - Get residue sequence 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 ShowCavi<Atom|Res|Mol|Obj|All> - Show cavities ShowCom - Show command description ShowCon<Atom|Res|Mol|Obj> - Show contacts ShowCone - Show a cone, cylinder, pyramid or prism ShowDoc - Show documentation ShowESP - Show electrostatic potential ShowHBo<Atom|Res|Mol|Obj|All> - Show hydrogen bonds ShowHUD<Atom|Res|Mol> - Show in head-up display ShowImage - Show images ShowIonSites<Obj|All> - Show ion binding sites ShowKBP - Show knowledge-based potential ShowMessage - Show text message at the bottom ShowPolygon - Show polygon between atoms or points ShowRest<Atom|Res|Mol|Obj|All> - Show restraints ShowRing<Atom|Res|Mol|Obj|All> - Show polygon inside ring 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 ShowWire<Obj|All> - Show polygon mesh as wire frame 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 SolvPar - Set/get solvation parameters SpaceballButton - Assign command to Spaceball button SpaceballPar - Set Spaceball parameters Span<Atom|Res|Obj> - Determine first and last unit spanning a selection Speed<Atom|Res|Mol|Obj|All> - Set/get speed and velocity of atoms 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 SupMulti<Atom|Res|Mol|Obj> - Superpose multiple objects SupOrdered<Atom|Res|Mol> - Superpose objects on ordered units Surf<Atom|Res|Mol|Obj|All> - Calculate surface areas SurfDis<Atom|Res|Mol|Obj> - Calculate distance from surface SurfESP<Atom|Res|Mol|Obj|All> - Calculate electrostatic surface potentials 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 Transformation - Get previously applied transformations 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