°  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 °  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 (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 Windows 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. °  LoadSim - Load simulation snapshot in sim format °  LoadXTC<Obj|All> - Load simulation snapshot in XTC format °  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 °  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 °  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 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 optimize 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. The geometry of small molecules can be optimized using semi-empirical quantum chemistry. 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 °  Optimize<Res|Mol|Obj|All> - Optimize molecular geometry °  Regularize<Obj|All> - Regularize covalent 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 and delete Add missing hydrogens at default positions and use an energy minimization to place them correctly. Change their order within the residue and delete them when needed. In 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 °  Force<Atom|Res|Mol|Obj|All> - Set/get force on atoms °  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 °  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 fix and free atoms or correct cis-peptide bonds and wrong isomeres on the fly, reporting these errors when needed. °  CorrectCis - Correct cis-peptide bonds during simulation °  CorrectConv - Correct naming conventions during simulation °  CorrectIso - Correct wrong isomeres during simulation °  Fix<Atom|Res|Mol|Obj|All> - Fix atoms during simulation °  Free<Atom|Res|Mol|Obj|All> - Free atoms during simulation °  Sim - Control simulation °  WarnIsError - Treat warnings as errors °  Analyze - Analyze the soup °  Atom position - Calculate average positions and RMSFs Get or set the position of selected atoms, sum up positions to calculate averages and root mean square fluctuations. °  AddPos<Atom|Res|Mol> - Sum atom positions to calculate average and standard deviation °  AveragePos<Atom|Res|Mol> - Average atom positions °  Pos<Atom|Res|Mol> - Set/get atom positions °  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 or all together and calculate the resulting RMSDs. °  RMSD<Atom|Res|Mol|Obj> - Calculate RMSDs °  SupMulti<Atom|Res|Mol|Obj> - Superpose multiple objects °  Sup<Atom|Res|Mol|Obj> - Superpose objects °  Alignment - Align objects and find related sequences Protein structures can be aligned automatically in pairs or all together based on either their structure or sequence with certain parameters. Alignments can be saved in various formats. Similar sequences can be retrieved from the PDB, SwissProt and TrEMBL with a built-in Blast. °  AlignMulti<Obj|All> - Align multiple objects °  AlignPar - Set/get alignment parameters °  Align<Mol|Obj> - Align objects and molecules °  Blast<Res|Mol|Obj|All> - Blast protein sequence °  SaveAli - Save alignment between objects °  Contacts - 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 °  Energy - Calculate energies Analyze the overall energy including individual terms, binding energies, solvation energies 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 °  SolvEnergy - Calculate solvation energy °  Electrostatics - Calculate electrostatic potentials and charges Display an electrostatic potential grid inside the periodic cell, sum up the charges in a selection of atoms or calculate the resulting dipole moment. °  Charge<Atom|Res|Mol|Obj|All> - Set/get the summed up charge °  Dipole<Atom|Res|Mol|Obj> - Calculate electric dipole moments °  ShowESP - Show electrostatic potential °  Geometry analysis - Measure distances, angles, dihedrals and radii 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, 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. °  Angle - Set/get angle between atoms °  Dihedral - Set/get dihedral angle between atoms °  Distance - Set/get distance between atoms °  GroupAngle - Get angle between two atom groups °  GroupDihedral - Get dihedral angle between two atom groups °  GroupDistance - Get distance between two atom groups °  GroupLine - Get optimal line through atom group °  GroupPlane - Get optimal plane through atom group °  Radius<Atom|Res|Mol|Obj|All> - Calculate the VdW radius °  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 °  Secondary structure - Calculate secondary structure content List the secondary structure per residue and the overall secondary structure content. °  HideSecStr<Res|Mol|Obj|All> - Hide secondary structure °  SecStrPar - Set secondary structure display parameters °  SecStr<Res|Mol|Obj|All> - Set/get secondary structure °  ShowSecStr<Res|Mol|Obj|All> - Show secondary structure °  Surface areas - Calculate VdW, molecular and accessible surfaces Calculations of surface areas 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 surface atom(s) or residue(s) and area(s) °  Surf<Atom|Res|Mol|Obj|All> - Calculate surface areas °  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 °  Scene content - List, count and compare units, get boundaries List the properties of atoms to objects, including names, numbers and secondary structure, count how many units are contained in a selection, find differences between selections, determine the first and last atom or object spanning a selection and sum up atom masses. °  Compare<Atom|Res> - Compare selections °  Count<Atom|Res|Mol|Obj> - Count selected units °  List<Atom|Res|Mol|Obj> - List selection °  Mass<Atom|Res|Mol|Obj|All> - Calculate mass °  Span<Atom|Res|Obj> - Determine first and last unit spanning a selection °  Checks - Search for errors Check objects for cis-peptide bonds, wrong isomeres, deviations from naming conventions and incorrectly placed water molecules and calculate the current solvent density. If you have the Twinset installed, you can run over 20 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 colors of covalent bonds, hydrogen bonds and the background. The default colors for chemical elements, secondary structure, B-factors etc. can also be adjusted. °  ColorBonds - Color bonds °  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 - 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 °  SecStr<Res|Mol|Obj|All> - Set/get secondary structure °  ShowSecStr<Res|Mol|Obj|All> - Show secondary structure °  Surfaces - Show VdW, molecular and solvent 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 °  Hydrogen bonds - Show hydrogen bonds 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 °  ShowHBo<Atom|Res|Mol|Obj|All> - Show hydrogen bonds °  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 °  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 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 Spaceball, or let them move automatically in a certain direction or to a certain spot. °  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 °  MoveMesh - Move polygon mesh °  Move<Atom|Res|Mol|Obj|All> - Move atoms, objects or the scene °  Pos<Obj|All> - Set/get object or scene position <