Here you can check which improvements to expect from a YASARA update. The list below only contains new features and major bug fixes since the first publically available release
(3.9.1), small changes are not included.
| Version | New feature |
| 8.6.21 | Workaround for a bug in some new ATI drivers that left the startup screen visible and did not clear the screen. |
| 8.6.8 | New command: 'SupOrdered' superposes an arbitrary number of selections in an ordered way. Click Analyze > Superpose > Two objects on ordered... |
| 8.6.6 | Fixed a problem with running 'Experiment Neutralization' multiple times on the same protein: pKa predictions from the first run were reused for subsequent runs, even if the protein conformation had changed. |
| 8.5.29 | Improved selection language: the 'with occurrence in' operator selects atoms that occur in both selections, see Selections > Selections can be combined with explicit operators. |
| 8.5.27 | New command: 'GDT' calculates the CASP global distance test, i.e. the percentage of atoms that can be superposed below a certain distance cutoff. Click Analyze > Global distance test of (Model+). |
| 8.5.26 | Improved commands: 'BuildRes', 'SwapRes' and 'AddRes' accept a new 'Isomer' parameter to build also D-amino acids. |
| 8.5.25 | Fixed a matching problem in 'Sup' and 'RMSD' that occured when more than two objects were superposed with 'Match=Yes', i.e. an RMSD matrix was calculated. |
| 8.5.7 | New command: 'ElementAtom' gets the chemical element of selected atoms. |
| 8.5.6 | Improved command: 'RadiusObj' can also obtain the radii of polygon meshes. |
| 8.4.15 | New command: 'SavePNG' saves a screenshot in compressed PNG format. |
| 8.3.30 | Improved command: 'Align' initializes the atomic properties to reflect sequence similarity between aligned residues. Coloring by properties thus helps to visualize the structural alignment. |
| 8.3.27 | Improved command: The minimization experiment supports a new convergence parameter to define how far the minimization should proceed. |
| 8.3.11 | Improved command: The 'Label' format supports a new 'CHARGE' keyword to display charges of entire units. 'ATOMCHARGE' is deprecated. |
| 8.3.3 | Improved command: 'Clean' sorts atoms in amino acids in their default order. |
| 8.3.1 | Reduced CPU usage on some graphics cards, e.g. nVIDIA. |
| 8.2.21 | Improved selections: the properties 'Ring', 'Aromatic' and 'Visible' are now available in atom selection menus. |
| 8.2.19 | Improved command: 'SupMulti' now employs the latest version 1.2.7 of Theseus (Linux+MacOSX). |
| 8.2.14 | Improved YAMBER3 force field: Stronger planarity constraints significantly increase structural quality with only a marginal effect on accuracy. |
| 8.2.10 | Improved typing of small molecules: 27 additional difficulties are now handled. |
| 8.2.3 | New feature: the 'SolvEnergy' command also calculates the Van der Waals solvation energy and returns it as the second result. A surface area is no longer returned, PLEASE UPDATE macros that use the second return value. |
| 8.2.2 | Improved macros: The examples macros at the 'BindEnergy' command now include Van der Waals solvation energies and the entropic cost of exposed surface. |
| 8.2.1 | Improved command: 'Rotate' can now also rotate atoms in the local coordinate system, the order of rotation is now about the X-, Z- and Y-axes. |
| 8.1.31 | New command: 'GroupLine' calculates the optimal line through a group of atoms, for example to move atoms along a helical axis. |
| 8.1.30 | Improved command: 'Clean' corrects incorrectly defined chemical elements, like OD2 ASP A 186 in 1F6W. |
| 8.1.29 | New command: 'GroupPlane' calculates the optimal plane through a group of atoms. |
| 8.1.28 | Improved command: Per-atom energy calculations with 'EnergyAtom/Res/Mol' add the dihedral energy to the two dihedral core atoms 2 and 3 instead of 1 and 4. This makes sure that the Phi and Psi dihedral energies stay inside the amino acid they belong to. The same holds for bond angles now. |
| 8.1.26 | Improved macro language: lists can be assigned to each other, e.g. MyOtherList=MyList. |
| 8.1.20 | New highlight: YASARA supports side-by-side stereo (parallel and cross-eyed), click Window > Stereo (Model+). |
| 8.1.18 | Improved command: 'AddRes' accepts a new 'End' parameter to add residues also to the front end of a peptide chain. |
| 8.1.17 | Fixed an issue where LoadSim complained that simulation snapshots created in the second half of 2007 were corrupted. |
| 8.1.10 | Improved feature: Object names can now be up to 12 characters long. |
| 8.1.7 | New highlight: A scene content browser with context menus in the top right head-up display allows to easily and quickly navigate and modify the scene. As a side-effect, <Ctrl> needs to be held down when grabbing an object for movement in the HUD. |
| 8.1.6 | Improved command: 'CheckObj Bumps' no longer considers crystal symmetry to avoid unexpected results. |
| 8.1.5 | New commands: 'ShowHUD' and 'HideHUD' toggle the display of selected units in the scene content browser. Click Window > Show/Hide in HUD. |
| 8.1.1 | New workaround for a backward compatibility bug in MacOSX 10.5. YASARA now also runs in Leopard. |
| 7.12.27 | Improved support for non-ASCII characters in filenames (UTF-8 etc.). |
| 7.12.25 | Improved command: 'StyleWin' can adapt YASARA's look to MacOSX 10.5 Leopard. Click Window > Style. |
| 7.12.22 | Improved secondary structure assignment. |
| 7.12.18 | Improved command: 'LoadPDB' supports a 'download' flag to automatically download missing PDB files. |
| 7.12.5 | Fixed a problem with showing hydrogen bonds from version 7.11.25. |
| 7.12.5 | Fixed an issue with the 'ShowPolygon' command, please update and add the polygons again. |
| 7.12.4 | Fixed some Twinset issues in Windows Vista and a cygwin1.dll problem. |
| 7.12.1 | Improved console: commands typed in can now be longer than the YASARA window. |
| 7.11.28 | New command: 'ShowPolygon' draws a polygon connecting points or atoms. Read Commands > Effects > Polygons. |
| 7.11.28 | New command: 'HidePolygon' hides a polgon connecting atoms. |
| 7.11.27 | Fixed an issue in the attribute selection list. |
| 7.11.26 | Improved Python interface: Selection can now be passed as Python lists [] to YASARA functions in Python modules and plugins. |
| 7.11.25 | New feature: YASARA's treatment of hydrogen bonds has been reimplemented and accelerated, including angle dependence, more details at the ListHBo command. |
| 7.11.23 | Improved command: 'Print' accepts an additional parameter 'Convert' to toggle the conversion of escape codes in strings. |
| 7.11.22 | Improved command: 'ListHBo' also lists the energies of hydrogen bonds. |
| 7.11.18 | Improved selection language: 'Ring' selects ring atoms, 'Aromatic' aromatic atoms. |
| 7.11.16 | Improved selection language: 'BFactor','Property' and 'Occupancy' calculate averages over the current selection type. |
| 7.11.14 | New highlight: YASARA can be used as a Python module, just 'import yasara'. Read Scripts > Use YASARA as a Python module. |
| 7.11.10 | Improved typing of small molecules: 23 additional pitfalls are now considered. |
| 7.11.3 | Improved selection windows: The 'Belongs to' list on the right side allows to select segments. |
| 7.11.3 | New command: 'Seg' complements 'NameSeg' (which performs segment inflation now) and sets or gets segment names of selected units, which helps storing complex selections permanently. See also Selections > Yanaconda helps to define selection subsets. |
| 7.11.2 | Improved consistency: ListObj also lists inactive objects. |
| 7.10.29 | New support for NFS mounted multi-user YASARA installations. Read Essentials > Running YASARA in special environments > Running YASARA from an NFS mounted volume. |
| 7.10.27 | New feature: when a simulation is switched off, YASARA wraps molecules that crossed a periodic boundary such that a maximum number of atoms are placed inside the cell. |
| 7.10.26 | Improved command: MUSTANG based structural alignments using 'Align' have been speeded up by an order of magnitude in Windows. |
| 7.10.18 | New guide and features for running YASARA on clusters: read Essentials > Running YASARA in special environments > Running YASARA on a cluster. |
| 7.10.15 | Improved command: 'Align' accepts an additional parameter to help MUSTANG align difficult oligomers. |
| 7.10.12 | New behavior: LoadSce now only sets surface parameters if a change of settings is requested with 'Settings=Yes'. |
| 7.10.10 | Improved command: pKaRes can determine the pKas predicted during a neutralization experiment. |
| 7.9.9 | New macro: md_runsteered.mcr runs a steered molecular dynamics simulations. More details in the documentation at Recipes > Run molecular dynamics simulations. |
| 7.9.5 | Improved commands: 'SaveSim' and 'LoadSim' protect the simulation snapshots with a checksum to minimize problems with hard disk data corruption. |
| 7.9.2 | New highlight: YASARA includes Arun S. Konagurthu's MUSTANG program to create pairwise and multiple structural alignments. Click Analyze > Align > Objects with MUSTANG. |
| 7.8.28 | Improved command: 'Tabulate' can add strings to a table. |
| 7.8.20 | New command: 'SaveAli' saves structural or sequence alignments in YASARA or FASTA format. Click Analyze > Align > Save alignment. |
| 7.8.15 | New highlight: YASARA supports local Smith&Waterman and global Needleman&Wunsch sequence alignments. Click Analyze > Align. |
| 7.8.10 | New command: 'AlignPar' sets various alignment parameters. Click Analyze > Align > Parameters. |
| 7.8.5 | Fixed an issue with numerical molecular surfaces that occurred after changing the standard probe radius of 1.4 A. |
| 7.7.31 | New highlight: The 'SupMulti' command superposes multiple objects together using the Theseus maximum likelihood approach developed by Douglas Theobald. This puts more emphasis on structurally conserved regions, allowing to superpose NMR bundles automatically without having to specify a target region. Click Analyze > Superpose > Multiple objects. |
| 7.7.28 | Improved force field parameter assignment for 3- and 4-rings. |
| 7.7.26 | New feature: The radii of sticks in balls&sticks and sticks alone can now be set independently. Click View > Stick > Parameters. |
| 7.7.10 | Improved command: 'Clean' deletes water molecules that overlap with other atoms or each other. |
| 7.7.4 | New feature: YASARA builds nucleic acids, DNA and RNA in all conformations. The 'BuildRes' command builds the first nucleotide, 'AddRes' appends at the 3' end, 'BuildMol' builds an entire nucleic acid based on a sequence. |
| 7.7.3 | Improved commands: 'ShowTorus' and 'ShowSphere' support a new 'Alpha' parameter to create transparent objects. For 'ShowSphere', this change is not entirely backward compatible. |
| 7.7.2 | Improved command: 'ListHBo' provides more intuitive output by listing atoms in the first selection that are hydrogen bonded with atoms in the second selection (i.e. bonds are listed in only one direction now). |
| 7.7.1 | Improved Yanaconda macro language: the 'in' operator checks if a list contains a certain value, the priority of the bitlogical operators has been set higher than comparisons, just like in Python. The variables 'FirstObj' and 'LastObj' store the number of the first/last *active* object and -1 of no object is active. |
| 7.6.29 | Improved commands: 'ListRes', 'ListMol', 'ListConRes', 'ListConMol', 'ListHBoRes' and 'ListHBoMol' now return unique residue and molecule ids instead of potentially ambiguous residue numbers and molecule names. |
| 7.6.27 | Fixed selection inconsistency: DelAtom Occupancy<0.5 deletes all atoms with occupancy<50% (meant 0.5% before) |
| 7.6.19 | New feature: Commands like 'SavePDB' now support the forthcoming new PDB format V3.0. Since it is less consistent and likely to cause problems with other programs, the original PDB format stays the default. |
| 7.6.17 | New commands: 'AddPos' adds atom positions to an internal table, 'AveragePos' and 'RMSF' use these data to calculate average positions and root mean square fluctuations. |
| 7.6.10 | Improved macro: 'md_analyze' calculates B-factors and the time-average structure from the simulation trajectory. |
| 7.6.5 | Improved macro: 'md_analyzeres' also calculates per-residue fluctuations |
| 7.5.30 | Improved command: 'SolvEnergy' is significantly faster, and the results have been optimized for accuracy. |
| 7.5.20 | Improved command: 'Clean' deletes residues that overlap significantly with other residues and are most likely slightly different ligands bound to the same active site, like BTN/BTQ in 2F01. |
| 7.5.14 | Improved command: 'Wait' can wait until the users marks an atom, distance, angle or dihedral. |
| 7.5.11 | Improved command: 'MarkAtom' returns the numbers of the currently marked atoms. |
| 7.5.8 | New command: 'CorrectConv' corrects errors in naming conventions (methylenes, Val/Leu side-chain flips) during a simulation to aid high-temperature NMR structure determination protocols. Click Simulation > Automatic correction of > wrong naming conventions (Dynamics+). |
| 7.5.6 | Fixed a startup problem on some Mandrake/Mandriva Linux distributions. |
| 7.5.5 | Improved command: 'BuildLoop' mutates all anchor residues if requested with 'Mutate=Yes' |
| 7.5.4 | New feature: The 'Check' command performs a new 'NameConv' check of naming conventions (methylenes, Val/Leu side-chain flips) and also handles the checks for cis-peptide bonds and wrong isomers. The old commands 'CheckCis' and 'CheckIso' are now deprecated. |
| 7.5.3 | Improved command: 'ShowHBo' supports a new 'Extend' flag to extend selections to hydrogen bonding partners, making it easy to show hydrogen bonds involving selected atoms. Click View > Show hydrogen bonds. |
| 7.4.29 | New movie: Proteins for beginners, NMR structure determination, information content of NOE restraints, refining NMR structures and error detection by Sander Nabuurs, separate download from www.yasara.org/movies. |
| 7.4.27 | Improved commands: 'Label' and 'Unlabel' can now also (un)label individual segments. |
| 7.4.26 | New movie: Methionine synthase, example for visualizing enzymatic mechanisms with YASARA, by Richard Deth, separate download from www.yasara.org/movies. |
| 7.4.24 | Improved command: 'Clean' renames left-over single OT1/OT2 atoms to O. |
| 7.4.22 | New highlight: YASARA now features an accurate and fast, multi-threaded algorithm to calculate molecular surfaces in real-time including all cavities. Click View > Show surface > Parameters > Numeric. |
| 7.4.18 | Improved feature: molecular surface calculations using the Gaussian approximation have been calibrated to reproduce the results of the new, more accurate molecular surface algorithm above. |
| 7.4.16 | New macro: md_analyzesecstr creates a 3D plot and text table of the secondary structure changes during a simulation. |
| 7.4.13 | Improved speed: YASARA is now compiled with a higher optimization level. |
| 7.4.1 | New plugin: The ConSurf interface developed by Joost Van Durme and Sebastian Maurer-Stroh colors proteins by sequence conservation (using the ConSurf server by Landau et al.). Click View > Color > Molecule by ConSurf. The similar PDBFinderII color mapping has been moved to View > Color > Residue by feature. |
| 7.3.30 | Improved surfaces: Calculations involving surface environments have been speeded up by 25%, surfaces also require significantly less memory. |
| 7.3.28 | Improved command: 'Transfer' supports three different ways of handling local atom coordinates during an object transfer. When an object is transferred into the simulation cell, its CRYST1 record is set, so that the simulation cell can be saved in PDB files. Click Edit > Transfer. |
| 7.3.21 | New feature: The 'SurfPar' command allows to choose between two sets of radii for molecular and solvent accessible surfaces. Standard VdW and more realistic effective solvation radii. Click View > Show surface > Parameters. |
| 7.3.20 | Improved command: 'Dihedral' also sets and gets improper dihedrals if 'bound' is set to 'yes'. |
| 7.3.15 | New workarounds for many bugs in Linux OpenGL drivers, especially for older video cards like e.g. Radeon 9X00, Intel integrated chipsets, Matrox G400. |
| 7.3.11 | New highlight: YASARA has been ported to Mac OS X, including special support for Mac gadgets like the Mighty Mouse. Watch the help movie 'Working with YASARA' for details. |
| 7.3.4 | New command: 'SeqSelector' toggles the display of the sequence selector at the bottom. Click Window > Show sequence. |
| 7.2.26 | Improved support and workarounds for MESA indirect software rendering in Linux. |
| 7.2.25 | Improved command: 'FramesPerSec' can also deactivate screen redraws when YASARA is idle to save CPU power. The SavePower command is deprecated. |
| 7.2.24 | New feature: Hydrogens can be selected by their name according to many different nomenclatures. Read Selections > Additional selection types allow to filter for various properties > 'PDB', 'PDBRev'... |
| 7.2.22 | Improved command: 'LoadPDB' corrects the hydrogen nomenclature unless 'Correct' is set to 'No'. |
| 7.2.20 | Improved command: 'AddHyd' adds amide and guanidine hydrogens matching PDB naming conventions. |
| 7.2.18 | New command: 'AtomSymbol' toggles the display of the chemical element symbol inside atoms that are cut open. Click Effects > Atom appearance > Element symbol. |
| 7.2.15 | Improved command: 'Clean' swaps amide and guanidine hydrogens to match PDB naming conventions. |
| 7.2.10 | Improved support for ATI Radeon cards in Linux: if driver >=8.X.Y is installed, graphics run significantly faster. |
| 7.2.7 | New feature: Compressed files with '.Z' extension can now be loaded directly just like '.gz' files. |
| 7.2.6 | Improved command: 'CD' allows to always change the working directory on startup, click Options > Change directory. |
| 7.2.5 | New command: 'ShowButton Continue' shows a continue button and sets the Yanaconda variable 'ContinueButton' to true if pressed. |
| 7.2.4 | Improved command: 'List' accepts a new 'Compress' parameter to return a compressed selection list, see Commands > Analyze > Scene content > List. |
| 7.2.3 | New feature: The 'Charge' command has improved capabilities to not only set net charges but also individual atom charges. This change is not entirely backward compatible. |
| 7.2.2 | Improved user interface: file selection menus provide various shortcuts to Home, Documents, Pictures etc. |
| 7.2.1 | New command: 'Install' automatically installs POVRay or Python, click Help > Install program. |
| 7.1.30 | Improved command: 'Raytrace' creates PNG images by default to save disk space. |
| 7.1.28 | New feature: The neutralization experiment allows to request a certain NaCl contration and thus add more salt ions than needed to neutralize the cell (click Options > Experiment > Neutralization). |
| 7.1.27 | Improved command: 'Mass' also lists the summed up mass. |
| 7.1.26 | New command: 'ShowTorus' draws a ring-, horn- or spindle-torus. Click Effects > Show solid > Torus (Model+). |
| 7.1.25 | Improved window manager: if all animations are disabled, clicks on icons and buttons now provide more visual feedback. |
| 7.1.24 | Improved Yanaconda macro language: the 'rnd' function can randomize strings, e.g. to create random RGB colors. |
| 7.1.17 | Improved command: 'JoinObj' can now also join polygon meshes like arrows, spheres, boxes etc. |
| 7.1.14 | New feature: Dummy atoms (element 0) can now be included in a simulation without causing an error message. |
| 7.1.11 | Fixed a YASARA for Windows issue where pulldown menus could not be closed after using the right mouse button to move a molecule behind an open window. |
| 7.1.10 | Improved command: 'SavePower' now reduces YASARA's CPU requirements to truly 0 if no input is made. Click Window > Save power. |
| 7.1.9 | Improved command: 'Wait' supports the new unit 'Femtoseconds' to make waiting during a simulation more straightforward. |
| 7.1.7 | New highlight: YASARA's graphics engine now supports diffuse shadows and ambient lighting for balls to sticks, even on very old video cards. Watch the new help movie 'Lighting and shadows'. |
| 7.1.6 | Improved commands: 'Sup' and 'RMSD' have improved flipping capabilities for equivalent atoms to minimize the RMSD: Hydrogens are now also considered and flipped atoms are listed in the console. |
| 7.1.5 | Improved selection language: 'Segment' switches to a selection of macromolecular segments, read Selections > Additional selection types > Segment. |
| 7.1.4 | New command: 'UndoLevels' sets the number of undo levels without having to edit yasara.ini. Click Options > Undo levels (Model+). |
| 7.1.3 | Improved command: 'LoadPDB' allows to configure the path of a local PDB installation, click File > Load > PDB file from local PDB. |
| 7.1.2 | Improved command: The 'Lightsource' command now also configures ambient lighting and shadows, the 'Shadow' command is deprecated. |
| 7.1.1 | New highlight: YASARA now has a newly styled look, that also adapts to your current operating system, see www.yasara.org/looks. Click Window > Style (Model+). |
| 6.12.31 | Improved commands: 'LoadSce' and 'SaveSce' now also load/save the projection, antialiasing, point & line appearance, fog and hbond colors, lighting parameters, surface parameters and cell boundary. |
| 6.12.30 | Improved command: 'WinFont' now allows to choose between 6 different fonts, click Window > Font. |
| 6.12.29 | Improved command: The 'HUD' command can show the head up display with an antialiased font, click Window > HUD > Antialiasing. |
| 6.12.28 | Improved command: The 'ConsolePar' command can show the console with an antialiased font, click Window > Console > Parameters. |
| 6.12.27 | Improved command: 'AnimateWin' command supports a new 'tilting' animation, click Window > Animation > Tilt. |
| 6.12.26 | Improved plugins: The 'CheckBoxMenu' allows to set the default checkbox states by appending '(Checked)' to the box text. |
| 6.12.19 | New feature: While a window is on screen (e.g. to interactively adjust dihedral angles), the scene can still be moved and rotated by holding down a mouse button outside the window. |
| 6.12.17 | New feature: When specifying a macro as a command line argument, it is now possible to add variables, see Essentials > The command line parameters. |
| 6.12.13 | Improved selection language: The 'with bond angles to' operator analyzes second neighbors in the molecule. Read Selections > Selections can be combined.. > The 'with <>X bond angles to' operator. |
| 6.12.10 | Improved typing and force field parameter assignment for small molecules. |
| 6.12.8 | Improved commands: Load* and Save* now support many more OpenBabel based fileformats. |
| 6.12.3 | New highlight: The 'Processors' command activates support for multiple CPUs, heavily speeding up molecular simulations, see www.yasara.org/parallelmd and click Options > Processors (Dynamics+). |
| 6.12.1 | Improved commands: 'Fix' and 'Free' are now included in the undo/redo history. |
| 6.11.29 | New feature: Up to four bond lengths, bond angles and bond dihedrals can now be changed together interactively. Mark two atoms, then click Geometry > Bond .. in the atom context menu. For more details, check the 'Distance', 'Angle' and 'Dihedral' commands (Model+). |
| 6.11.27 | Improved support for Windows Vista. |
| 6.11.24 | Improved command: 'LoadPDB' accepts a 'Model' parameter to load only one model from an NMR bundle. |
| 6.11.22 | New command: 'SwapBond' changes an existing bond order, the use of 'AddBond' for this purpose is deprecated. Click Edit > Swap > Bond. |
| 6.11.21 | Improved Yanaconda macro language: the 'join' function concatenates a list to a single weak string. |
| 6.11.20 | Improved selection language: the 'without contribution to .. surface' selects buried residues that do not contribute to a certain surface. |
| 6.11.11 | New command: 'MoveMesh' moves a polygon mesh in the local coordinate system to facilitate rotations around certain points. |
| 6.11.5 | New feature: YASARA's assembly language core now supports the SSE3 instruction set found in PentiumIV Prescott, Athlon64 Venice, Opteron 90nm and newer CPUs. On AMD Opteron, the speedup for MD simulations is ~10%. Make sure to either select 'Many' or a CPU architecture with SSE3 on the download page. |
| 6.11.3 | Improved command: 'Temp' accepts a new 'reassign' parameter to toggle the reassignment of atom velocities according to a Maxwell-Boltzmann distribution. |
| 6.11.1 | Improved command: 'LoadPDB' automatically adds missing CONECTs if the 'Correct' flag is set. Using LinkAtom is no longer needed. |
| 6.10.30 | New example macro: md_refine.mcr refines a homology model and analyzes individual snapshots, check the docs at Recipes > Refine a homology model. |
| 6.10.28 | Improved command: 'Link' does a better job ignoring bumps instead of assigning covalent bonds. |
| 6.10.26 | Improved command: 'ListObj' now also lists those objects that do not contain atoms. |
| 6.10.24 | New feature: The new parameter 'SetPar' of the 'ForceField' command allows to set optimal default simulation parameters, click Simulation > Force field (Dynamics+). |
| 6.10.19 | Improved simulations: If the simulation cell includes only a small part of the protein, the simulation runs much faster now with (Y)AMBER force fields. |
| 6.10.8 | New highlight: The 'Crystallize' command fills the unit cell with symmetry related copies of the selected object. Click Edit > Crystallize (Dynamics+). |
| 6.10.4 | Improved macro language: the 'chr' function converts an ASCII number to a character string. |
| 6.9.22 | New feature: Amino acid side-chains bound to ligands or metals are now shown when choosing one of the trace, ribbon or cartoon scene styles. |
| 6.9.20 | Improved commands: 'LoadPDB' and 'SavePDB' preserve the crystallographic symmetry REMARK 290. |
| 6.9.18 | New command: 'Compare' finds differences between atom and residue selections. Click Analyze > Compare. |
| 6.8.19 | Improved command: 'NiceOri' can choose a nice orientation for the entire scene. Click Effects > Orientation > Set nicely for scene (Model+). |
| 6.8.13 | Improved command: 'SwapRes' can swap nucleotides to Uridine and handle nucleotides like ATP or GDP. |
| 6.8.6 | Improved command: 'BuildRes' supports a 'Center' flag to disable centering of the newly built residue. |
| 6.8.1 | Improved command: 'SwapRes' keeps all useful side-chain dihedral angles to minimize reorientations (Model+). |
| 6.7.25 | Improved command: 'RayTrace' supports a new 'Background' parameter to create transparent backgrounds. |
| 6.7.15 | New highlight: The YAMBER3 force field provides another improvement in force field accuracy (Dynamics+). |
| 6.7.10 | Improved command: 'SurfPar' can display the current surface parameters. |
| 6.7.8 | Improved graphics: Lines are now drawn with antialiasing if requested (Window > Antialiasing) and supported by your OpenGL driver. |
| 6.7.6 | Improved command: 'ColorPar' allows to choose all rainbow colors for the secondary structure elements. Click View > Color > Parameters > Secondary structure. |
| 6.6.25 | Improved selection language: the 'with distance >X from' operators provide more intuitive results for 'Res', 'Mol' and 'Obj' selection types. |
| 6.6.19 | New feature: MD simulations with solvents other than water are now much easier. Check the documentation of the commands 'FillCellObj' and 'PressureCtrl' (Dynamics+). |
| 6.6.18 | New command: 'Mass' sums up atomic masses, click Analyze > Mass of. |
| 6.6.17 | Improved command: FillCellObj allows to specify a density to easily fill the simulation cell with special solvents. Click Simulation > Fill cell with (Dynamics+). |
| 6.6.16 | New command: 'SolvDensity' measures the density of any solvent, the 'WaterDensity' command is now deprecated. |
| 6.6.12 | New feature: The current energies are displayed in the simulation HUD on the right side and can be quickly recalculated by pressing the key left to '1'. |
| 6.6.11 | Improved commands: 'CorrectCis' and 'CorrectIso' can now also correct unusual amino acids. |
| 6.6.10 | New feature: Having grabbed a single object for movement, it is now possible to grab the entire scene again by clicking a second time on the object name in the top right HUD. |
| 6.6.9 | Improved commands: 'Sup' and 'RMSD' can now perform full matching of atom and residue names. |
| 6.6.6 | New highlight: YASARA can now calculate force field energies individually for objects, molecules, residues and atoms. This makes it easy to localize regions of high-energy. Click Analyze > Energy (Dynamics+). |
| 6.5.29 | New feature: The commands 'Sup' and 'RMSD' can now also shuffle atoms around within a residue to easily superpose molecules with different atom orders. |
| 6.5.20 | New default: The 'CorrectCis' command does not correct cis-prolines by default now. |
| 6.5.15 | Improved command: 'TransformObj' supports a flag to keep the global object position after transformation of atom coordinates. This is now the default. |
| 6.5.7 | New command: 'RenumberObj' reorders the objects in the scene, helpful to close gaps in the HUD if objects have been deleted. Click Edit > Renumber > Objects. |
| 6.4.30 | Improved command: 'Clean' adds cysteine bridges between close CYS SG atoms. |
| 6.4.29 | New feature: Atoms causing an error message are now automatically highlighted. |
| 6.4.28 | Improved command: 'LoadPDB' supports a 'correct' option to automatically delete unusually long CONECT bonds. |
| 6.4.27 | Improved command: 'Clean' detects alternate conformations of entire molecules put on top of each other and deletes the one with the lower occupancy. |
| 6.4.26 | Improved commands: 'LoadPDB' and 'Clean' detect and correct shifted atom names. |
| 6.4.25 | Improved commands: Virtually all YASARA commands now support compression when reading or writing files whose names end with '.gz'. |
| 6.4.23 | Improved commands: 'Sup' and 'RMSD' display a warning when trying to superpose atoms with different names. |
| 6.4.21 | Improved plugin: The PDBFinder2 interface retrieves data from a new server and better handles proteins with chain-breaks. Click Analyze > PDBFinder2 properties. |
| 6.4.15 | Improved command: 'Clean' sorts backbone and side-chain atoms within each residue. |
| 6.4.9 | Improved commands: 'BuildRes', 'AddRes' and 'SwapRes' can now select specific Asp, Glu, His and Cys protonation states via special residue names. |
| 6.4.8 | Improved command: 'Tabulate' now also adds string return values to a table, e.g. 'Tabulate NameRes all' tabulates all residue names. |
| 6.4.7 | Improved command: 'Experiment minimization' checks for regions with strong bumps and performs a local steepest descent minimization without electrostatics first to avoid nuclear fusion caused by Coulomb attraction exceeding VdW repulsion. |
| 6.4.5 | Improved command: 'Energy' explicitly returns a planarity energy also for the NOVA force field to identify severe planarity problems. Total NOVA energies therefore change a bit. |
| 6.4.3 | New feature: YASARA now calculates solvent accessible surfaces using optimized 'effective' Van der Waals radii that implicitly consider hydrogen bonds. For best results, the probe radius should be set to 1.4 A (click View > Show surface > Parameters). |
| 6.3.27 | Improved command: 'List' supports a new 'Format' parameter to also get names in specific formats, not only numbers. |
| 6.3.26 | New commands: 'PosMol' and 'PosRes' set and get the position of the geometric center of molecules and residues, click Effects > Position. |
| 6.3.25 | Improved command: 'SecStrRes' returns the secondary structure as a list of character strings 'H','E','T' and 'C'. Numerical codes are deprecated. |
| 6.3.24 | New highlight: the commands 'GroupDistance', 'GroupAngle' and 'GroupDihedral' calculate the distance between geometric centers and the angles between lines and planes optimally fit through groups of atoms, e.g. the angles between two helices or phenyl rings. Click Analyze > Geometry (Model+). |
| 6.3.23 | Improved command: 'SaveMOL2' stays closer to the file format when saving proteins. |
| 6.3.20 | New feature: The 'Surf' command supports a new 'unit' parameter to calculate surface areas per molecule, residue or atom. |
| 6.3.16 | Improved command: 'Color' accepts multiple sequence alignment also in FASTA format when coloring by sequence conservation. |
| 6.2.12 | New command: 'Name' sets or gets the names of objects, molecules, residues and atoms. The 'Rename' command is now deprecated. |
| 6.2.10 | New command: 'UnlabelDis' deletes distance labels between selected atoms. Click Effects > Unlabel > Distance. |
| 6.2.7 | New workaround for flickering problems on Intel GMA 9xx graphics chips when running YASARA fullscreen. |
| 6.2.5 | Improved command: When 'Raytrace'ing with outlines, black labels are excluded to allow proper labelling of schematic figures. |
| 6.1.24 | Improved bond typing: A weighted average of bond length and bond angle deviations is now used to determine hybridization states. |
| 6.1.23 | Improved command: 'SwapAtom' knows all standard (order dependent) bond lengths between organic elements and updates them accordingly. |
| 6.1.22 | New feature: 'Check WaterPos' calculates normality Z-scores for water molecules to identify those at unlikely positions, e.g. a hydrophobic protein cavity. Click Analyze > Check (Dynamics+). |
| 6.1.19 | Improved command: 'Experiment Neutralize' uses an improved algorithm to avoid placing water molecules in cavities where a vacuum would be energetically more favorable. |
| 6.1.17 | Improved macro language: the 'dirname' function extracts the directory name from a string. |
| 6.1.15 | New improved algorithm to remove center-of-mass-motion from a simulation, solutes are now less likely to pass periodic boundaries, which makes visualization easier (Dynamics+). |
| 6.1.14 | Improved command: 'Sim Pause' can now be used to pause a simulation after a given time. Click Simulation > Simulator > Pause in... |
| 6.1.13 | Improved commands: 'Label' and 'Unlabel' are now restricted to create and delete labels of a given unit type. Click 'Effects > Unlabel > All above' to delete all labels at once. |
| 6.1.12 | Improved commands: 'Sup' and 'RMSD' can determine the chemical equivalence of molecules with exotic atoms to minimize the RMSD via the 'flip' flag. |
| 6.1.11 | Improved command: 'ForceField' allows to set the charge assignment scheme: AutoSMILES, AM1BCC or AM1 (for comparison and validation only). |
| 6.1.10 | New feature: The 'AutoSMILES' algorithm automatically splits long aliphatic lipids that contain too many atoms for QM charge derivation (Dynamics+). |
| 6.1.9 | Improved command: 'Clean' makes external single atoms bound to a residue part of this residue, e.g. three oxygens bound to Cys SG atoms. |
| 6.1.8 | Improved command: 'Experiment' automatically cleans the soup in case hydrogens are missing, 'Neutralization' does a better job removing waters from the protein core. |
| 6.1.7 | Improved command: 'Clean' deletes terminal residues with incomplete backbone, which are usually X-ray artifacts. |
| 6.1.6 | Improved feature: automatic force field parameter assignment and QM optimization in water are now 6x faster in YASARA for Windows. |
| 6.1.1 | New highlight: The 'AutoSMILES' algorithm fully automatically parameterizes organic molecules for simulation, including assignment of point charges by combining the high-throughput AM1BCC approach with a large SMILES-based library of optimal RESP charges, making it possible to run MD simulations of most PDB files at the touch of a button. Read www.yasara.org/autosmiles or Recipes > Running molecular dynamics simulations > Preparing the force field > Deriving new (Y)AMBER parameters (Dynamics+). |
| 5.12.31 | Improved typing of double bonds outside rings. |
| 5.12.30 | Improved selection language: the 'Charge' operator allows to select by net charge. Look at the end of the 'Belongs to or has' list or read Selections > Additional selection types > Charge. |
| 5.12.29 | New help movie: 'Simulation and quantum mechanics of small molecules' introduces fractional bond orders and pH dependency, shows how to build and simulate small molecules, and how to use quantum mechanics to optimize geometries and compare tautomers. Click Help > Play help movie > Simulation and QM of small molecules. (Dynamics+) |
| 5.12.28 | Improved command: 'LabelDis' accepts a new 'bound flag' to label only distances between bound atoms. |
| 5.12.27 | New highlight: The 'QuantumMechanics' command activates the semi-empirical MNDO, AM1 or PM3 quantum chemistry methods provided by the built-in YAPAC, a customized and validated derivative of MOPAC. Click Options > Quantum mechanics (Dynamics+). |
| 5.12.26 | Improved command: 'Label' supports two new format options 'ATOMTYPE' and 'ATOMCHARGE' to label with atom type and charge respectively. |
| 5.12.25 | New feature: 'pH' sets the implicit solvent model used in quantum chemistry calculations, either none when working in vacuo or COSMO by A.Klamt when working in solution. |
| 5.12.24 | Improved command: 'Sim Init' automatically adds springs to enforce virtual bonds to metal ions (i.e. headless arrows added by ShowArrow or by CONECT records in the original PDB file) (Dynamics+). |
| 5.12.23 | New highlight: The 'Optimize' command tunes the geometry of molecules containing up to ~100 atoms using semi-empirical quantum chemistry. Click Edit > Optimize. |
| 5.12.22 | Improved command: 'AddBond' accepts a new 'bound flag' to modify only existing bonds. Click Edit > Add > Bond. |
| 5.12.21 | New command: 'FormEnergy' calculates the heat of formation using semi-empirical quantum chemistry. Click Analyze > Energy > Formation. |
| 5.12.20 | Improved command: 'AutoMoveImage' supports two ways of repeating the automatic image movement: 'Cycle=MoveBack' and 'Cycle=JumpBack'. |
| 5.12.19 | New command: 'TypeAtom' retrieves the currently assigned force field atom types, for example to label atoms accordingly. |
| 5.12.18 | Improved command: When importing molecules with OpenBabel using 'Load*', the 'Resonate' flag allows to automatically replace alternating single/double bonds with the proper resonance form. |
| 5.12.16 | Improved command: 'Clean' replaces seleno-methionine with methionine and deletes NMR dummy atoms (element 0). |
| 5.12.15 | New highlight: The new General AMBER Force Field (GAFF) provides force field parameters for any organic molecule. |
| 5.12.14 | Improved typing of bonds and handling of alternate atoms. |
| 5.12.10 | New WHAT IF released as part of the Twinset. WHAT IF's homology modeling module now also works in the Twinset. |
| 5.12.7 | Improved handling of cyclic peptides: Traces, tubes and ribbons are now drawn without a gap, provided that the cyclic peptide bond is indicated with a 'CONECT' in the PDB file. |
| 5.12.3 | New command: 'KekulizeBond' converts resonance bonds with fractional bond orders to alternating single/double bonds. Click Edit > Adjust bond orders > Kekulize bond. |
| 5.12.2 | Improved command: 'RMSD' accepts a 'flip' flag like 'Sup' to minimize the calculated RMSD by flipping chemically equivalent atoms. |
| 5.12.1 | New command: 'ResonateBond' converts alternating single/double bonds to the proper resonance form. Click Edit > Adjust bond orders > Resonate bond. |
| 5.11.26 | Improved command: 'ShowTrace' displays a trace also for Calpha only proteins when you press <F4>. |
| 5.11.25 | Improved command: 'Clean' detects residues with missing bonds and invokes 'Link' to find them before adding hydrogens. |
| 5.11.24 | Improved command: 'LoadPDB' automatically searches and types links in standard residues with non-standard atom names. |
| 5.11.23 | New workaround for a new ATI Radeon OpenGL Linux driver bug (missing secondary structure), updated installation hints at Troubleshooting > YASARA runs slowly > You are running Linux with an ATI Radeon. |
| 5.11.22 | Improved command: 'Link' uses a new algorithm to find also large numbers of bonds quickly. |
| 5.11.20 | Improved command: The tubes and ribbon created by 'ShowSecStr' stay correct when the protein crosses a periodic boundary. |
| 5.11.19 | Improved command: 'PosAtom' can now set and get the mean position of an atom selection. |
| 5.11.18 | New highlight: The improved 'TypeBond' command employs a new algorithm combining graph theory with chemical knowledge on valence ambiguities and preferred tautomers to type complicated hetero-polycycles, e.g. in PDB file ligands. See www.yasara.org/typing or click Edit > Type bonds. |
| 5.11.14 | Improved command: 'LoadPDB' provides special support for ancient but still official PDB files with weird atom names. |
| 5.11.10 | Improved plugin: the OpenOffice Impress import filter now supports OpenOffice 2.0. Click Options > Macro & movie > Import movie |
| 5.11.6 | New Yanaconda function: 'ord' returns the summed ASCII code of the given string |
| 5.11.4 | Improved command: 'Dihedral' can now change improper dihedrals, also interactively from the atom context menu. |
| 5.11.3 | New command: 'Dipole' calculates the electric dipole moment. Click Analyze > Dipole moment of (Dynamics+). |
| 5.11.2 | Improved selection language: the operator 'within sequence' selects units belonging to a given sequence, e.g. ColorRes Lys within sequence Arg Lys Phe,yellow. |
| 5.11.1 | New workaround for a Mandriva Linux 2006 AMD64 problem, which is lacking the library 'libncurses'. |
| 5.10.15 | Improved selection language: Single or double quotes can be used to span unusual atom/residue/object names with special characters like spaces. |
| 5.10.9 | New highlight: Structural alignments using the CE, Multiprot and Sheba methods are available for Windows and Linux thanks to a plugin and webserver developed by Emmanuel Bettler and Mikael Roche. Click Analyze > Align. |
| 5.10.8 | Improved command: 'BuildAtom' allows to define the position of the new atom, which helps to place dummy atoms e.g. in the center of a phenly ring to measure distances. |
| 5.10.7 | New command: 'pKaRes' assigns pKa values to selected residues that override the predictions made during the neutralization experiment. Click Options > Residue pKa. |
| 5.10.5 | Improved command: 'SwapRes' can swap residues to Uracil and keeps the chi1 dihedral intact. |
| 5.10.1 | New highlight: The commands 'ShowSphere', 'ShowBox' and 'ShowCone' display solid spheres, ellipsoids, cubes, boxes, cylinders, cones, prisms and pyramids. Click Effects > Show solid. Click Help > Play help movie > 'Buckynut Island' for a demonstration (Model+, download from www.yasara.org/movies in YASARA View). |
| 5.9.25 | New Yanaconda function: 'trunc' returns the integer part of a number, rounded towards zero. |
| 5.9.18 | New command: 'MoveMesh' translates a polygon mesh in its local coordinate system to allow off-center rotations. Click Effects > Move > Mesh. |
| 5.9.15 | New command: 'SearchDoc' googles the YASARA documentation. Click Help > Search documentation. |
| 5.9.10 | Improved command: 'Experiment Neutralize' does a better job at keeping original water molecules very close to metal ions instead of replacing them with newly added ones. |
| 5.9.6 | Improved command: 'Link' now uses the atomic bond radii and an 'allowed deviation' parameter to find bonds. The bond orders are also assigned automatically. |
| 5.9.2 | New highlight: The 'pH' command sets the default pH, YASARA now has extensive knowledge about pH dependent bond orders and protonation patters of organic molecules and assigns bond orders and hydrogen atoms according to the chosen pH. Read Commands > Options > Default pH (Model+). |
| 5.8.30 | Improved command: 'SampleLoop' allows to select the preferred secondary structure. |
| 5.8.24 | Improved command: 'LoadPDB' automatically topologyfies ligands in PDB files and assigns bond orders. |
| 5.8.21 | New highlight: The 'TypeBond' command analyzes any organic molecule and assigns fractional bond orders, making it easy to add hydrogen atoms. It is no longer required to manually add topologies for unknown molecules to yasara.def. Read Commands > Edit > Bonds > TypeBonds. |
| 5.8.19 | Improved command: 'AddHyd' contains a new 'update' parameter to adjust bond orders to the newly added hydrogens. |
| 5.8.15 | New feature: Bonds to metals (which are not considered real bonds by MD force fields) are converted to virtual bonds and shown as cylinders when reading/writing PDB files. Read Commands > Edit > Bonds > AddBond. |
| 5.8.10 | Improved command: 'AddBond' now accepts fractional bond orders to express resonance effects and a parameter to update hydrogens. Read Commands > Edit > Bonds > AddBond. |
| 5.8.2 | New highlight: The PovRay interface has been heavily improved and now includes fog, textures (MakeImageObj), fore- and background images (ShowImage), exact background colors and the ability to add outlines for comic style graphics. Read Commands > File > Screenshots > Raytrace. |
| 5.8.1 | Improved command: 'Color' accepts RGB atom colors and finds the closest matching color in YASARA's own color scheme. |
| 5.7.30 | New command: 'SaveMacro' creates a macro that restores selected parts of YASARA's current state: scene, visualization parameters, images, simulation parameters, window parameters. Click Options > Macro & Movie > Save macro. |
| 5.7.29 | Improved command: 'PressCtrl' can exclude axes from rescaling. |
| 5.7.28 | New highlight: The 'Projection' command toggles between perspective and parallel projection. Click View > Projection. |
| 5.7.21 | Improved command: 'RayTrace' and 'SavePOV' now also include the black outline of the comic atom texture (View > Atom appearance > Texture > Comic). |
| 5.7.20 | Improved command: 'AddHyd' automatically corrects bond orders and atom names of carboxyl groups. |
| 5.7.19 | Improved command: 'SaveXTC' and 'LoadXTC' have improved LFS support to handle trajectories larger than 2 GB in Linux. |
| 5.7.18 | New highlight: A new plugin automatically converts OpenOffice/PowerPoint presentations to YASARA movies, which makes it easy to augment them with hi-quality molecular animations. Read Recipes > Create your own YASARA movies > Movies can be imported from OpenOffice and PowerPoint (Model+). |
| 5.7.17 | Improved command: 'Clean' corrects bond orders and atom names of carboxyl groups. |
| 5.6.30 | Improved command: 'AddBond' now gained the 'UpdateHyd' option to suppress the update of hydrogen atoms. |
| 5.6.29 | Improved plugins: Error reports and update requests now function without having to add an email server in plg/reporter.cnf |
| 5.6.23 | Improved command: 'ScaleForce Planarity' now includes not only improper dihedrals, but also normal dihedrals in planar systems. |
| 5.6.21 | Improved multi-monitor support: Set 'CorrectWin' in yasara.ini to 0 to disable the window size correction, which helps if the YASARA window is on monitor 2. |
| 5.6.16 | Improved command: 'WaterDensity' works better in non-periodic cells, where the vacuum layer between cell wall and atoms (caused by repulsive wall forces) is now excluded from the density calculation. |
| 5.6.14 | Improved command: 'PressureCtrl' now rescales only the simulation cell and not the atom coordinates if there are atoms outside a non-periodic cell. |
| 5.5.25 | Improved command: 'BuildMol' now also reads FASTA sequences to build a linear peptide chain (Model+). |
| 5.5.22 | New highlight: The 'Volume' command calculates VdW, molecular and solvent accessible volumes. Click Analyze > Volume of (Model+). |
| 5.5.20 | New command: 'ScaleForce' scales bond, angle, dihedral, planarity and non-bonded forces during a simulation. Click Simulation > Scale forces. The commands ScaleBSFC and ScaleNBI are now deprecated (Dynamics+). |
| 5.5.18 | New feature: Yanaconda macros can contain 'include' statements to include other macros (read Macros > Yanaconda macros can include each other). |
| 5.5.16 | Improved commands: 'CorrectIso' and 'CorrectCis' use a new dihedral-angle based algorithm to enforce correct stereochemistry during high temperature simulations. |
| 5.5.13 | New command: 'NiceOri' orients an object nicely (along its major axes). Click Effects > Orientation > Set nicely for object (Model+). |
| 5.5.12 | Improved command: 'CorrectCis' allows to exclude proline residues from cis-peptide bond correction. |
| 5.5.9 | Improved command: 'Clean' swaps methylene hydogens to match PDB/XPLOR conventions for stereoassigned NOEs. |
| 5.5.1 | Improved force field parameter assignment for DNA/RNA bases. |
| 5.4.5 | New IMPORTANT feature: YASARA's internal force field representation has been changed. If you modified force fields, recompile them with 'yasara -upd' now. |
| 5.3.31 | Improved command: OpenBabel export with 'Save*' now offers a 'transform' option to restore original atom coordinates and a 'nameformat' option to choose among different atom naming conventions. A few OpenBabel for Windows issues have been fixed. |
| 5.3.30 | New feature: the order of covalent bonds can be shown in Ball&Stick style with 'ColorBonds Order'. |
| 5.3.28 | Improved command: 'SavePDB' allows to select the YASARA PDB format variant in addition to PDB standard and Xplor. |
| 5.3.20 | New IMPORTANT feature: The conventions for triclinic (=non-rectangular) simulation cells have been changed to match the PDB format. .sce or .sim files with non-rectangular cells have to be converted. Please update YASARA Dynamics (as a bonus, the PME code runs a bit faster now). |
| 5.2.28 | Improved detection of unusual DNA/RNA bases to display them as part of the DNA/RNA backbone. |
| 5.2.26 | New command: 'SecStr' assigns a custom secondary structure and analyzes the secondary structure content. The commands 'ShowSec' and 'HideSec' changed their names to 'ShowSecStr' and 'HideSecStr'. Click Analyze > Secondary structure of. |
| 5.2.24 | New feature: OpenBabel has been updated to version 1.100.2, the command 'Save*' now also exports atom charges assigned by the current force field. Click File > Save as > Other fileformat. |
| 5.2.17 | Improved command: If there are residues with alternate locations, 'Clean' keeps only the one with highest occupancy. |
| 5.2.13 | New highlight: The 'Check' command performs 20+ different WHAT_CHECKs of protein structures: bonds, angles, torsions, omega angle, Ramachandran plot, side-chain rotamers, proline rings, chirality, planarity, backbone conformation, peptide-plane flips, bumps, 3D packing quality, inside-outside distribution, unsatisfied H-bonds, flipped Asn/Gln/His side-chains, B-factors and atom occupancies. Click Analyze > Check (Twinset). |
| 5.2.11 | New command: 'PointPar' sets the style and thickness of point/wireframe objects (ShowESP,ShowSimGrid,WHAT IF MolObjects). Click View > Point & line appearance. |
| 5.2.9 | New highlight: The 'Align' command performs a structural alignment with the MOTIF algorithm. Click Analyze > Align (Twinset). |
| 5.2.7 | Improved command: 'LoadPDB' now searches a local PDB automatically if 'PDBPath' is defined in yasara.ini |
| 5.2.5 | New highlight: The 'OptHyd' command optimizes the hydrogen bonding network and flips Asn/Gln/His side-chains if that improves the network. Click Edit > Add > hydrogens to: object & optimize (Twinset). |
| 5.2.3 | Improved command: 'SaveMPG' now uses a quality instead of bitrate setting, which avoids encoding failures with some animations. |
| 5.2.1 | New highlight: The 'Regularize' command optimizes bond lengths, angles and chirality. Click Edit > Geometry > Regularize (Twinset). |
| 5.1.30 | Improved commands: 'Raytrace' and 'SavePOV' now also work in console mode, e.g. on a web-server creating molecular graphics with YASARA. |
| 5.1.28 | New highlight: The 'ShowRota' command shows the backbone dependent rotamer distribution for selected residues. Click Analyze > Rotamers (Twinset). |
| 5.1.21 | Improved command: 'ScreenSize' also works in console mode and defines the aspect ratio of ray-traced output. |
| 5.1.20 | Improved selection language: the 'Property' operator selects atoms by their property value. |
| 5.1.19 | Improved command: 'ColorPar' can change the default color range for atom properties. |
| 5.1.18 | New command: 'Prop' gets and sets the new atomic property value that maps to WHAT IF's 'atomic value' and becomes very helpful in the Twinset. |
| 5.1.17 | Improved command: 'PosAtom' now also gets/sets atom positions in the global coordinate system. |
| 5.1.12 | Improved command: 'SaveXTC' wraps molecules around periodic boundaries to avoid saving 'broken' ones with bonds that span the simulation cell. |
| 5.1.11 | Improved command: 'TransferObj' can now also correctly transfer static surfaces and similar geometry to another coordinate system. |
| 5.1.10 | Improved commands: 'LoadSim' and 'LoadXTC' now have an option to disable secondary structure reassignment. |
| 5.1.9 | Improved commands: 'RayTrace' and 'SaveMPG' allow to disable the PovRay window. |
| 5.1.5 | New highlight: The 'SaveMPG' command creates MPEG movies, plain or ray-traced. Click File > Save as > MPEG movie (Model+). |
| 4.12.31 | Improved support for resolution independent movies. See Recipes > Create movies > The look of the movie. |
| 4.12.29 | Improved command: 'LoadXTC' applies the transformation history of the target object to avoid unwanted shifts. |
| 4.12.25 | New highlight: The 'SolvEnergy' command calculates solvation energies using a fast boundary element approach. Click Analyze > Energy > Solvation (Dynamics+). |
| 4.12.19 | Improved commands: 'AddHyd' and 'Clean' make better choices when inventing hydrogen names. |
| 4.12.17 | Improved command: 'Label' supports new format components: OBJNAME,OBJNUM,ATOMNAME and ATOMNUM. Click Effects > Label. |
| 4.12.15 | New highlight: YASARA now supports copy&paste, the console at the bottom has been heavily improved with history and selections. Click Essentials > The keys and mouse buttons > Using the console. |
| 4.12.13 | Improved commands: 'ListCon' and 'ListHBo' now also return the selected units, e.g. atomlist()=ListConAtom Mol A,Mol B. |
| 4.12.11 | New command: ConsolePar changes the size and font of the extended console (press <Space> twice to bring it up). Click Window > Console > Parameters. |
| 4.12.9 | Improved selection operators: 'with distance' and 'with atoms among' now consider periodic boundaries during a simulation. |
| 4.12.7 | Improved command: 'Experiment Neutralization' does a better job at reaching the requested water density. |
| 4.11.30 | Improved secondary structure assignment for double beta bulges. |
| 4.11.29 | Improved support for hires notebook screens up to 1680x1050. |
| 4.11.24 | New feature: hydrogen bonds can now inherit the color of the bound atoms, click View > Color > Hydrogen bonds. |
| 4.11.23 | Improved quad-buffered stereo and ray-tracing of stereo images. |
| 4.11.14 | New command: 'FlipTab' flips a pair of table axes (columns, rows, pages). Click Options > Tables > Flip. |
| 4.11.13 | New feature: YASARA can now work with 250 objects at the same time (Model+) |
| 4.11.12 | Improved commands: 'Sup' and 'RMSD' calculate all permutations if several objects are selected and support a 'unit' parameter. Averages and standard deviations are no longer returned. |
| 4.11.11 | New Yanaconda functions: 'mean' and 'stddev' calculate the average and standard deviation of a list. |
| 4.11.10 | Improved command: 'Center' now also allows to center on atoms, residues and molecules. E.g. click Center > Atom in the atom context menu. |
| 4.11.9 | New highlight: Tables have been reimplemented and heavily improved. They can now be one-, two- or three-dimensional. The 'ShowTab' command visualizes tables using various styles. Click Options > Table > Show. |
| 4.11.8 | New command: 'MakeTab' creates a new table with one to three dimensions. Click Options > Table > Make. |
| 4.11.7 | New command: 'DelTab' deletes tables. Click Options > Table > Delete. |
| 4.11.7 | New command: 'Tab' sets or gets table cells, columns, rows, pages and entire tables. Click Options > Table > Set/get cells. |
| 4.11.6 | New command: 'Tabulate' adds new cells to a growing table and replaces the deprecated 'AddTab' command. |
| 4.11.6 | New command: 'SelectTab' selects a table for use by the new 'Tabulate' command. Click Options > Table > Tabulate. |
| 4.11.5 | New command: 'LoadTab' loads a table in plain text format from disk. Click Options > Table > Load. |
| 4.11.5 | Improved command: SaveTab allows to select a table, which supports the forthcoming release of heavily improved tables. This is one of the rare changes that are not backwards compatible but required for consistency. |
| 4.11.4 | Improved plugin: Emmanuel Bettler added an option to check for YASARA updates. Click Help > Check for update. |
| 4.11.3 | Improved command: 'Link' now also assigns the order of covalent bonds for residues with topology information in yasara.def. |
| 4.11.1 | Improved command: 'FillCellObj' allows to define the maximum allowed sum of bumps. |
| 4.10.31 | New Yanaconda functions: 'sum' and 'average' sum up list elements and calculate the average. |
| 4.10.30 | Improved windows: all load/save dialogs have been enlarged so that long filenames are easier to read. |
| 4.10.29 | New command: 'Radius' calculates Van der Waals radii. Click Analyze > Radius of. |
| 4.10.28 | Improved commands: 'Occup' and 'BFactor' now allow to set unusual atom occupancies and B-factors from -99.99 to 999.99 for programs that expect different data like charges and radii in these columns of the PDB file. |
| 4.10.24 | New feature: YASARA now reads gzip compressed files (.gz extension) transparently. Time to compress your local copy of the PDB? |
| 4.10.21 | New command: 'MouseWheel' assigns one of four functions to the mouse wheel. Click Window > Mouse wheel command. |
| 4.10.20 | New command: 'SavePower' enters a special power saving mode for notebooks running on battery. Click Window > Save power. |
| 4.10.19 | New command: 'WinFont' changes the fonts used by YASARA's window manager. Click Window > Font. |
| 4.10.16 | New highlight: The 'FirstSurf' command combined with the new selection operators 'with distance from surface' and 'with contribution to surface' enables very flexible surface analysis. See Commands > Analyze > Surfaces > FirstSurf (Model+). |
| 4.10.15 | Improved command: 'Color' now returns the colors of the selected atoms: collist() = ColorAtom Obj 1crn |
| 4.10.14 | New Yanaconda feature: You can now loop over the content of a file, e.g. a list of PDB IDs: for id in file /home/id.txt, see Macros > There a four types of loops > Loops can run over a list. |
| 4.10.13 | Improved secondary structure assignment for some beta bulges. |
| 4.10.4 | New feature: 'yasara -txt' runs the program in plain text mode, see Essentials > Running YASARA in special environments > Running without graphics. |
| 4.10.3 | New movie available: 'PhD defence', a summary about the technology and science behind YASARA at www.yasara.org/multimedia. |
| 4.10.2 | Improved filename handling: loading a file with missing extension is now possible, and the working directory is searched before any subdirectories. |
| 4.10.1 | New feature: The mouse wheel scrolls through lists and selects the previous and next atoms. |
| 4.8.31 | Improved command: 'AddSpring' can now add springs to atoms without intramolecular interactions (ions). |
| 4.8.27 | Improved selection language: 'LocalX|Y|Z' and 'GlobalX|Y|Z' allow to select atoms by their positions. Selections by 'BFactor' and 'Occupancy' are now also possible. |
| 4.8.26 | New highlight: Emmanuel Bettler contributed a Linux plugin to create MPEG movies and animated GIFs. Click File > Save as > MPEG/GIF movie. |
| 4.8.24 | Improved command: 'SwapRes' can now also swap non-standard amino acids like seleno-methionine. |
| 4.8.22 | New highlight: Mikael Roche & Emmanuel Bettler developed a structural alignment plugin using SHEBA (by J.Jung & B.Lee). Click Analyze > Superpose > Objects automatically (Linux only). |
| 4.8.18 | New command: 'ColorPar' sets various default color schemes for chemical elements, secondary structure, B-factors. Click View > Color > Parameters. |
| 4.8.18 | Improved command: 'Zoom' now also considers the visibility of surfaces when fitting atoms on the screen and is much faster for large proteins. |
| 4.8.17 | Improved command: 'RayTrace' does a better job putting special textures (selected with 'AtomTexture') on the atoms |
| 4.8.13 | New command: 'PrintHUD' allows plugins to print to YASARA's head-up-display and is now also available in YASARA View. |
| 4.8.13 | New highlight: Several improvements make building small molecules very easy. Get an update and watch the new help movie 'Building small molecules' (Model+). |
| 4.8.12 | Improved command: 'AddBond' now automatically adapts the hydrogen atoms (if the object contains any) to the new bond order. |
| 4.8.8 | New feature: Python plugins can be run directly from the command line: yasara MyPlugin.py MyRequest ('MyRequest' is sent to the plugin, no selections are available). |
| 4.8.8 | Improved plugin: The PDBFinder2 plugin to analyze proteins now uses the BioASP server at www.bioasp.nl |
| 4.8.6 | New command: 'AddHydAtom' allows to add hydrogens to individual atoms, e.g. to quickly force Histidine protonation. |
| 4.8.3 | Improved command: 'AddHyd' is orders of magnitude faster now and places aliphatic hydrogens more intelligently. |
| 4.7.21 | Improved command: 'FillCellWater' and 'Experiment Neutralize' are now less likely to place waters inside homology models with a loose core packing. The second parameter had to be changed. Post-processing steps to delete these waters are not absolutely required anymore. |
| 4.7.18 | New Python plugin command: yasara.Finish() synchronizes the plugin with YASARA, more info at Plugins > Python plugins run in a separate thread |
| 4.7.10 | Improved sequence selector: atoms behind it are clickable while the sequence selector is transparent. |
| 4.7.4 | New highlight: A 'neutralizing plasma' allows to run Particle Mesh Ewald simulations also with non-neutral simulation cells. Simulation algorithms and energy calculations have been improved and run a bit faster now. Update now! |
| 4.7.3 | Improved command: 'Surf' calculates surface areas 0.1% more accurately. |
| 4.6.25 | Renumbering residues is now restricted to the 'RenumberRes' command. To renumber the residues in object 1crn, type 'RenumberRes Obj 1crn'. The shortcut 'RenumberObj 1crn' is deprecated. |
| 4.6.18 | New movie feature: When a movie ends (or you click on Options > Macro & Movie > Stop), the scene including background colors+working directory is restored. To avoid that, run the movie as a macro. |
| 4.6.17 | New command: 'ShowCom' opens the documentation for a given command in the browser. |
| 4.6.16 | Improved command: The default Calpha color 'cyan' is now passed on to the ribbon/tubes/cartoons if all backbone atoms are cyan, not only if all residue atoms are cyan. |
| 4.6.15 | New command: 'ShowDoc' opens the documentation in a browser window. |
| 4.6.14 | Improved commands: During a simulation, static surface objects ('ShowSurf') and calculated surface areas ('Surf') consider all objects simultaneously. |
| 4.6.7 | Improved command: 'CenterAll' centers all objects together, which keeps the superposition intact after loading multiple PDB files with centering disabled. |
| 4.6.5 | Improved command: 'LoadPDB' handles incorrect/single-sided CONECT records. |
| 4.6.1 | Improved commands: 'AddHyd' and 'Clean' now do a better job when working with alternate atoms and Val/Leu residues with swapped CG/CD atom names. |
| 4.5.20 | New highlight: Support for Spaceball 3D input devices has been added (Linux only for now). Click Window > Spaceball to adjust the settings (Model+). |
| 4.5.19 | New commands: 'GrabNext' and 'GrabPrev' grab the next and previous object for movement with mouse or SpaceBall. Helpful when assigned to SpaceBall buttons (Model+). |
| 4.5.18 | Improved command: 'Clean' now automatically deletes bonds to cations, which may not be present during simulations. |
| 4.5.17 | New optimized algorithms for several tasks that became bottle-necks when working with giant structures (300000 atoms). Many things run 100x faster now. See also the hints at Essentials > Working with extremely large structures. |
| 4.5.12 | Improved support for NFS mounted multi-user installations: In the docs, click Essentials > Running YASARA in special environments. |
| 4.5.12 | New release of the YASARA Models@Home distributed computing system with support for Redhat 9, Fedora Core, Mandrake 9, Windows XP. |
| 4.5.11 | New highlight: Three new surface movies available from www.yasara.org/movies: Introduction, Environments and Electrostatics. |
| 4.5.11 | Improved command: 'CountObj' now counts all objects, not just those with atoms. |
| 4.5.10 | New highlight: The 'ShowSurf' command shows Van der Waals, molecular and solvent accessible surfaces, either static or dynamically updated. |
| 4.5.9 | Improved command: 'MarkAtom' can now mark up to four atoms. |
| 4.5.8 | New highlight: The 'ColorSurf' command assigns surface colors and transparency, options include coloring by atom and electrostatic potential. |
| 4.5.7 | Improved selection language: 'with <>X bonds to' allows to select by the number of bound atoms. |
| 4.5.6 | New highlight: The 'SurfPar' command sets the surface resolution and activates an interface to Michel Sanner's MSMS program which calculates analytic molecular surfaces. |
| 4.5.4 | New highlight: The 'Surf' command allows to calculate VdW, molecular and solvent accessible surface areas (YASARA Model+). |
| 4.5.3 | Improved handling of unusual amino acids: even those forgotten in the official PDB hetgroup dictionary are recognized correctly. |
| 4.5.3 | New highlight: The 'AddEnv' and 'RemoveEnv' commands allow to define surface environments to analyze partial surfaces (YASARA Model+). |
| 4.5.2 | Improved experiment: 'Experiment Minimization' converges faster now. |
| 4.5.1 | Improved selection language: 'visible' and '!visible' allow to select (in)visible atoms. |
| 4.4.30 | New Yanaconda operator: Like in Python, '//' performs a division with truncation of the result's fractional part, e.g. 3//2 = 0 |
| 4.4.29 | Improved logs: Specifying a filename with .log extension as a command line argument will automatically record a log. |
| 4.4.28 | Improved command: Logs recorded with 'RecordLog' are now flushed continuously and do not lag behind. |
| 4.4.25 | New Yanaconda function: 'onein' returns a random list element. |
| 4.4.15 | Improved command: 'Clear' now also clears the 'Tabulate'/'SaveTab' table. Use 'Del' instead of 'Clear' when adding values to a table. |
| 4.4.14 | Improved command: 'Tabulate' now accepts an arbitrary number of values to add to a table. |
| 4.4.12 | New command: 'SpeedUp' allows to toggle the speedup of movements when graphics are slow |
| 4.4.9 | Improved documentation: Click Commands > Index to get an alphabetic list of all YASARA commands |
| 4.4.7 | Improved installation: In Linux, you can now install YASARA as user A (e.g. 'root') and then work as user 'B' as long as you run it once as user 'A'. |
| 4.4.3 | Improved Yanaconda macro language: up to 1000 times faster (better list handling, reduced printout in the console) |
| 4.4.3 | Improved command: 'AddObj' returns the numbers of the first and last atom in the newly added object, e.g. first,last=AddObj 7 |
| 4.4.2 | Improved command: 'SplitObj' and 'OligomerizeObj' return a list of created objects, e.g. objlist()=SplitObj 5 |
| 4.4.2 | New Yanaconda feature: iterate over a list, e.g. selection()=ListAtom CA / for atom in selection |
| 4.4.1 | Improved command: 'ListAtom' and 'ListObj' return a list of atom and object numbers. |
| 4.4.1 | New Yanaconda feature: Assign the return values of YASARA commands to a list, e.g. mylist()=ListAtom CA |
| 4.4.1 | Improved command: 'MakeImageObj' returns the number of the created image. |
| 4.3.26 | Improved help movies: the 'OnError Continue' command makes sure that they will not stop if you make an error. |
| 4.3.16 | New ATI Radeon Linux HOWTO (click Troubleshooting>YASARA runs slowly), workaround for a Radeon Linux driver bug in 'ShowMessage'. |
| 4.3.14 | New highlight: A plugin for Bert de Groot's CONCOORD program allows to quickly sample conformational space and analyze protein flexibility. Click Edit > Sample. |
| 4.3.14 | New Yanaconda functions: 'min MyList' and 'max MyList' return the smallest and largest list element. |
| 4.3.13 | Improved command: 'Span' can now also determine the first and last residue number in a selection |
| 4.3.13 | New command: 'BFactor' gets and sets the BFactor. |
| 4.3.13 | Improved command: 'Temp' now also returns the current simulation temperature (YASARA Dynamics+) |
| 4.3.12 | New command: 'Charge' gets and sets the net charge. The old command 'NetCharge' is now deprectated (YASARA Dynamics+) |
| 4.3.12 | Improved command: 'Color' can now color by atom occupancy. |
| 4.3.12 | New command: 'Occup' gets and sets the atom occupancy. |
| 4.3.1 | Improved plugin support: 'NumberInputMenu[1-6]' allows to input 1 to 6 numbers and pass them to the plugin. |
| 4.2.27 | Improved commands: 'LoadSce', 'LoadPDB' and several other commands are now much faster for large files. |
| 4.2.15 | Workaround for an ATI Radeon Linux driver bug that caused color problems and showed random triangles (verified for fglrx 4.3.0-3.7.0 and Radeon 9600Pro) |
| 4.2.14 | New Yanaconda functions: 'sqr X' function returns X*X, 'cube X' function returns X*X*X |
| 4.2.11 | New command: 'Transfer' an object to the coordinate system of another object (e.g. if you moved one of two superposed objects away and want to get it back). |
| 4.2.1 | Improved command: 'AtomSize' can now freely change the atom sizes, which is the same as moving the near clipping plane. Helpful when cutting surfaces open. |
| 4.2.1 | Inconvenience solved: Showing just the side-chain and CA atom (e.g. in a ribbon) is now trivial (click on 'Show atoms'). |
| 4.1.25 | Improved pKa prediction accuracy in the 'Neutralization' experiment (YASARA Dynamics+) |
| 4.1.15 | Workaround for a SiS OpenGL driver bug that crashed YASARA (verified for SiS 650M chipset) |
| 3.12.24 | New Yanaconda functions: 'abs' function returns absolute values, 'sign' returns the sign (-1,0 or 1) |
| 3.12.23 | Improved command: 'Clean' automatically corrects CG/CD atoms in Val/Leu that got swapped. |
| 3.12.21 | Improved secondary structure assignment for wrong structures with lots of bumps. |
| 3.12.18 | New command: 'Span' allows to determine the first and last atom or object spanning a selection. Very useful in macros. |
| 3.12.11 | Command line arguments that do not end in .mcr, .yob, .sce are assumed to be PDB files and loaded instantly. |
| 3.11.24 | Improved command: 'DelLink' now handles problems caused by incorrect PDB files with single-sided bonds. |
| 3.11.23 | New plugin support: Python error messages are now displayed directly on screen including a traceback, also under Windows. |
| 3.11.17 | New highlight: The 'SwapAtom' command now also adjusts the bond lengths, making building easier. E.g. to add a methyl group to a hydroxyl group, just swap the hydroxyl hydrogen to carbon. |
| 3.11.16 | New command: 'UserInput' allows to disable disturbing user input during a non-interactive movie. |
| 3.11.16 | Improved command: 'RayTrace' now also works for electrostatic potentials and simulation grids. |
| 3.11.14 | New command: 'OnError' allows to handle errors in a running macro. This command replaces 'ErrorExit', which is now deprecated. |
| 3.10.27 | New command: 'RequireVersion' allows to check if a minimum YASARA version is installed. |
| 3.10.26 | New plugin support: Various workarounds for bugs in Windows solve some cases where Python plugins could not be run. |
| 3.10.26 | New graphics engine: YASARA now runs better on old cards, especially those with Riva TNT chips. |
| 3.10.25 | Improved command: 'Cell' now also returns the coordinates of the cell center and can be used to create non-centered cells (YASARA Dynamics+). |
| 3.10.24 | New Yanaconda function: 'rnd' function returns random numbers, variables 'Linux' and 'Windows' define operating system. |
| 3.10.20 | Improved command: 'MakeTextObj' returns the number of the created object (YASARA Model+). |
| 3.10.19 | New highlight: Distances, angles and dihedrals can be changed interactively by marking up to four atoms and clicking on 'Geometry' in the atom context menu (YASARA Model+) |
| 3.10.19 | Improved command: 'Distance', 'Angle' and 'Dihedral' can now actively change the geometry. |
| 3.10.17 | Improved command: 'CheckCis' and 'CheckIso' can now be applied to individual residues, e.g. non-prolines |
| 3.10.16 | New command: 'Count' the number of atoms to objects that are contained in a selection. |
| 3.10.15 | Improved feature: Macros can now use the predefined variables 'Residues' and 'Objects' (in the soup). |
| 3.10.15 | Improved command: CheckCis and CheckIso now return the number of cis-peptide bonds or wrong isomers. |
| 3.10.15 | Improved feature: Press <CTRL>+<M> to rerun the last macro, including those chosen from the command line. |
| 3.10.15 | New feature: RightClick in the VISibility column of the 'Scene Content' head-up-display to switch all other objects off. |
| 3.10.11 | Improved plugin: The error report plugin adds an option to request YASARA updates from the Help menu. |
| 3.10.11 | New command: 'RenameSeg' allows to change the segment ID for an atom selection. |
| 3.10.11 | Improved selection syntax: the 'not' operator allows to negate entire selection blocks. |
| 3.10.10 | New loop database (YASARA Structure). |
| 3.10.10 | Improved support: ATI Radeon 9600 cards under Linux now fully tested. |
| 3.10.5 | New highlight: Press the top right button in the sequence selector to display structural alignments. |
| 3.10.5 | Important bug fix: Playing YASARA Movies from YASARA View works again. Click Help > Play movie > 'Interactive Simulations for Modeling'. |
| 3.10.4 | Improved secondary structure assignment for unusual helices. |
| 3.9.24 | Improved command: LoadPNG now imports the alpha channel as well. |
| 3.9.23 | New command: 'UnrestImage' lets an animated image disappear immediately (YASARA Model+). |
| 3.9.19 | Improved command: PlayMacro and PlayMovie can be repeated by pressing <Ctrl>+<M> |
| 3.9.11 | Improved graphics: If an atom makes more than four bonds (defined via CONECT records in the PDB file), YASARA makes a better choice which four bonds to show. |
| 3.9.10 | Improved command: 'Link' uses more sensitive cutoffs when searching for bonds. |
| 3.9.8 | Improved PDB writer: If multiple NMR models are saved in one PDB file, the CONECT records are now collected at the end and atom numbers do not restart at 1. |
| 3.9.8 | Improved PDB reader: Single amino acid ligands are graphically displayed as HetGroups and not linked if they have both C-terminal oxygens |
| 3.9.8 | Improved command: 'Clean' now replaces missing backbone oxygens including both C-terminal ones |
| 3.9.7 | New command: 'Move<Atom|Res|Mol>' moves atoms in the local coordinate system of an object |
| 3.9.7 | New command: 'SwapImage' changes the priority of bitmaps when displayed on screen |
| 3.9.3 | New plugin: Interface to the PDBFinder2 database. Click Analyze->PDBFinder2 to color your protein according to HSSP sequence conservation, entropy and PDBReport quality indicators. |
