CAP - Catabolite gene Activating Protein (1BER)

Endonuclease PvuII bound to palindromic DNA recognition site CAGCTG (1PVI)

GCN4 - leucine zipper transcription factor bound to palindromic DNA recognition site ATGAC(G)TCAT (1YSA)

Your guide to YASARA View

°

Essentials

-

What you really have to know

°

Selections

-

Tell YASARA what you want

°

Commands

-

Tell YASARA what to do

°

-

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

°

-

Change content and properties of the soup

°

-

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.

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 (including the loop database) 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

°
BuildLoopDB
-
Build loop data base

°
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
-
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

°
GroupAngle
-
Get angle between two atom groups

°
GroupDihedral
-
Get dihedral angle between two atom groups

°
GroupDistance
-
Get distance between two atom groups

°
Optimize<Res|Mol|Obj|All>
-

Optimize molecular geometry

°
Radius<Atom|Res|Mol|Obj|All>
-

Calculate the VdW radius

°
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 .

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

°

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

°
Superposition
-
Align atoms and calculate RMSDs

Superpose objects based on a selected set of atoms and calculate the resulting RMSDs . Structures can be aligned automatically in the Twinset.

°
AlignObj
-

Align objects

°
RMSD<Atom|Res|Mol|Obj>
-

Calculate RMSDs

°
Sup<Atom|Res|Mol|Obj>
-

Superpose 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
-
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.

°
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

°
Optimize<Res|Mol|Obj|All>
-

Optimize molecular geometry

°
Radius<Atom|Res|Mol|Obj|All>
-

Calculate the VdW radius

°
Regularize<Obj|All>
-

Regularize covalent geometry

°
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

°
Soup 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.

°
BallRadius
-
Set ball radius 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 scene

°
Pos<Obj|All>
-

Set/get object or scene position

°
Orientation
-
Orient and rotate objects

Orient or rotate objects, continuously, until a certain orientation is reached or to a nice view.

°
AutoRotateTo<Obj|All>
-

Rotate objects or scene automatically to a certain orientation

°
AutoRotate<Obj|All>
-

Rotate objects or scene automatically

°
NiceOri<Obj|All>

-

Orient objects nicely

°
Ori<Obj|All>
-
Set/get object or scene orientation

°
Rotate<Obj|All>
-

Rotate objects or scene

°
Labels
-
Display text labels

Label anything from atoms to the entire scene and distances, change the label style including font, color or perspective, finally delete atom- and distance labels again.

°
LabelDis
-
Label atom distances

°
LabelPar
-

Set label parameters

°
Label<Atom|Res|Seg|Mol|Obj|All>
-

Add labels

°
UnlabelDis
-

Delete distances labels

°
Unlabel<Atom|Res|Seg|Mol|Obj|All>
-

Delete labels

°
Marks and zooms - Mark atoms with fireflies and zoom in

Mark one atom and display its properties in the head up display, then zoom in closely on one or more atoms .

°
MarkAtom
-

Mark atom with fireflies

°
Zoom<Atom|Res|Mol|Obj|All>
-

Zoom in on atoms

°
Arrows
-

Show arrows connecting atoms or points

Show arrows and hide those connecting atoms and those connecting points.

°
HideArrow<Atom|Res|Mol|Obj|All>
-

Hide arrows

°
ShowArrow
-
Show arrows between atoms or points

°
Solids
-
Show spheres, boxes, pyramids, cylinders, tori and others

Show solid spheres & ellipsoids, boxes & cubes, cones, cylinders, pyramids & prisms or a torus.

°
ShowBox
-
Show a rectangular box

°
ShowCone
-

Show a cone, cylinder, pyramid or prism

°
ShowSphere
-

Show a sphere or ellipsoid

°
ShowTorus
-
Show a torus

°
Images
-

Show and animate bitmaps

Load a bitmap in Windows BMP- or PNG-format, show it on screen , move it around or do more complicated animations and let the image disappear again. You can also swap images, attach them to objects , toggle fogging, hide them and finally delete them.

°
AnimateImage
-
Animate appearance and disappearance of images

°

AutoMoveImage
-
Move images automatically

°
DelImage
-

Delete images

°
HideImage
-
Hide images

°
ImageFog
-

Switch image fog on/off

°
LoadBMP
-
Load image from BMP file

°
LoadPNG
-

Load image from PNG file

°
MakeImageObj
-
Make object with attached image

°
ShowImage
-
Show images

°
SwapImage
-

Swap images

°
UnrestImage
-
Let animated image disappear

°

Text
-
Print text, possibly in 3D letters

By default, printing is done to the console. To get fancier text output, create a text object and redirect printing . Choose a font, possibly with fog , position the cursor, then print three-dimensional characters . When writing a plugin or macro, it sometimes helps to show a text message at the bottom and hide it afterwards, show a button to click or print to the top right head up display .

°
Font
-

Set font for 3D letters

°
FontFog
-
Switch font fog on/off

°
HideMessage
-

Hide text message at the bottom

°
MakeTextObj
-
Make text object to print 3D letters

°
PosText
-
Position and justify text

°
Print
-

Print text

°
PrintCon
-
Print to console

°
PrintHUD
-

Print to head up display

°
PrintObj
-
Print to text object

°
ShowButton
-

Show clickable button

°
ShowMessage
-
Show text message at the bottom

°

Options

-

Other commands

°

Experiments

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Let YASARA cook for you

Some things are non-trivial. Nevertheless, YASARA delivers the answer at the touch of the 'Experiment' button. During an experiment, YASARA takes over control and uses its 'artificial intelligence' to do various things in the right order. A message at the bottom will keep you informed. Some experiments accept additional parameters, look at the example macros to see how it works.

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Experiment
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Choose and control experiments

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Macros
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Watch YASARA do the work for you

Save YASARA's current state in a macro or record your input as a macro (excluding mouse movements), play back your own macros or those made by others with a higher stage of YASARA, stopping whenever you want. You can use the back/forward icons in the top right corner to jump around in the macro. Macros can wait for certain events before they continue, raise errors if something goes wrong, take a certain action if an error occurs, disallow user input, speedup animations if the graphics get slow , require a minimum YASARA version, and be applied to a certain target. You can save a lot of time by running macros in text console mode (start YASARA with command line parameter -con).

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Go
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Go to another position in the macro

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MacroTarget
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Set macro target

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OnError
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Set error action

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PlayMacro
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Play back macro

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PlayMovie
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Play back macro as a movie

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RaiseError
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Display error message

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RecordMacro
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Record all following commands in a macro

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RequireVersion
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Require a minimum YASARA version

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SaveMacro
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Save a macro to restore the current state

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SpeedUp
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Speed up movements when graphics are slow

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StopMacro
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Stop macro playback or recording

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UserInput
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Set user input

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Wait
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Wait for certain time period or condition

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Tables
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Collect, visualize and export data

When analyzing data, you often want to visualize it. This is achieved by creating a one-, two- or three-dimensional table , selecting it for data collection, tabulating the results and showing a graphical representation of the data . Tables can also be listed and manipulated on the column, row and page level, flipped, deleted entirely, imported and exported for use with other programs like Excel and XMGrace.

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Tabulate
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Add cells to table

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DelTab
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Delete tables

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FlipTab
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Flip table axes

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LoadTab
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Load formatted table

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MakeTab
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Make a table

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SaveTab
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Save formatted table

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SelectTab
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Select table to add cells

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ShowTab
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Show table data as 3D object

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Tab
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Set/get table cells

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Formats
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Choose the residue output format

Many commands output a list of residues. Change the format for residue names if you log this output.

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FormatRes
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Format residue output

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Logs
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Redirect output to a file

Many YASARA commands, especially those in the Analyze section, write their output to the console. You can log all output or just the result of the next command to a file and stop logging at a later point.

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LogAs
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Log output of next command

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RecordLog
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Record all console output in a log file

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StopLog
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Stop log recorder

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Plugins
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Run plugins from a macro

Normally plugins are run by clicking on the options they add to the menus. In some rare cases, it may help to create a plugin input file and then run a plugin directly. If there is a bug in the plugin and it crashes, you must additionally stop it before it can be run again.

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RunPlugin
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Run Python plugin

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SavePLI<Atom|Res|Mol|Obj>
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Save plugin input file

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StopPlugin
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Stop running plugin

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Default pH - Set the H+ ion concentration and residue pKas

YASARA normally assigns bond orders and protonation patterns according to pH 7.0. Here you can change this value and also assign pKas to certain residues, overriding YASARA's predictions made during the neutralization experiment.

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pH
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Set/get default pH

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pKaRes
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Set/get residue pKa

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Quantum mechanics - Configure YAPAC

YASARA provides semi-empirical quantum chemistry based on YAPAC, a derivative of James Stewart's MOPAC. Choose one of the MNDO, AM1 or PM3 methods, optimize geometries (possibly in water) and calculate formation energies .

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QuantumMechanics
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Set quantum mechanics method

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Coordinate system - Live in a left or right handed world

YASARA's default is a left-handed coordinate system, feel free to live in a right-handed world .

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CoordSys
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Set coordinate system

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Units
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Choose your favorite units

By default, YASARA displays energies in kJ/mol. Here you can switch to kcal/mol .

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EnergyUnit
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Set energy unit

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Parallel computations - Configure multi CPU core usage

Today's CPUs contain more than one core to speed up calculations. Here you can change the number of CPUs YASARA should use.

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Processors
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Set/get number of processors to use

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Input devices - Configure the interaction with YASARA

Choose between three different pointer styles , change the function of the mouse wheel , activate the P5 data glove or configure the Spaceball and its buttons .

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MouseWheel
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Assign command to mouse wheel

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P5
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Set state of p5 data glove

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PointerStyle
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Set style of mouse pointer

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SpaceballButton
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Assign command to Spaceball button

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SpaceballPar
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Set Spaceball parameters

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Shell
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Execute shell commands

Change or print your current working directory, delete files, get their size or run any other shell command.

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CD
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Change working directory

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DelFile
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Delete file on disk

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FileSize
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Get file size

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PWD
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Print working directory

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Shell
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Execute shell command

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Window

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Change the display properties

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Location

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Place the YASARA window

The YASARA window can be resized , cover the entire screen and be fixed on one of multiple connected screens .

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FullScreen
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Switch fullscreen mode on/off

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Screen
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Fix YASARA window on a certain screen

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ScreenSize
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Set/get window and fullscreen size

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Menus
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Change the appearance of menus

Adapt the style to match your operating system, animate windows in various ways, choose your favorite background texture and font, or hide all menus , including the head up display and the sequence selector at the bottom.

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AnimateWin
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Animate Windows

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HUD
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Switch head up display

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Menu
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Switch menu on/off

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SeqSelector
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Switch sequence selector on/off

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StyleWin
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Style Windows

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WinFont
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Set window font

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WinTexture
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Set window background texture

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Console
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Configure the console

YASARA's command console can be extensively configured and hidden to speed up calculations and movies. Several console functions like copy/paste are explained here.

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Console
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Switch console on/off

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ConsolePar
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Set console parameters

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Antialiasing
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Smooth is better

Toggle YASARA's built in antialiasing and note that it only affects atom balls. Activate fullscreen antialiasing separately in your OpenGL settings.

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Antialias
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Switch antialiasing on/off

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Frequency
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Change the frames per second and save battery power

Depending on the power of your computer, you can let YASARA update the screen more often or enter a special power saving mode when running on a notebook.

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FramesPerSec
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Set screen update frequency

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Stereo
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Time to touch your molecules

Choose a stereo mode and adjust the stereo parameters to let molecules fly out of the screen.

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Stereo
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Set stereo mode

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StereoPar
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Set stereo parameters

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Help

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Access the documentation and solve problems

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Manual

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Browse the HTML documentation

Enter the manual at the top level, jump directly to a certain command or search for individual keywords.

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SearchDoc
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Search documentation

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ShowCom
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Show command description

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ShowDoc
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Show documentation

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Installation
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Download missing programs

YASARA uses other programs to perform additional tasks, here you can install them.