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

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Essentials

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What you really have to know

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Selections

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Tell YASARA what you want

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Commands

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Tell YASARA what to do

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Load and save the scene or parts of it

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Change content and properties of the soup

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Change the appearance of the soup

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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