Endonuclease PvuII (1PVI) DNA - GATTACAGATTACA
CAP - Catabolite gene Activating Protein (1BER)
DNA - GATTACAGATTACAGATTACA Endonuclease PvuII bound to palindromic DNA recognition site CAGCTG (1PVI) DNA - GATTACAGATTACAGATTACA TBP - TATA box Binding Protein (1C9B)
CAP - Catabolite gene Activating Protein (1BER)
GCN4 - leucine zipper transcription factor bound to palindromic DNA recognition site ATGAC(G)TCAT (1YSA)
GCN4 - leucine zipper transcription factor bound to palindromic DNA recognition site ATGAC(G)TCAT (1YSA)
GCN4 - leucine zipper transcription factor bound to palindromic DNA recognition site ATGAC(G)TCAT (1YSA)
GCN4 - leucine zipper transcription factor bound to palindromic DNA recognition site ATGAC(G)TCAT (1YSA)
GCN4 - leucine zipper transcription factor bound to palindromic DNA recognition site ATGAC(G)TCAT (1YSA)
TBP - TATA box Binding Protein (1C9B)
 

Your guide to YASARA View



° 

Essentials

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What you really have to know


° 

Selections

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Tell YASARA what you want


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Commands

-

Tell YASARA what to do


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File

-

Load and save the scene or parts of it

° 

Edit

-

Change content and properties of the soup

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Simulation

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Simulate the soup

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Analyze

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Analyze the soup

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View

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Change the appearance of the soup

° 

Effects

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Change and animate the scene

° 

Options

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Other commands


° 

Experiments

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Let YASARA cook for you

° 

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

-

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

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Formats

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Choose the residue output format

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Logs

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Redirect output to a file

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Plugins

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Run plugins from a macro

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

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Quantum mechanics - Configure YAPAC

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Coordinate system - Live in a left or right handed world

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Units

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Choose your favorite units

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Parallel computations - Configure multi CPU core usage

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Input devices - Configure the interaction with YASARA

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Shell

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Execute shell commands

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Window

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Change the display properties

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Help

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Access the documentation and solve problems

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Index

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All commands in alphabetic order


° 

Recipes

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Answer complex questions


° 

Macros

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Automate your work with Yanaconda


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Plugins

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Extend YASARA with your own functions


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Scripts

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Use YASARA as a Python module


° 

Troubleshooting

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Get things going