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



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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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File

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Load and save the scene or parts of it

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Edit

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Change content and properties of the soup

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Simulation

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Simulate the soup


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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 .

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Boundary

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Set cell boundary

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Cell

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Set/get simulation cell dimensions

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FillCellObj

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Fill simulation cell with object

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FillCellWater

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Fill simulation cell with water

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Force fields - Get the recipe

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Simulation parameters - Choose your favorite ingredients

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Restraints

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Enforce distances and dihedral angles

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Running a simulation - Keep the soup from boiling

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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

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Effects

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Change and animate the scene

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Options

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Other 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


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Recipes

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Answer complex questions


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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


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Troubleshooting

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Get things going