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)

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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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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Colors

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Add a fourth dimension to your figures

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Visibility

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Show and hide, switch on and off

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Style

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Display atoms as balls, balls&sticks, sticks and traces

°	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 .

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HideSecStr<Res|Mol|Obj|All>
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Hide secondary structure

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SecStrPar
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Set secondary structure display parameters

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SecStr<Res|Mol|Obj|All>
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Set/get secondary structure

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ShowSecStr<Res|Mol|Obj|All>
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Show secondary structure

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Surfaces
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Show VdW, molecular and solvent accessible surfaces

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Hydrogen bonds - Show hydrogen bonds

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Atoms
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Choose atom styles

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Projection
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Switch the perspective

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Lighting
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Light the scene

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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