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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History

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Undo and redo changes

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Objects

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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.

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Add<Obj|All>
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Add objects to the soup

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Center<Atom|Res|Mol|Obj|All>
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Center atoms

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Del<Atom|Res|Mol|Obj|All>
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Delete atoms

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Remove<Obj|All>
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Remove objects from the soup

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Transfer<Obj|All>
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Transfer objects into another coordinate system

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Transform<Obj|All>

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Transform objects

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Split points - Edit split points, split and join entire objects

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Bonds
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Add, type and delete bonds

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Building
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Build atoms to molecules, oligomers, crystals and loops

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Geometry
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Set or optimize distances, angles and dihedrals

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Sampling
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Search conformational space

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Surface environments - Define the context of surface analysis

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Hydrogens
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Add, swap and delete

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Water
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Delete all waters

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Names and numbers - Set or get properties of atoms to objects

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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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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