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

°	Atom position - Calculate average positions and RMSFs

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Superposition

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Align atoms and calculate RMSDs

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Contacts

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List contacts and hydrogen bonds

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Energy

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Calculate energies

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Electrostatics

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Calculate electrostatic potentials and charges

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Geometry

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Measure distances, angles, dihedrals and radii

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Rotamers

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Show rotamer distributions

°	Secondary structure - Calculate secondary structure content

°	Surface areas - Calculate VdW, molecular and accessible surfaces

Calculations of surface areas are influenced by the current surface environment and the resolution of the surface grid. If a protein has cavities, they can be treated separately.

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FirstSurf<Atom|Res>
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Get first surface atom(s) or residue(s) and area(s)

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Surf<Atom|Res|Mol|Obj|All>
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Calculate surface areas

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Volumes
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Calculate VdW, molecular and solvent accessible volumes

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Soup content - List, count and compare units, get boundaries

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Checks
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Search for errors

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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