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

In addition to coloring atoms , you can also change the colors of covalent bonds , hydrogen bonds and the background . The default colors for chemical elements, secondary structure, B-factors etc. can also be adjusted.

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ColorBonds
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Color bonds

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ColorBG
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Color background

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ColorPar
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Set default color parameters

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Color<Atom|Res|Mol|Obj|All>
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Set/get atom colors

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Visibility
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Show and hide, switch on and off

Show and hide atoms, switch entire objects on and off . Look in the essentials section for details.

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

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

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Switch<Obj|All>
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Switch objects on/off

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

Display atoms as space filling balls (CPK), balls of a certain radius connected with sticks or just plain sticks of a given radius. Show and hide a trace through a selection of atoms (e.g. Calpha atoms). When showing a trace, it may help to additionally hide atoms that are not traced.

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BallRadius
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Set ball radius in balls&sticks

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BallStick<Atom|Res|Mol|Obj|All>
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Style atoms as balls&sticks

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Ball<Atom|Res|Mol|Obj|All>
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Style atoms as balls

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HideTrace
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Hide trace through atoms

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PointPar
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Set point and line radius and plasticity in wire frames

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ShowTrace
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Show trace through atoms

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StickRadius
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Set stick radius

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Stick<Atom|Res|Mol|Obj|All>
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Style atoms as sticks

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Style
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Set general display style

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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

Show or hide three kinds of surfaces at various resolutions , color them afterwards or extract fragments by defining a surface environment .

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ColorSurf<Obj|All>
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Color surface

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HideSurf<Atom|Res|Mol|Obj|All>
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Hide surface

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ShowSurf<Atom|Res|Mol|Obj|All>
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Show surface

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SurfPar
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Set/get surface parameters

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Hydrogen bonds - Show hydrogen bonds

Show or hide all hydrogen bonds made by selected atoms and choose their color and transparency level.

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ColorHBo
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Color hydrogen bonds

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HideHBo<Atom|Res|Mol|Obj|All>
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Hide hydrogen bonds

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ShowHBo<Atom|Res|Mol|Obj|All>
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Show hydrogen bonds

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Atoms
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Choose atom styles

Set the overall atom size , attach various textures to the atoms , and toggle the display of the chemical element symbol or a whobbling plasma inside those atoms that are cut open by the viewplane.

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AtomPlasma
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Switch plasma inside atoms on/off

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AtomSize
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Set size of atoms

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AtomSymbol
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Switch element symbol inside atoms on/off

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AtomTexture
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Set texture style of atoms

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Projection
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Switch the perspective

Switch between perspective and parallel projection .

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Projection
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Set perspective or parallel projection

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Lighting
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Light the scene

Configure the lightsource including shadows and ambient influence, and add fog of a certain color to the scene.

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ColorFog
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Color fog

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Fog
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Set fog density

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LightSource
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Configure the light source

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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