CAP - Catabolite gene Activating Protein (1BER)

Endonuclease PvuII bound to palindromic DNA recognition site CAGCTG (1PVI)

GCN4 - leucine zipper transcription factor bound to palindromic DNA recognition site ATGAC(G)TCAT (1YSA)

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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Effects

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Change and animate the scene

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Position

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Place and move objects

Choose object positions on an absolute or relative scale (including polygon meshes), grab either one , the next or the previous object for movement with mouse and Spaceball, or let them move automatically in a certain direction or to a certain spot .

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AutoMoveTo<Obj|All>
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Move objects or scene automatically to a certain location

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AutoMove<Obj|All>

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Move objects or scene automatically

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GrabNext
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Grab next object for mouse movement

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GrabPrev
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Grab previous object for mouse movement

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Grab<Obj|All>
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Grab object or scene for mouse movement

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MoveMesh
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Move polygon mesh

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Move<Atom|Res|Mol|Obj|All>
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Move atoms, objects or scene

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Pos<Obj|All>
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Set/get object or scene position

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Orientation
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Orient and rotate objects

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Labels
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Display text labels

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Marks and zooms - Mark atoms with fireflies and zoom in

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Arrows
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Show arrows connecting atoms or points

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Solids
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Show spheres, boxes, pyramids, cylinders, tori and others

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Images
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Show and animate bitmaps

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Text
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Print text, possibly in 3D letters

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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