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

°	Preparing a simulation - Define and fill the cell

°	Force fields - Get the recipe

Choose the force field and the force cutoff for non-bonded interactions, calculate electrostatic forces without a cutoff using PME for accurate results. In special cases, you may want to scale or exclude some force field components. The force field and AM1BCC atom types can also be retrieved to visualize YASARA's assignments.

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Cutoff
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Set force cutoff distance

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ForceField
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Set force field

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Force<Atom|Res|Mol|Obj|All>
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Set/get force on atoms

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Interactions
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Set force field terms

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Longrange
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Set long range interactions

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ScaleForce
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Set/get force scaling factors

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ShowSimGrid
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Show simulation grid

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SimSpeed
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Set simulation speed

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TypeAtom
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Get the atom type

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Simulation parameters - Choose your favorite ingredients

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Restraints
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Enforce distances and dihedral angles

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Running a simulation - Keep the soup from boiling

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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