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

°

Essentials

-

What you really have to know

°

Selections

-

Tell YASARA what you want

°

Commands

-

Tell YASARA what to do

°

File

-

Load and save the scene or parts of it

°

Edit

-

Change content and properties of the soup

°

Simulation

-

Simulate the soup

°

Analyze

-

Analyze the soup

°

View

-

Change the appearance of the soup

°

Colors

-

Add a fourth dimension to your figures

°

Visibility

-

Show and hide, switch on and off

°

Style

-

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

°	Secondary structure - Show tubes, ribbons and cartoons

°

Surfaces

-

Show VdW, molecular and solvent accessible surfaces

°	Hydrogen bonds - Show hydrogen bonds

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

°
ColorHBo
-
Color hydrogen bonds

°
HideHBo<Atom|Res|Mol|Obj|All>
-

Hide hydrogen bonds

°
ShowHBo<Atom|Res|Mol|Obj|All>
-

Show hydrogen bonds

°
Atoms
-

Choose atom styles

°
Projection
-
Switch the perspective

°
Lighting
-

Light the scene

°

Effects

-

Change and animate the scene

°

Options

-

Other commands

°

Window

-

Change the display properties

°

Help

-

Access the documentation and solve problems

°

Index

-

All commands in alphabetic order

°

Recipes

-

Answer complex questions

°

Macros

-

Automate your work with Yanaconda

°

Plugins

-

Extend YASARA with your own functions

°

Scripts

-

Use YASARA as a Python module

°

Troubleshooting

-

Get things going