Endonuclease PvuII (1PVI) DNA - GATTACAGATTACA
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)
CAP - Catabolite gene Activating Protein (1BER)
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)
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



° 

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

° 

Effects

-

Change and animate the scene

° 

Options

-

Other commands


° 

Experiments

-

Let YASARA cook for you

° 

Macros

-

Watch YASARA do the work for you

° 

Tables

-

Collect, visualize and export data

° 

Formats

-

Choose the residue output format

° 

Logs

-

Redirect output to a file

° 

Plugins

-

Run plugins from a macro

Normally plugins are run by clicking on the options they add to the menus. In some rare cases, it may help to create a plugin input file and then run a plugin directly. If there is a bug in the plugin and it crashes, you must additionally stop it before it can be run again.

° 

RunPlugin

-

Run Python plugin

° 

SavePLI<Atom|Res|Mol|Obj>

-

Save plugin input file

° 

StopPlugin

-

Stop running plugin

° 

Default pH - Set the H+ ion concentration and residue pKas

° 

Quantum mechanics - Configure YAPAC

° 

Coordinate system - Live in a left or right handed world

° 

Units

-

Choose your favorite units

° 

Parallel computations - Configure multi CPU core usage

° 

Input devices - Configure the interaction with YASARA

° 

Shell

-

Execute shell 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