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

°

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

When analyzing data, you often want to visualize it. This is achieved by creating a one-, two- or three-dimensional table , selecting it for data collection, tabulating the results and showing a graphical representation of the data . Tables can also be listed and manipulated on the column, row and page level, flipped, deleted entirely, imported and exported for use with other programs like Excel and XMGrace.

°
Tabulate
-
Add cells to table

°
DelTab
-

Delete tables

°
FlipTab
-
Flip table axes

°
LoadTab
-

Load formatted table

°
MakeTab
-
Make a table

°
SaveTab
-

Save formatted table

°
SelectTab
-
Select table to add cells

°
ShowTab
-
Show table data as 3D object

°
Tab
-

Set/get table cells

°
Formats
-
Choose the residue output format

°
Logs
-

Redirect output to a file

°
Plugins
-
Run plugins from a macro

°
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