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

°	Preparing a simulation - Define and fill the cell

°	Force fields - Get the recipe

°	Simulation parameters - Choose your favorite ingredients

Switch between normal molecular dynamics at a given temperature , simulated annealing with a certain cooling level and energy minimization with a maximum step size . Control the pressure in the cell, set the simulation time, the time step and the number of screen updates per simulation step .

°
AnnealSteps
-

Set simulated annealing steps

°
MinStep
-
Set energy minimization step

°
PressureCtrl
-
Set pressure control

°
SimSteps
-

Set number of simulation steps per screen update

°
Temp
-
Set/get simulation temperature

°
TempCtrl
-
Set temperature control

°
Time
-

Set/get simulation time

°
TimeStep
-
Set simulation time step

°
Restraints
-

Enforce distances and dihedral angles

°
Running a simulation - Keep the soup from boiling

°

Analyze

-

Analyze the soup

°

View

-

Change the appearance of the soup

°

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