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

°	New scene - Start again

Clear all objects and bitmaps for a fresh start or reset YASARA entirely, including simulation parameters and undo-history.

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Clear
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Clear scene

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Reset
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Reset YASARA to startup state

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PDB files - Load and save objects in plain PDB format

Load PDB files and save them again in standard PDB or X-Plor format .

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LoadPDB
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Load Protein Data Bank file

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SavePDB
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Save Protein Data Bank file

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YASARA objects - Load and save complete objects

Load single objects in YASARA's own format , including styles and items and save them to disk .

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LoadYOb
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Load YASARA object

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SaveYOb
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Save YASARA object

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YASARA scenes - Load and save the entire scene

Load all objects together and save them including styles,items and the view .

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LoadSce
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Load complete scene

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SaveSce
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Save complete scene

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OpenBabel
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Import and export molecules using OpenBabel

When working with more exotic file formats, import and export structures with OpenBabel.

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Load*
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Import file with OpenBabel

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Save*
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Export file with OpenBabel

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Screenshots
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Save plain or ray-traced screenshots

Save simple screenshots (optionally including the menu), save scene descriptions for PovRay or run it immediately to create photorealistic images including shadows.

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RayTrace
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Create raytraced screenshot using POVRay

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SaveBMP
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Save screenshot as Windows bitmap

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SavePOV
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Save POVRay scene description

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MPEG movies - Encode plain or ray-traced animations

Save MPEG movies (optionally including the menu).

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SaveMPG
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Save MPEG video

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Simulation snapshots - Load and save simulation states

Load simulation snapshots to restore atom positions and velocities at a certain time or save them in periodic time intervals. Atom positions without velocities can also be saved and restored in XTC format, which minimizes the required storage space.

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LoadSim
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Load simulation snapshot in sim format

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LoadXTC<Obj|All>
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Load simulation snapshot in XTC format

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SaveSim
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Save simulation snapshots in sim format

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SaveXTC
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Save simulation snapshots in XTC format

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Exit
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Quit YASARA

Exit YASARA immediately .

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Exit
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Exit YASARA

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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

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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