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



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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

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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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Preparing a simulation - Define and fill the cell

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Force fields - Get the recipe

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Simulation parameters - Choose your favorite ingredients

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Restraints

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Enforce distances and dihedral angles

In addition to simply linking atoms with a spring , you can determine NMR structures using the same functions as XPLOR to restrain distances and dihedral angles individually or all together via a restraint file . The violation energies and statistics can be obtained using various potential functions and parameters like distance averaging . The restraints can be listed , selectively shown (satisfied restraints in green, violated ones in red), styled, hidden or deleted. Floating assignments can also be analyzed.

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AddSpring

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Link atoms with a spring

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DelRest<Obj|All>

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Delete restraints

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HideRest<Atom|Res|Mol|Obj|All>

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Hide restraints

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LoadTbl

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Load XPLOR distance and dihedral angle restraints

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ListFloat<Obj|All>

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List floating assignments

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ListRest<Atom|Res|Mol|Obj|All>

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List restraints and energies

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RestEnergy<Obj|All>

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Calculate restraint energies

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RestViol<Obj|All>

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Get restraint violation statistics

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RestrainDis

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Restrain distance

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RestrainDih

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Restrain dihedral angle

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RestrainPar

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Set/get restraining parameters

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RestrainPot

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Set/get restraining potential function

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SaveTbl

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Save XPLOR distance and dihedral angle restraints

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ScaleRest<Atom|Res|Mol|Obj|All>

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Scale restraints

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ShowRest<Atom|Res|Mol|Obj|All>

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Show restraints

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Running a simulation - Keep the soup from boiling

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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