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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Analyze

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Analyze the soup


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Atom position - Calculate average positions and RMSFs

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Superposition

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Align atoms and calculate RMSDs

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Contacts

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List contacts and hydrogen bonds

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Energy

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Calculate energies

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Electrostatics

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Calculate electrostatic potentials and charges

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Geometry

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Measure distances, angles, dihedrals and radii

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Rotamers

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Show rotamer distributions

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Secondary structure - Calculate secondary structure content

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Surface areas - Calculate VdW, molecular and accessible surfaces

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Volumes

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Calculate VdW, molecular and solvent accessible volumes

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Soup content - List, count and compare units, get boundaries

List the properties of atoms to objects, including names, numbers and secondary structure, count how many units are contained in a selection, find differences between selections , determine the first and last atom or object spanning a selection and sum up atom masses.

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Compare<Atom|Res>

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Compare selections

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Count<Atom|Res|Mol|Obj>

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Count selected units

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List<Atom|Res|Mol|Obj>

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List selection

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

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Calculate mass

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Span<Atom|Res|Obj>

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Determine first and last unit spanning a selection

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Checks

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Search for errors

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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