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

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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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History

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Undo and redo changes

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Objects

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Center, transform, transfer, remove, add and delete

°	Split points - Edit split points, split and join entire objects

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Bonds

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Add, type and delete bonds

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Building

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Build atoms to molecules, oligomers, crystals and loops

Swap chemical elements , atom positions, residue side-chains and entire objects. Create individual atoms , or residues, build loops (including the loop database) or entire proteins, extending them at the C-terminus , possibly adding missing oxygens and protection caps. To prepare a molecular dynamics simulation, clean the structures. When looking at oligomers, duplicate objects, use the BIOMT transformations in the PDB file to create the biological oligomeric state or add the crystal symmetry related copies .

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AddCap<Obj|All>
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Add N/C-terminal capping groups

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AddRes
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Add terminal residue

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AddTer<Obj|All>
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Add C-terminal oxygens

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BuildAtom
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Build single atom

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BuildLoop
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Build central or terminal loop

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BuildLoopDB
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Build loop data base

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BuildMol
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Build peptide chain

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BuildRes
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Build single residue

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Clean<Obj|All>
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Clean objects for molecular dynamics simulation

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Crystallize<Obj|All>
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Crystallize objects to fill the unit cell

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Duplicate<Obj|All>

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Duplicate objects

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Oligomerize<Obj|All>
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Oligomerize objects to generate the biologically active form

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SwapAtom
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Swap chemical element of atoms

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SwapObj
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Swap two objects in the list

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SwapPosAtom
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Swap atom positions

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SwapRes
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Swap residue side-chains

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Geometry
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Set or optimize distances, angles and dihedrals

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Sampling
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Search conformational space

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Surface environments - Define the context of surface analysis

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Hydrogens
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Add, swap and delete

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Water
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Delete all waters

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Names and numbers - Set or get properties of atoms to objects

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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