Your guide to YASARA View
°
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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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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Experiments
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Let YASARA cook for you
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Macros
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Watch YASARA do the work for you
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Tables
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Collect, visualize and export data
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Formats
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Choose the residue output format
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Logs
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Redirect output to a file
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Plugins
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Run plugins from a macro
Normally plugins are run by clicking on the options they add to the menus. In some rare cases, it may help to
create a plugin input file
and
then run a plugin directly
. If there is a bug in the plugin and it crashes, you must
additionally stop it
before it can be run again.
°
RunPlugin
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Run Python plugin
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SavePLI<Atom|Res|Mol|Obj>
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Save plugin input file
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StopPlugin
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Stop running plugin
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Default pH - Set the H+ ion concentration and residue pKas
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Quantum mechanics - Configure YAPAC
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Coordinate system - Live in a left or right handed world
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Units
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Choose your favorite units
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Parallel computations - Configure multi CPU core usage
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Input devices - Configure the interaction with YASARA
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Shell
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Execute shell 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