Your guide to YASARA View
°
Essentials
-
What you really have to know
°
Selections
-
Tell YASARA what you want
°
Commands
-
Tell YASARA what to do
°
File
-
Load and save the scene or parts of it
°
Edit
-
Change content and properties of the soup
°
Simulation
-
Simulate the soup
°
Preparing a simulation - Define and fill the cell
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Force fields - Get the recipe
°
Simulation parameters - Choose your favorite ingredients
°
Restraints
-
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
.
°
AddSpring
-
Link atoms with a spring
°
DelRest<Obj|All>
-
Delete restraints
°
HideRest<Atom|Res|Mol|Obj|All>
-
Hide restraints
°
LoadTbl
-
Load XPLOR distance and dihedral angle restraints
°
ListFloat<Obj|All>
-
List floating assignments
°
ListRest<Atom|Res|Mol|Obj|All>
-
List restraints and energies
°
RestEnergy<Obj|All>
-
Calculate restraint energies
°
RestViol<Obj|All>
-
Get restraint violation statistics
°
RestrainDis
-
Restrain distance
°
RestrainDih
-
Restrain dihedral angle
°
RestrainPar
-
Set/get restraining parameters
°
RestrainPot
-
Set/get restraining potential function
°
SaveTbl
-
Save XPLOR distance and dihedral angle restraints
°
ScaleRest<Atom|Res|Mol|Obj|All>
-
Scale restraints
°
ShowRest<Atom|Res|Mol|Obj|All>
-
Show restraints
°
Running a simulation - Keep the soup from boiling
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Analyze
-
Analyze the soup
°
View
-
Change the appearance of the soup
°
Effects
-
Change and animate the scene
°
Options
-
Other commands
°
Window
-
Change the display properties
°
Help
-
Access the documentation and solve problems
°
Index
-
All commands in alphabetic order
°
Recipes
-
Answer complex questions
°
Macros
-
Automate your work with Yanaconda
°
Plugins
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Extend YASARA with your own functions
°
Scripts
-
Use YASARA as a Python module
°
Troubleshooting
-
Get things going