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

°

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

°

Analyze

-

Analyze the soup

°

View

-

Change the appearance of the soup

°

Effects

-

Change and animate the scene

°

Position

-

Place and move objects

Choose object positions on an absolute or relative scale (including polygon meshes), grab either one, the next or the previous object for movement with mouse and Spaceball, or let them move automatically in a certain direction or to a certain spot.

°
AutoMoveTo<Obj|All>
-

Move objects or scene automatically to a certain location

°
AutoMove<Obj|All>

-

Move objects or scene automatically

°
GrabNext
-
Grab next object for mouse movement

°
GrabPrev
-
Grab previous object for mouse movement

°
Grab<Obj|All>
-
Grab object or scene for mouse movement

°
MoveMesh
-
Move polygon mesh

°
Move<Atom|Res|Mol|Obj|All>
-

Move atoms, objects or scene

°
Pos<Obj|All>
-

Set/get object or scene position

°
Orientation
-
Orient and rotate objects

Orient or rotate objects, continuously, until a certain orientation is reached or to a nice view.

°
AutoRotateTo<Obj|All>
-

Rotate objects or scene automatically to a certain orientation

°
AutoRotate<Obj|All>
-

Rotate objects or scene automatically

°
NiceOri<Obj|All>

-

Orient objects nicely

°
Ori<Obj|All>
-
Set/get object or scene orientation

°
Rotate<Obj|All>
-

Rotate objects or scene

°
Labels
-
Display text labels

Label anything from atoms to the entire scene and distances, change the label style including font, color or perspective, finally delete atom- and distance labels again.

°
LabelDis
-
Label atom distances

°
LabelPar
-

Set label parameters

°
Label<Atom|Res|Seg|Mol|Obj|All>
-

Add labels

°
UnlabelDis
-

Delete distances labels

°
Unlabel<Atom|Res|Seg|Mol|Obj|All>
-

Delete labels

°
Marks and zooms - Mark atoms with fireflies and zoom in

Mark one atom and display its properties in the head up display, then zoom in closely on one or more atoms .

°
MarkAtom
-

Mark atom with fireflies

°
Zoom<Atom|Res|Mol|Obj|All>
-

Zoom in on atoms

°
Arrows
-

Show arrows connecting atoms or points

Show arrows and hide those connecting atoms and those connecting points.

°
HideArrow<Atom|Res|Mol|Obj|All>
-

Hide arrows

°
ShowArrow
-
Show arrows between atoms or points

°
Solids
-
Show spheres, boxes, pyramids, cylinders, tori and others

Show solid spheres & ellipsoids, boxes & cubes, cones, cylinders, pyramids & prisms or a torus.

°
ShowBox
-
Show a rectangular box

°
ShowCone
-

Show a cone, cylinder, pyramid or prism

°
ShowSphere
-

Show a sphere or ellipsoid

°
ShowTorus
-
Show a torus

°
Images
-

Show and animate bitmaps

Load a bitmap in Windows BMP- or PNG-format, show it on screen , move it around or do more complicated animations and let the image disappear again. You can also swap images, attach them to objects , toggle fogging, hide them and finally delete them.

°
AnimateImage
-
Animate appearance and disappearance of images

°

AutoMoveImage
-
Move images automatically

°
DelImage
-

Delete images

°
HideImage
-
Hide images

°
ImageFog
-

Switch image fog on/off

°
LoadBMP
-
Load image from BMP file

°
LoadPNG
-

Load image from PNG file

°
MakeImageObj
-
Make object with attached image

°
ShowImage
-
Show images

°
SwapImage
-

Swap images

°
UnrestImage
-
Let animated image disappear

°

Text
-
Print text, possibly in 3D letters

By default, printing is done to the console. To get fancier text output, create a text object and redirect printing . Choose a font, possibly with fog , position the cursor, then print three-dimensional characters . When writing a plugin or macro, it sometimes helps to show a text message at the bottom and hide it afterwards, show a button to click or print to the top right head up display .

°
Font
-

Set font for 3D letters

°
FontFog
-
Switch font fog on/off

°
HideMessage
-

Hide text message at the bottom

°
MakeTextObj
-
Make text object to print 3D letters

°
PosText
-
Position and justify text

°
Print
-

Print text

°
PrintCon
-
Print to console

°
PrintHUD
-

Print to head up display

°
PrintObj
-
Print to text object

°
ShowButton
-

Show clickable button

°
ShowMessage
-
Show text message at the bottom

°

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

-

Extend YASARA with your own functions

°

Scripts

-

Use YASARA as a Python module

°

Troubleshooting

-

Get things going