°
View
-
Change the appearance of the soup
°
Colors
-
Add a fourth dimension to your figures
In addition to
coloring atoms
, you can also change the colors of
covalent bonds
,
hydrogen bonds
and the
background
. The default colors for chemical elements, secondary structure, B-factors etc.
can also be adjusted
.
°
ColorBonds
-
Color bonds
°
ColorBG
-
Color background
°
ColorPar
-
Set default color parameters
°
Color<Atom|Res|Mol|Obj|All>
-
Set/get atom colors
°
Visibility
-
Show and hide, switch on and off
Show
and
hide atoms
,
switch entire objects on and off
. Look in the
essentials section
for details.
°
Hide<Atom|Res|Mol|Obj|All>
-
Hide atoms
°
Show<Atom|Res|Mol|Obj|All>
-
Show atoms
°
Switch<Obj|All>
-
Switch objects on/off
°
Style
-
Display atoms as balls, balls&sticks, sticks and traces
Display atoms as
space filling balls (CPK)
, balls of a
certain radius
connected
with sticks
or just
plain sticks
of a
given radius
.
Show
and
hide
a trace through a selection of atoms (e.g. Calpha atoms). When showing a trace, it may help to additionally hide atoms that are not traced.
°
BallRadius
-
Set ball radius in balls&sticks
°
BallStick<Atom|Res|Mol|Obj|All>
-
Style atoms as balls&sticks
°
Ball<Atom|Res|Mol|Obj|All>
-
Style atoms as balls
°
HideTrace
-
Hide trace through atoms
°
PointPar
-
Set point and line radius and plasticity in wire frames
°
ShowTrace
-
Show trace through atoms
°
StickRadius
-
Set stick radius
°
Stick<Atom|Res|Mol|Obj|All>
-
Style atoms as sticks
°
Style
-
Set general display style
°
Secondary structure - Show tubes, ribbons and cartoons
Indicate the secondary structure by
showing a plain tube, ribbons, and cartoons with cylindric helices
. Change the
radius, width and height of the secondary structure elements
and
hide
them again later. It is also possible to
override YASARA's secondary structure assignment
.
°
HideSecStr<Res|Mol|Obj|All>
-
Hide secondary structure
°
SecStrPar
-
Set secondary structure display parameters
°
SecStr<Res|Mol|Obj|All>
-
Set/get secondary structure
°
ShowSecStr<Res|Mol|Obj|All>
-
Show secondary structure
°
Surfaces
-
Show VdW, molecular and solvent accessible surfaces
Show
or
hide
three kinds of surfaces at
various resolutions
,
color them afterwards
or extract fragments by
defining a surface environment
.
°
ColorSurf<Obj|All>
-
Color surface
°
HideSurf<Atom|Res|Mol|Obj|All>
-
Hide surface
°
ShowSurf<Atom|Res|Mol|Obj|All>
-
Show surface
°
SurfPar
-
Set/get surface parameters
°
Hydrogen bonds - Show hydrogen bonds
Show
or
hide
all hydrogen bonds made by selected atoms and choose their
color and transparency level
.
°
ColorHBo
-
Color hydrogen bonds
°
HideHBo<Atom|Res|Mol|Obj|All>
-
Hide hydrogen bonds
°
ShowHBo<Atom|Res|Mol|Obj|All>
-
Show hydrogen bonds
°
Atoms
-
Choose atom styles
Set the
overall atom size
,
attach various textures to the atoms
, and toggle the display of
the chemical element symbol
or a
whobbling plasma
inside those atoms that are cut open by the viewplane.
°
AtomPlasma
-
Switch plasma inside atoms on/off
°
AtomSize
-
Set size of atoms
°
AtomSymbol
-
Switch element symbol inside atoms on/off
°
AtomTexture
-
Set texture style of atoms
°
Projection
-
Switch the perspective
Switch between perspective and parallel
projection
.
°
Projection
-
Set perspective or parallel projection
°
Lighting
-
Light the scene
Configure
the lightsource
including shadows and ambient influence, and
add fog
of a
certain color
to the scene.
°
ColorFog
-
Color fog
°
Fog
-
Set fog density
°
LightSource
-
Configure the light source
