Draw Structure

Description

Transform the molecule structure data into graphic objects for display.

Input Ports

structure_in MoleculeType Molecular structure data to be rendered.

Parameters

Atoms rendering list Select the visualization format for the structure atoms. The available formats are:
Normal
Ball and Stick.
Licorice
Only bonds are show with rounded edges, but also orphan atoms are show as small spheres.
Lic. if bounded
Like licorice, but orphan atoms are not show.
CPK
Usual space filling format.
No atoms
The atoms are not show.
From data
The rendering method of each atom is determined by its corresponding render field. This field can be set using the Set Rendering Mode module.
Bonds rendering list Select the visualization format for the structure bonds. The available formats are:
Tubes
Bonds are represented as tubes; H-bonds as dashed lines.
Lines
Bonds are represented as continuous lines; H-bonds as dashed lines.
All tubes
All bonds are represented as tubes.
All lines
All bonds are represented as continuous lines.
H as lines
Bonds are represented as tubes; normal bonds to H are represented as lines; H-bonds as dashed lines.
No bonds
The bonds are not show.
Atoms coloring list Select the coloring method for the structure atoms. The available formats are:
Atom type
The atoms are colored by their atom type.
Monochrome
All atoms are colored using the default color.
(Atom scalar variable)
The atoms are colored by the corresponding scalar value.
Bonds coloring list Select the coloring method for the structure atoms. The available formats are:
Same as atom
The bonds are colored by their bonded atom colors.
Atom type
The atoms are colored by their bonded atom type.
Monochrome
All bonds are colored using the default color.
(Bonds scalar variable)
The bonds are colored by the corresponding scalar value.
colormap list List of possible color schemas to map values to colors.
Rainbow
The usual rainbow continuous colormap.
Blue-Red
Blue for negative values, red for positive values and white for zero values.
Greyscale
The usual grayscale continuous colormap.
White-Blue
From white to blue.
Split color toggle Set the coloring of bonds to be two uniform bands instead of an interpolated color between the two atoms colors.
Force grey toggle Convert the colors into a luminosity colorscale using the formula: R * 0.299 + G * 0.587 + B * 0.114
Use manual limits toggle For the value color mapping use the limits entered below. If not set the value limits are computed by the module and show in the fields below.
Min, Max numeric fields Limits of the values.
Labels (atoms) list Select the labeling method for the structure atoms. The available methods are:
No atom label
No label is visualized.
Atom name
Label each atom with the atom name (if available) or with the atom element type.
Element type
Label each atom with its element type.
Atom index
Label each atom with its index in the structure. The numbering starts at one.
Labels (fragments) list Select the labeling method for the structure fragments. The available methods are:
No fragm. label
No label is visualized.
On atoms
Label each atom with the name of the fragment to which the atom pertains.
On fragments
Put the fragment name label at the fragment centroid.
Resolution radio buttons Sets the resolution of ball and sticks. Useful with big molecules. The available resolutions are:
Ultra
Use 26 facets for tubes and spheres.
High
Use 18 facets for tubes and spheres.
Mid
Use 10 facets for tubes and spheres.
Low
Use 3 facets for tubes and spheres.
Fast rot. toggle If set the atom structure is replaced in the viewer by a lighter representation during manipulations. This is useful with big structures to speedup manipulations.
normal scale numeric field Size scale for atoms in ball and stick representation. The scale is related to the atom VdW radius.
licorice sc. numeric field Size scale for atoms in licorice representation. The scale is related to the bonds radius.
cpk scale numeric field Size scale for atoms in CPK representation. The scale is related to the atom VdW radius.
bonds radius numeric field Bond tube radius.
line width numeric field Width of the lines used by H-bonds or bonds with line representation.
Use Info Set list List of possible atom types and size values to be used for the geometric mapping. The available info sets are edited and created using the Info Set Editor.
Atom label standard font parameters selector Set the font used for the atom labels.
Fragment label standard font parameters selector Set the font used for the fragment labels.
Default color standard color selector Set the color used for monochrome atoms and bonds rendering.

Output Ports

obj DefaultObject Graphic representation to be sent to the viewer.
display_parameters DisplayParamsType Structure display settings data.
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