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[ Surfaces | Meshes | Macroshape | Google 3D | Display or Undisplay | Display Options | Move/Resize | Mesh/Display | Mesh Clipping | Save Mesh | Occlusion ]
Click on the tab button entitled 'meshes' and more graphics tools for surfaces are available. In ICM surfaces are sometimes referred to as meshes or graphical objects (Grobs).
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Surface | Plain Solid |
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Electrostatic Surface | Binding Property Surface |
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Macroshape Solid | Macroshape Transparent |
5.2.1 Surfaces |
The surface of your structure can be displayed and colored by electrostatics or binding properties. To do this:
5.2.2 Meshes |
A variety of shapes can be constructed automatically using ICM. These shapes are referred to as meshes. The types of shapes you can build are shown below:
All the buttons for creating these shapes are shown here:
To make a shape select it from the menu by clicking on the down arrow and then click the button next to the menu. The shape will then be displayed in the 3D graphics window.
5.2.3 Macroshape |
A macroshape can be constructed and allows easy viewing and manipulation of the structural representation. A macroshape representation is ideal for large structures which allows the user to easily identify important regions of the structure and facilitate the return to the 'standard' view of a particular molecule. All the buttons needed to display a macroshape structure are shown below in the 'meshes' tab.
To construct a macroshape:
Macroshape can also be used from the View menu: View/Macro Shape
5.2.4 Google 3D Objects (Sketchup) |
To read in a 3D Mesh from Google in KMZ or COLLADA format:
An example of a KMZ file can be found in the distribution (a squirrel model by ilikipie, provided with author's permission).
5.2.5 Display or Undisplay Meshes or Surfaces |
To display or undisplay the surface click in the box in the ICM workspace as shown below:
NOTE: All surfaces, meshes and macroshapes come under the one heading of meshes in the workspace panel. |
5.2.6 Mesh Options. |
A number of options relating to meshes can be used by right clicking on the mesh in the ICM Workspace. This section describes some of these options.
5.2.7 Move and Resize Mesh |
Once a mesh has been created you can move it and resize it. To do this, locate the mesh you wish to either move or resize in the ICM Workspace and right click on it as shown below.
A purple box as shown below will surround the molecule.
To resize the mesh click on one of the corners of the box and drag to the required size. The number displayed on the edges of the box represent the dimensions.
To move the mesh click on it with the center mouse button or selct the connect option.
5.2.8 Color and Mesh Display |
There are a number of options to color and change the display of the mesh. These options can be accessed simply by right clicking on the mesh name in the ICM Workspace as shown below.
The lighting and display can be changed by selecting the options 'Display Mode' or 'Invert Lighting'.
There are five different display modes as shown below:
To change the lighting effects select 'Invert Lighting'.
The mesh colors can be changed by using the 'Color' option in the menu.
5.2.9 Mesh Clipping |
Clipping tools can be used to adjust the frames of the mesh independently of other objects.
The buttons shown below can be used for this purpose.
The buttons used for clipping are described in the section entitled Clipping Tools.
5.2.10 Save Mesh |
You can save a mesh as a wavefront object by right clicking on the mesh in the ICM Workspace and selecting SaveAs.
5.2.11 Occlusion Shading |
The occulusion shading option provides better representation of depth within a cavity. The color of each surface element of a grob (mesh) is changed by mixing its own color with the background depending on the burial of the surface element
To add occlusion shading:
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