Sep 13 2018
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).
The surface of your structure can be displayed and colored by electrostatics or binding properties. To do this:
MolSkin is a new macro that instantly makes publication quality graphics and it gives each molecule a color and colors contact patches. It undertakes the following:
To use MolSkin:
To color a surface by proximity to neighboring molecules:
To color a surface by a selection:
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 in the drop down option in the meshesh tab
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.
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
To read in a 3D Mesh from Google in KMZ or COLLADA format:
To display or undisplay the surface click in the box in the ICM workspace as shown below:
A number of options relating to meshes can be found by right clicking on the mesh in the ICM Workspace. This section describes some of these options.
Once a mesh has been created you can move it and resize it. To do this:
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 a mesh:
There are five different display modes:
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.
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.
To clip the skin independently of the object as shown in the image above:
You can save a mesh as a wavefront object by right clicking on the mesh in the ICM Workspace and selecting SaveAs.
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:
See example here.
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