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[ Molecule Representation and Color | Annotation | Labels | 2D and 3D Labels | Graphical Selections Tutorial | Basic Selections | Sequence Selections | Spherical Selection | Filter Selection | Residue Propogate | 3D Documents | Plots and Histograms | Histogram | Plot ]
22.1.1 Change Molecule Representation and Color |
22.1.2 Annotation |
22.1.3 Labels |
22.1.4 2D and 3D Labels |
22.1.5 Graphical Selections Tutorial |
All buttons relating to graphical selections are shaded green. These buttons are shown here and are located at the top of the graphical user interface and along the side.
The File/New window is a great place to start learning how to use ICM as it provides a quick and easy way to generate new peptides, compounds, DNA/RNA, sequences and graphical objects.
The examples in this section will take you through the basics of making selections in the graphical user interface using objects generated from File/new.
22.1.6 Making Basic Selections |
Now let us display the peptide in wire format and remove the ribbon and xstick representation
To do this:
Now we will display different parts of the peptide in different representations.
Other ways of making selections.
22.1.7 Making Sequence Selections in the ICM Workspace |
Selections can be made on the sequence of the peptide. This can be done by expanding the sequence display in the ICM Workspace and clicking and dragging on the sequence as shown below. Non-contiguous selections can be made by clicking/dragging over the sequence whilst holding down the Ctrl key.
22.1.8 Making a Spherical Selection. |
In this example we will select the residues surrounding a ligand.
22.1.9 Filtering a Selection. |
In this example we will filter the selection made in the previous example and select only His, Asn, Gln and Pro residues surrounding the ligand.
NOTE: Only amino acid residues in the current selection will be available in the Filter. |
Display the selected residues in wire format.
22.1.10 Propogating a selection to all atoms in a residue. |
Sometimes it is useful to propogate a selection to all atoms in a residue. For example when selecting the residues surrounding a ligand within a certain angstrom radius the selection will only pick up certain atoms of a residue. The button shown below can be used to propogate the selection to all atoms in a residue.
22.1.11 Creating Fully Interactive Slides for PowerPoint and the Web Tutorial |
See the ActiveICM How To Guide for instructions on how to view in the web and PowerPoint.
22.1.12 How to Generate Plots and Histograms |
22.1.13 How to make a histogram. |
22.1.14 How to make an X-Y scatter plot. |
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