[ Neigh/Graphical | Neigh/Workspace ]

In some instances you may only want to display or select only a subset of a structure. For example you may only wish to display the residues surrounding a ligand (as shown below (ligand red; graphical selection green crosses). The "Selecting Neighbors" option selects the residues within a shpere of a defined radius.

There are two ways of selecting neighbours to a particular atom or residue in ICM. Either by right clicking on the atom or residue in the graphical display or by right clicking in the ICM workspace.

6.3.1 Selecting Neighbors: Graphical

To select neighboring atoms or residues around a sphere of a certain radius:

• First select the residue(s) or atom(s) around which you wish to select neighbors. (See the Selection Toolbar Section)
• Right click on the selection and a menu as shown below will be displayed or choose Tools/Geometry/Neighbors.

• Select the Neigbors option and a data entry box as shown below will be displayed.

• Enter the selection radius around which you wish to select.
• Select from which object you wish to make the selection from the drop down list in the "type" data entry box.

• Select whether you wish your original selection to be selected by checking the "exclude source" box.
• Select whether you wish water molecules to be selected by checking the "unselect water" box.
• There are also options to change the current selection to expand to residues, molecules, or flexible side-chains.
• Click OK and your selection will be displayed as green crosses.

NOTE: The selection you have made is always recorded at the top of the ICM workplace. If you are familiar with using the ICM terminal (See language manual) the atoms, residues, molecules or objects selected interactively in the graphics window are automatically saved in the variable as_graph. Graphical selections are shown in green (crosses) or highlighted in blue in the ICM Workspace.

6.3.2 Selecting Neighbors: Workspace

To select neighboring atoms or residues around a sphere of a certain radius from a residue in the ICM workspace:

• First select the residue in the ICM workspace around which you wish to select neighbors. (See the Residue Selection)
• Right click on the selection and a menu as shown below will be displayed.

• Select the Neigbors option and a data entry box as shown below will be displayed.
• Follow the instructions in the previous section.

NOTE: The selection you have made is always recorded at the top of the ICM workplace. If you are familiar with using the ICM terminal (See language manual) the atoms, residues, molecules or objects selected interactively in the graphics window are automatically s