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There will be many occasions when you will have to make selections. For example, if you want to display a particular region or molecule contained within your protein structure or if you want to select residues around a binding pocket. If you have a molecule displayed in the graphics window, then selections will be displayed as green crosses. The selection you have made is also displayed at the top of the ICM Workspace. It is always a good idea to keep an eye on what is selected and what isnt.
There are four basic levels of selection
You can make selections in:
3.2.1 Graphical Selections |
In this section you will learn how to select parts and certain regions of molecules from the 3D graphical display. Graphical and molecule selections are required for many operations within ICM. For example, if you wanted to display graphically part of a molecule or if you wanted to perform a minimization of residues within a sphere of an imporant atom.
3.2.2 Selection Tools |
The following buttons can be used to make a selection once a structure is displayed.
NOTE: All selection tool buttons are colored green. Graphical selections are represented as green crosses. |
3.2.3 Basic Selections |
To make a basic selection (ie nothing too complicated!) the following buttons can be used.
To select parts of your structure:
OR
To pick individual atoms:
You can also change the level of a selection using the button shown below. Click and hold the button to choose the level of selection. For example, if you have selected atoms you can convert the selection to all atoms at the residue level by choosing the Residues option.
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 stored in the as_graph variable. |
3.2.4 Clear Selection |
To unselect everything you have previously selected:
OR
3.2.5 Altering a Selection |
Once you have made a selection you may wish to add or remove parts of the selection. The buttons shown below allow you to accomplish this.
To add or remove from your current selection:
You may also wish to invert your selection in a specific part of the structure.
The parts that are currently selected will become unselected, and the unselected parts will become selected.
In order to invert a selection:
If you wish to select and unselect certain regions of a selection the toggle selection button is very useful.
NOTE: The selection you have made is recorded at the top of the ICM workplace. Any selection is stored in the variable as_graph. |
3.2.6 Filter Selection |
You may want to be very specific about a selection you want to make. For example you may only want to select protein backbone atoms.
The button shown below enables you to filter your selection:
Or
Right click on a selection and a menu as shown below will be displayed.
If you wish to filter and select by residue or atom type:
To select just the protein or just the hetatoms as well:
To filter by residue type or secondary structure:
NOTE: You may need to click on the button marked with a '+' symbol to expand the options. |
To filter by atom type.
NOTE: You may need to click on the button marked with a '+' symbol to expand the options. |
To select neighbors to a particular selection.
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 |
3.2.7 Workspace Selections |
In the default GUI layout the workspace panel is located to the left of the 3D graphics display. It is a great tool for keeping track of all your sequences, pdb structures, objects, tables and alignments. As you will see in this section it also provides a way of making selections.
3.2.8 Workspace Navigation |
Once you have mastered how to navigate the ICM workspace making a selection will become easier. Each object is divided into 3 levels:
NOTE: You can expand each level of the ICM workspace by clicking the "+" button as shown above. |
3.2.9 Selecting the Whole Object |
To select the whole object:
3.2.10 Selecting Amino Acids |
There are three options to select individual amino acid residues:
OPTION 1:
OPTION 2:
OPTION 3:
NOTE: Ctrl + A will select everything in the ICM workspace, and Ctrl + Shift + A will unselect your objects. |
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 |
3.2.11 Selecting Neighbors |
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.
3.2.12 Selecting Neighbors: Graphical |
To select neighboring atoms or residues around a sphere of a certain radius:
This option will allow you to make a spherical selection.
The window will open as displayed as below:
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. <>
3.2.13 Selecting Neighbors: Workspace |
To select neighboring atoms or residues around a sphere of a certain radius from a residue in the ICM workspace:
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 |
3.2.14 Alignment and Table Selections |
Descriptions on how to make selections in Alignments and Tables are in the sections entitled Making Selections in Alignments and Making Table Selections.
3.2.15 Making Links |
It is sometimes necesary to make links between sequences objects and alignments. A link enables you to make selections in one environment such as an alignment and then these selections are transfered to the object such as the PDB structure displayed.
If a link is made then a symbol will be displayed next to the object in the ICM workspace. In the example shown below subunit_a of the X-ray structure 1ql6 is linked to the sequence 1ql6_a and the alignment called 'alig'.
If an object is linked to an alignment a symbol as shown below will be displayed.
To link a sequence from an object - extract the sequence from the object.
To link a sequence and object to an alignment.
Use the extracted sequence as described above to build your alignment.
In addition a link can be made between a structure and alignment by:
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