Aug 4 2022
[ Selection | Quick Selection | Selection Levels | Selection Check | Orange Selection | Clear | Change Selection | Filter | Workspace Selections | Workspace Navigation | Select Object | Select Molecule | Select Residue | Select All | Neighbors | Neigh/Graphical | Neigh/Workspace | Residue Number | Alignment and Table | Links | Tags ]
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:
The following buttons can be used to make a selection once a structure is displayed.
To make a quick selection the following buttons can be used.
To select parts of your structure:
To pick individual atoms:
It is possible to change the level of selection before or during the building of a selection. The selection level drop-down button can be used to do this (see image below).
For example, a C-alpha of a residue is selected but one would like to select all atoms in the residue. You can change the level to Residues. This selection can then be changed into all atoms of the residue by then selecting the Atoms level again. Or you can use the Propagate Selection to all Atoms button (see image below).
It is also important to observe the selection mode that is being used. There are four modes:
All selections are displayed as green crosses in the graphical display and blue in the ICM Workspace. All green selections are returned to a variable called as_graph.
Sometimes it is necesary to have two different selections. The Orange selection allows you to do this it is useful for such operations as superposition and more technical procedures such as designing a protein loop. The orange selection is returned to a variable called as2_graph.
To unselect everything you have previously selected:
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.
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 or you might want to just select the charged residues.
The button shown below enables you to filter your selection:
Right click on a selection and a menu as shown below will be displayed.
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.
Once you have mastered how to navigate the ICM workspace making a selection will become easier. Each object is divided into 3 levels:
To select the whole object:
Use the CTRL button to select multiple non-contiguous objects or if they are continuous you can use double click and hold the tab button.
To select a molecule(s):
Use the CTRL button to select multiple non-contiguous molecules or if they are continuous you can use double click and hold the tab button.
There are different options to select residues:
Use the select residue button.
Ctrl + A will select everything in the ICM workspace, and Ctrl + Shift + A will unselect your objects.
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.
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. <>
To select neighboring atoms or residues around a sphere of a certain radius from a residue in the ICM workspace:
To select by residue number:
Descriptions on how to make selections in Alignments and Tables are in the sections entitled Making Selections in Alignments and Making Table Selections.
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:
It is sometimes convenient to tag selections so you can come back and use them at a later date. To do this:
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