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There is a quick and easy way to do this as described in the Tips section of the manual entitled "Quick Binding Pocket Display" or you may want to follow the instructions below for a more user-defined method.
- Double click on the ligand name in the ICM workspace and it will be highlighted in blue.
- Right click on the name and select the Neighbors option.
- Enter 6Å (or whatever distance is appropriate for the ligand) for the sphere radius selection. Green crosses represent selected residues.
- Select type from the drop down menu "same_object_other_chains".
- Convert your selection to a residue selection if you wish using the button shown in the example below.
- Go to the display tab and select the representation you would like for the residues surrounding the pocket. Next use the "Invert Graphical Selection" button to select everything else other than the residues around the pocket and undisplay them by clicking on the representation buttons in the display tab.
- Select the residues around the pocket using the spherical selection method as described above.
- Select the xstick representation button in the display panel
- Select the invert selection button
- Select the ribbon display button and the ribbon display will be removed from outside the pocket.
Steps shown graphically below for the kinase 1ql6 and the atp ligand.
Step 1: Receptor (1ql6.a) is in ribbon display:
Step 2: Double click and select the atp molecule in the ICM Workspace
Step 3: Right click on the selected atp molecule in the ICM Workspace and select Neighbors. Enter radius and type of selection. Click OK and you will see a graphical selection of green crosses around the pocket.
Step 4: Convert your selection to a residue selection if you wish. You will then see green "R" in the graphical selection rather than green crosses.
Step 5: Select the xstick representation and the residues around the ligand will be displayed.
Step:6: If you want to undisplay the rest of the receptor outside the pocket use the invert selection button and then click the ribbon representation button.
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