[ Delete | Delete All | Select All | Search in Workspace | Selection | Invert Selection | Clear Selection | Neighbor Selection | Undo | Redo | Restore | PDB Search | PDB Search by Field | PDB Search by Identity | PDB Search by Homology | PDB Search with External Sequence | Ligand Tools | Ligand Editor Preferences ]

3.2.1 Delete

This option will delete anything that is selected.

3.2.2 Delete All

This option will delete everything e.g. sequences, structures, tables ... Use with care!

3.2.3 Select All

This option will select everything e.g. sequences, structures, tables...

3.2.4 Search in Workspace

This option allow you to search for a particular text in the workspace

3.2.5 Selection

This option allows you to make a precise selection either by neighbors or specifying a particular atom or neighbor. Click on the tabs to jump between selection levels.

3.2.6 Invert Selection

This option will select everything that is not currently selected.

3.2.7 Clear Selection

This option will remove all selections. For more information on selections see the Making Selections Chapter.

3.2.8 Neighbor Selection

This option will allow you to make a spherical selection.

The window will open as displayed as below:

• Select the molecule you wish to select neighbors around. For example you can select a ligand in the ICM Workspace and then choose the Graphical Selection option in the "Select Neighbors For" dialog entry box. Or alternatively you can select the object by clicking on the drop down button next to the "Select Neighbors For" dialog entry box.
• Enter the radius in Angstroms for the neighbor selection. e.g. 5.
• Type - this option is important. This option relates to what is going to be selected. For example if you leave this option as visible and you only have ribbon representation displayed for your receptor (e.g. when selecting neighbors for a ligand) then only backbone atoms will be selected.

• visible - will select all atoms displayed within the radius selected.
• visible sidechains will select all visible side-chains - not backbone atoms.
• same_object_other_chains will select all atoms in other chains in the same object as the original selection.
• other objects will select atoms in objects other than the original selection.
• same object will select atoms in the same object as the original selection.
• all_objects will select atoms in all objects
• choose_from_list will allow you to select the object you wish to include in the neighbors selection.

• exclude source if checked will not include your original selection in the spherical selection.
• unselect water if checked will not select water molecules
• Undisplay Beyond Selection will only display the atoms selected.

3.2.9 Undo

Due to the complexities of working in an internal coordinates environment not everything can be undone or redone. Certain things like coloring and representations can be undone or redone.

3.2.10 Redo

Due to the complexities of working in an internal coordinates environment not everything can be undone or redone. Certain things like coloring and representations can be undone or redone.

3.2.11 Restore Recent Backup

ICM periodically makes a backup of your ICM project. If for whatever reason you lose an ICM session and you want to load the backup for the file use:

Edit/Restore Recent Backup

3.2.12 PDB Search

See PDB Search Tab

3.2.13 PDB Search by Field

See PDB Search Tab

3.2.14 PDB Search by Identity

See PDB Search Tab

3.2.15 PDB Search by Homology

See PDB Search Tab

3.2.16 PDB Search with External Seqeuence

See PDB Search Tab

3.2.17 Ligand Tools

See the ligand editor section of the manual.

3.2.18 Ligand Editor Preferences

See the ligand editor section of the manual.