Ligand Detection Preferences

Features

• Ligand molecule attributes section
  • Minimum # heavy atoms text box
  • Maximum # heavy atoms text box
  • Allow options
  • Small ion molecules option
  • Nucleic acids option
  • Amino acids option
• Add selected Workspace ligands to options and section
  • Add to Table button
• Excluded residues tab
• Included residues tab
• Restore Defaults button

Ligand molecule attributes section

In this section you can specify criteria for detecting ligand molecules.

Minimum # heavy atoms text box

Enter the minimum number of non-hydrogen atoms that a valid ligand molecule can have in this text box. Default: 5.

Maximum # heavy atoms text box

Enter the maximum number of non-hydrogen atoms that a valid ligand molecule can have in this text box. Default: 100.

Allow options

Choose options for molecule types that are allowed to be treated as ligands, where they would not be by default.

Small ion molecules option

Select this option to allow molecules that are small ions (less than 10 atoms) to be considered as ligands. This option is deselected by default.

Nucleic acids option

Select this option to allow molecules that consist entirely of nucleic acids to be considered as ligands.. Molecules that contain nucleic acids and other fragments are always detected as ligands. Detection of small nucleic acid chains could also detect a disconnected part of DNA or RNA, so it is important that the structure is properly prepared and any chain breaks fixed. This option is deselected by default.

Amino acids option

Select this option to allow molecules that consist entirely of amino acids to be considered as ligands. Molecules that contain amino acids and other fragments are always detected as ligands. Detection of small peptide chains could also detect a disconnected part of the protein, so it is important that the protein is properly prepared and any chain breaks fixed. This option is selected by default.

Add selected Workspace ligands to options and section

Choose whether the residues that are selected in the Workspace ligands are added to the list of included residues or the list of excluded residues, i.e. the selected ligands are valid ligands or are not valid ligands. (You can select objects other than ligands, such as single residues; the primary intention is to identify residues that should or should not be part of a ligand.) A ligand can be added to both lists, but it can only be marked as a ligand in one of the lists.

• Excluded residues list (not a ligand)—add the residues in the Workspace selection to the list of residues that are not considered to be part of a valid ligand.
• Included residues list (ligand)—add the residues in the Workspace selection to the list of residues that are considered to be part of a valid ligand. If any residues have an unknown name (UNK), the confirmation dialog box allows you to rename these residues to a name of your choice, and add that name to the list. Otherwise all UNK residues are added to the list.

Add to Table button

Add the residues in the ligand to the table in the appropriate tab. A dialog box opens, asking you to confirm the addition. This allows you to check whether the selection contains the desired residues.

Excluded residues tab

In this tab you can specify molecules that are not to be considered as ligands, by means of their residue code, which is usually 3 letters, but can be any length from 1 to 4 letters. The tab contains a table and tools to add and delete residues.

Exclude column

This column contains a checkbox for each residue. When the box is checked, the residue is excluded from consideration as a ligand. By default all residues are excluded. The checkboxes can be used to control the actual list that is used for ligand detection. If the residue is already checked as included in the Included residues tab, it is unchecked in that tab.

Residue column

This column lists the residue code for various common residues, such as cofactors and ions. The column is noneditable.

Description column

This column lists a description for each residue. The column is noneditable.

Residue to add text box

In this text box, enter the residue code of a residue that you want to add to the table.

Add button

Click this button to add the residue entered in the Residue to add text box to the table. An error is posted if the residue name is more than 4 characters long.

Delete button

Click this button to delete the selected residues from the table.

Included residues tab

In this tab you can specify residues that may validly be part of a ligand. Molecules that contain any of the listed residues are considered ligands. The residue codes are usually 3 letters, but can be any length from 1 to 4 letters. The tab contains a table and tools to add and delete residues. The table is empty by default.

Include column

This column contains a checkbox for each residue. When the box is checked, the residue is permitted to be part of a ligand. The checkboxes can be used to control the actual list that is used for ligand detection. If the residue is already checked as excluded in the Excluded residues tab, it is unchecked in that tab.

Residue column

This column lists the residue code for residues to be included as allowed in ligands. You can define custom residues by using the Workspace selection to add unknown (UNK) residues to the table with a chosen name; otherwise the residue name must be a known name.

Description column

This column lists a description for each residue. The column is noneditable.

Residue to add text box

In this text box, enter the residue code of a residue that you want to add to the table.

Add button

Click this button to add the residue entered in the Residue to add text box to the table. An error is posted if the residue name is more than 4 characters long.

Delete button

Click this button to delete the selected residues from the table.

Restore Defaults button

This button resets the settings to the defaults. It removes any residue codes added to the table and restores any default residue codes as well as redoing the settings.