Choose Ligands and Cofactors Dialog Box

Choose Ligands and Cofactors Dialog Box Features

• Select items to preserve table
• Keep all waters option
• Apply binding site proximity constraints option
• Constrain residues list
• Pick button

Select items to preserve table

Select the ligands or cofactors to include in the homology model. Click Select All or Clear All below the table to include all hets in the model, or exclude them all.

Only the ligands and cofactors within 5 Å of the chain used for the template are included in the list.

Keep all waters option

Keep all the waters from the template in the homology model. For a chimeric model, keep all the waters from each template that are closely associated with the region chosen for the model. By default, waters are not kept.

Apply binding site proximity constraints option

Apply constraints between residues in the binding site and the ligand or cofactors in the homology model, by picking residues in the target sequence. The Constrain residues list and tools are displayed when you select this option, and the ligand contact annotation is displayed in the sequence viewer, to guide the selection of residues.

Constrain residues list

This list displays the residues from the target sequence that have been selected for constraint to a ligand. Click Remove All below the list to clear the list. Instructions are given in the list before it is populated and also with the information icon.

Pick button

Click to pick the residues in the target sequence for constraint to the ligand. Ligand residues that have heavy atoms within 4 Å of a template residue heavy atom are marked in red in the ligand contact annotation, and in orange if they are within 6 Å. These can be used as a guide to picking constraints.