pocket_view
Visualize the binding pocket around a ligand as a colored surface, revealing chemical character, sidechains, H-bonds, and protein context for structural analysis.
Instructions
Visualizes the binding pocket cavity around a ligand as a colored surface.
The pocket (all residues within 5 Å of the ligand) is shown as a semi-transparent surface colored by chemical character: orange=hydrophobic, white=polar, skyblue=positive, salmon=negative. Pocket residue sidechains are shown as sticks. The ligand is shown as yellow sticks. H-bonds between the ligand and pocket are drawn as cyan dashes. The protein backbone is shown as a thin grey cartoon for context.
Input Schema
| Name | Required | Description | Default |
|---|---|---|---|
| resn | Yes | Ligand residue name (e.g. "ATP", "LIG", "ANP") | |
| obj_name | Yes | PyMOL object name (e.g. "1abc") |
Output Schema
| Name | Required | Description | Default |
|---|---|---|---|
| result | Yes |