How can I view only the ligand and surrounding residues rather than the whole protein-ligand complex?
Having loaded a protein-ligand complex in Hermes, you need to define how large you want your complex to look. To do so, right-click in Hermes and navigate to 'Selection', then 'Select', then 'Set Selection Radius', then input a value e.g. 10 for creating a 10 Angstroms selection around your ligand.
To select all atoms of the ligand, pick an atom in the ligand, right-click and navigate to 'Selection', then 'Select Molecule'.
To select the protein atoms within e.g. 10 Angstroms of your ligand, with the ligand already selected (highlighted) as above, right-click in the background and navigate to 'Selection', then 'Select', then 'Select Within Range of Selected (all proteins)'.
Then, right-click in an empty area in the Hermes 3D display and navigate to 'Show/Hide', then 'Show Only'.
You now have displayed in Hermes a protein-ligand complex focussed on the protein atoms within e.g. 10 Angstroms of the ligand.