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)'.

You now need to invert the selection; to do so, right-click and navigate to 'Selection', then 'Invert Selection'.

You now need to hide those atoms; to do so, go to Hermes to-level menu 'Display', navigate to 'Show/Hide', then 'Atoms...'. In the pop-up dialog click on the Hide radio button and then OK.

You now have displayed in Hermes a protein-ligand complex focussed on the protein atoms within e.g. 10 Angstroms of the ligand.

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