Edit

Structure editing and modification tools.

Commands

/edit hadd

Add hydrogen atoms.

/edit hadd protein
/edit hadd ligand

/edit remove

Remove atoms from a selection.

/edit remove solvent       # Remove water
/edit remove hydrogens     # Remove hydrogens

/edit alter

Alter atom properties.

/edit alter protein b=0     # Set all B-factors to 0
/edit alter chain A chain='B'  # Rename chain

/edit extract

Extract a selection into a new object.

/edit extract my_ligand organic
/edit extract chain_a chain A

/edit bond

Create a bond between two atoms.

/edit bond A/45/SG A/89/SG

/edit unbond

Remove a bond.

/edit unbond A/45/SG A/89/SG

/edit minimize

Energy minimize a selection.

/edit minimize ligand

/edit build

Build atoms/residues.

/edit build ALA    # Build alanine

/edit split

Split object into separate chains.

/edit split protein

/edit moveout

Move a selection to a new object.

/edit moveout ligand

/edit copy

Copy a selection to a new object.

/edit copy chain_a chain A

/edit fixchem

Fix chemistry issues (missing atoms, valence errors).

/edit fixchem protein