PyMol Editing Functions

Molecule Tutorials - Herong's Tutorial Examples

∟PyMol Editing Functions

This chapter provides quick introductions on using PyMol to edit molecule structure using 'edit' to identify picked atoms, and 'replace/attach' command to replace or attach new atoms to picked atoms in PyMol.

"pk1", "pk2", "pk3" and "pk4" Selections

"edit id n1, id n2, id n3, id n4" Commands

"remove pk*" and "remove_picked" Commands

"unbond pk1, pk2" and "bond pk1, pk2" Commands

"replace new_atom, ..." Replace pk1 with New Atom

"attach new_atom, ..." Attach to pk1 with New Atom

Build Alcohol Molecule with PyMol

Takeaways:

PyMol allows you to create 4 special atom selections, pk1, pk2, pk3 and pk4, by clicking atoms in mouse editing mode.
PyMol allows you to create 4 special atom selections, pk1, pk2, pk3 and pk4, using "edit id n1, id n2, id n3, id n4" command.
PyMol allows you to delete picked atoms using "remove pk*" and "remove_picked" commands.
PyMol allows you to unbond and bond two picked atoms using "unbond" and "bond" commands.
PyMol allows you to replace the first picked atom with a new atom using the "replace" command.
PyMol allows you to attach to the first picked atom with a new atom using the "attach" command.