Do we have method to mutate the iCode-containing residue?

[locitran]

Do we have a method to mutate the iCode-containing residue?
It seems applyMutations doesn't work.

For example, how can we mutate the residue GLY-9A-chainA of pdbID 1S9V?

[peastman]

This would be a useful feature to add to applyMutations(). A PR would be welcome!

If you know what residue you want to replace, it's pretty easy to do it yourself. applyMutations() is a very simple method. Here's the part that actually makes the change. It just changes the residue's name field and deletes any existing atoms that shouldn't be present.

pdbfixer/pdbfixer/pdbfixer.py

Lines 794 to 810 in 6bf10e1

	deleteAtoms = [] # list of atoms to delete
	# Find atoms that should be deleted.
	for residue in residue_map.keys():
	replaceWith = residue_map[residue]
	residue.name = replaceWith
	template = self.templates[replaceWith]
	standardAtoms = set(atom.name for atom in template.topology.atoms())
	for atom in residue.atoms():
	if atom.element in (None, hydrogen) or atom.name not in standardAtoms:
	deleteAtoms.append(atom)
	# Delete atoms queued to be deleted.
	modeller = app.Modeller(self.topology, self.positions)
	modeller.delete(deleteAtoms)
	self.topology = modeller.topology
	self.positions = modeller.positions

[locitran]

Thank you @peastman
I will give a try :-)