I am working with some chemically modified residues. For consistency with MMTK, I have to move non-natural atoms in the ATOM list of the pdb. I would like to do that directly from chimera and not editing the pdbfile.

 I thought that I could alter the heteroatom value of chimera's residues to get there. But whether this is not the right attribute  or I miss something.

What I do is:

build my system, select the atoms of the non-natural and  natural part of the residue. Make a new residue and then, having selected it:

atoms=chimera.selection.currentAtoms()

for a in atoms:

     a.residue.isHet=False

This indeed changes the isHet attribute but when saving the pdb, the residue is in the  HETATM field.

Any pointer?

Best,

JD