Hi Rex,

I have taken over a high resolution set of protein data which has H atoms built in.

For non-H atoms having 2 or three H atoms these H atoms each carry the same atom number

in the pdb file.

Phenix will not accept this format.

Should I delete all H-atoms and reassign them in the next Phenix refinement run?

if you got structure from somewhere (not Phenix) with H already present and Phenix does not recognize them, then it's best to remove H:

phenix.reduce -trim model_with_H.pdb > model_no_H.pdb

and then add them back

phenix.ready_set model_no_H.pdb

then use the new file with H added from this point on.

Note, you can do both steps using the GUI.

Pavel