[phenixbb] pdb file with duplicate atom names (Hydrogens)
pafonine at lbl.gov
Thu Jun 12 21:57:31 PDT 2014
> 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
then use the new file with H added from this point on.
Note, you can do both steps using the GUI.
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