[phenixbb] pdb file with duplicate atom names (Hydrogens)

Pavel Afonine pafonine at lbl.gov
Thu Jun 12 21:54:13 PDT 2014

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 from this point on.

Note, you can do both steps using the GUI.


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