[phenixbb] Question about Adding Hydrogens

Pavel Afonine pafonine at lbl.gov
Mon Feb 28 22:18:39 PST 2011

  Hi Jared,

> 2. In PyMOL (or another similarly capable program), load the molecule, remove the unwanted hydrogens, and save the new pdb. If you're not familiar with PyMOL selection syntax, try something like this:
> 	load model_reduce.pdb
> 	remove (elem H and not resi 10)
> 	save model_resi10_H.pdb, model_reduce

you could do it in PHENIX:

phenix.pdbtools model_with_H.pdb remove="element H and not (chain A and 
resseq 10)"


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