[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)"
Pavel.
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