On Tue, Mar 1, 2011 at 1:18 AM, Pavel Afonine <pafonine@lbl.gov> wrote:

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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