[phenixbb] Question about Adding Hydrogens
louisl at brandeis.edu
Tue Mar 1 08:09:26 PST 2011
Would just like to thank everyone for all of their helpful suggestions. Was
doing a lot of replies off list. Thanks again.
On Tue, Mar 1, 2011 at 1:18 AM, Pavel Afonine <pafonine at 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)"
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