[phenixbb] Question about Adding Hydrogens

Sampson, Jared Jared.Sampson at nyumc.org
Mon Feb 28 13:09:39 PST 2011

Hi Louis - Since, as others have mentioned, this functionality doesn't exist in phenix.refine alone, here's the 2-step workaround that I came up with.

1. Add hydrogens to the whole model using phenix.reduce.

	phenix.reduce model.pdb > model_reduce.pdb

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

I just tried it with my own pdb, and it seems as though it should achieve your desired end result.  Out of curiosity, what is the rationale for using only 1 residue's worth of hydrogens?

Good luck,
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
New York, NY 10016

On Feb 28, 2011, at 3:37 PM, Jeff Headd wrote:

> Hi Louis,
> Hydrogen atoms in Phenix are added using the Reduce program, and one
> of the real strengths of Reduce is that it determines H-atom positions
> by optimizing the local H-bond network. By only adding hydrogens to
> one residue, this step would be lost.
> Is there a reason that you'd like to add H atoms to just one residue?
> You can find out more about Reduce here:
> http://kinemage.biochem.duke.edu/software/reduce.php
> Thanks,
> Jeff
> On Mon, Feb 28, 2011 at 8:45 AM, Louis Lazar <louisl at brandeis.edu> wrote:
>> All,
>> I was curious if there is a way to add hydrogens to an individual residue.
>> For example, rather than running the command: phenix.ready_set model.pdb,
>> run something like:
>> phenix.ready_set model.pdb resid=X or
>> phenix.ready_set=resid 10 model.pdb
>> Any thoughts/recommendations on the subject are greatly appreciated. Thanks
>> in advance.
>> Louis
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