[phenixbb] Question about Adding Hydrogens

Louis Lazar louisl at brandeis.edu
Mon Feb 28 13:21:22 PST 2011


Jared,

Thanks for your response. Your workaround is useful if you just wanted
hydrogen atoms on one residue, but in actuality my problem/situation is a
little different.

I have a high resolution structure that I added hydrogen atoms to, and upon
further inspection of the model realized that a terminal residue in one of
my chains was oriented incorrectly (the terminal oxygen should be where the
R group was placed in the density, and vice versa). So I deleted that
residue, added a terminal residue back in with the OXT oxygen in Coot, but
during the add terminal residue step, it does not include hydrogens. This is
why I was curious if I could add the hydrogens back to that residue
specifically without altering the rest of the model. I could also have just
gone back to the model before hydrogens were added, fixed the model, then
added hydrogens, but was curious if there was a faster fix. Thanks again for
your response.

Regards,

Louis


On Mon, Feb 28, 2011 at 4:09 PM, Sampson, Jared <Jared.Sampson at nyumc.org>wrote:

> 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
> http://kong.med.nyu.edu
> 212-263-7898
>
> 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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> >>
> >>
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>
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