[phenixbb] Question about Adding Hydrogens

Robert Immormino immormino at gmail.com
Mon Feb 28 13:38:50 PST 2011


Hi Louis,

It may be mute at this point, but I think reduce can do this with the
--no-build flag.  If I understand right with the no-build flag missing
hydrogens are added, but a penalty is added to the optimization step
for the hydrogens that were already present such that the positions
they are in are unlikely to change.  Probably this was intended for
filling in missing hydrogens from neutron experiments or NMR where the
hydrogen positions are experimentally determined, but it may work
perfectly for your case.

Try
phenix.reduce --no-build my_protein.pdb > my_protein_H.pdb

Best Wishes,
-bob


On Mon, Feb 28, 2011 at 4:21 PM, Louis Lazar <louisl at brandeis.edu> wrote:
> 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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