[phenixbb] Question about Adding Hydrogens

[Jeff Headd]

Hi Louis,

In the case you've described, running your model through
phenix.ready_set or running phenix.reduce -build model.pdb >
modelFH.pdb will only add the missing hydrogens. The other H atom
positions will be optimized in terms of bond-lengths and H-bond
network, but the heavy atom positions will not be changed.

Is there a reason that you don't want the H atoms to move at all? If
there is, you should get the desired behavior with:

phenix.reduce -keep -noadjust model.pdb > modelH.pdb

If you have further questions, please let me know.

Thanks,
Jeff



On Mon, Feb 28, 2011 at 1:21 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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>> >>
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