Jared,<br><br>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.<br><br>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.<br>
<br>Regards,<br><br>Louis<br><br><br><div class="gmail_quote">On Mon, Feb 28, 2011 at 4:09 PM, Sampson, Jared <span dir="ltr"><<a href="mailto:Jared.Sampson@nyumc.org">Jared.Sampson@nyumc.org</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
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.<br>
<br>
1. Add hydrogens to the whole model using phenix.reduce.<br>
<br>
� � � �phenix.reduce model.pdb > model_reduce.pdb<br>
<br>
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:<br>
<br>
� � � �load model_reduce.pdb<br>
� � � �remove (elem H and not resi 10)<br>
� � � �save model_resi10_H.pdb, model_reduce<br>
<br>
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?<br>
<br>
Good luck,<br>
--<br>
Jared Sampson<br>
Xiangpeng Kong Lab<br>
NYU Langone Medical Center<br>
New York, NY 10016<br>
<a href="http://kong.med.nyu.edu" target="_blank">http://kong.med.nyu.edu</a><br>
212-263-7898<br>
<div><div></div><div class="h5"><br>
On Feb 28, 2011, at 3:37 PM, Jeff Headd wrote:<br>
<br>
> Hi Louis,<br>
><br>
> Hydrogen atoms in Phenix are added using the Reduce program, and one<br>
> of the real strengths of Reduce is that it determines H-atom positions<br>
> by optimizing the local H-bond network. By only adding hydrogens to<br>
> one residue, this step would be lost.<br>
><br>
> Is there a reason that you'd like to add H atoms to just one residue?<br>
><br>
> You can find out more about Reduce here:<br>
><br>
> <a href="http://kinemage.biochem.duke.edu/software/reduce.php" target="_blank">http://kinemage.biochem.duke.edu/software/reduce.php</a><br>
><br>
> Thanks,<br>
> Jeff<br>
><br>
> On Mon, Feb 28, 2011 at 8:45 AM, Louis Lazar <<a href="mailto:louisl@brandeis.edu">louisl@brandeis.edu</a>> wrote:<br>
>> All,<br>
>><br>
>> I was curious if there is a way to add hydrogens to an individual residue.<br>
>> For example, rather than running the command: phenix.ready_set model.pdb,<br>
>> run something like:<br>
>><br>
>> phenix.ready_set model.pdb resid=X or<br>
>><br>
>> phenix.ready_set=resid 10 model.pdb<br>
>><br>
>> Any thoughts/recommendations on the subject are greatly appreciated. Thanks<br>
>> in advance.<br>
>><br>
>> Louis<br>
>><br>
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