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 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 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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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 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 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 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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Would just like to thank everyone for all of their helpful suggestions. Was doing a lot of replies off list. Thanks again. Louis On Tue, Mar 1, 2011 at 1:18 AM, Pavel Afonine wrote:

Hi Jared,

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

you could do it in PHENIX:

phenix.pdbtools model_with_H.pdb remove="element H and not (chain A and resseq 10)"

Pavel.

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