Re: [phenixbb] Question about Adding Hydrogens

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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