[phenixbb] how to remove hydrogen from pdb

Pavel Afonine pafonine at lbl.gov
Thu Feb 6 11:47:06 PST 2014

Hi Afshan,

it not a good idea to do this for reasons explained in great details here:

see "On contribution of hydrogen atoms to X-ray scattering".

Yes, the easiest is

phenix.reduce -trim model_with_h.pdb > model_no_h.pdb

If you do this make sure you update refinement statistics (including 

All the best,

On 2/6/14, 9:12 AM, Afshan Begum wrote:
>  Dear Experts,
> Could you kindly tell me how can i remove hydrogen from my coordinate. 
> Actually i refine my structure with phenix along all hydrogen now its 
> almost done but before submitting the molecule into PDB data bank i 
> want to remove hydrogen from the coordinate which i do not know how to 
> do,  suggestion would be appreciated
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