Hi Afshan,

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

http://www.phenix-online.org/newsletter/CCN_2012_01.pdf
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 R-factors!).

All the best,
Pavel

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