Hi Afshan, This is from the documentation online. http://www.phenix-online.org/documentation/refinement.htm 7.To remove hydrogens from a model: % phenix.pdbtools model.pdb remove="element H or element D" or Reduce programs can be used for this: % phenix.reduce model_h.pdb -trim > model_noH.pdb We strongly recommend to not remove hydrogen atoms after refinement since it will make the refinement statistics (R-factors, etc...) unreproducible without repeating exactly the same refinement protocol. Ryan From: [email protected] [mailto:[email protected]] On Behalf Of Afshan Begum Sent: Thursday, February 06, 2014 9:12 AM To: [email protected] Subject: [phenixbb] how to remove hydrogen from pdb 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 Best Regards AFSHAN =========================================== Dr. Afshan Begum