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

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Dr. Afshan Begum