[phenixbb] how to remove hydrogen from pdb

Ryan Spencer rspencer at uci.edu
Thu Feb 6 10:31:44 PST 2014

Hi Afshan,

This is from the documentation online. 



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.





From: phenixbb-bounces at phenix-online.org
[mailto:phenixbb-bounces at phenix-online.org] On Behalf Of Afshan Begum
Sent: Thursday, February 06, 2014 9:12 AM
To: phenixbb at phenix-online.org
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


Dr. Afshan Begum 


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