[phenixbb] how to remove hydrogen from pdb

Zhijie Li zhijie.li at utoronto.ca
Thu Feb 6 14:43:57 PST 2014

Hi Afshan,

Here is my little Linux shell script for removing hydrogen atoms from PDB. It uses the PDBCUR program in CCP4 package (my apologies to the PhenixBB!). With little modification you can also turn it into scripts for other things, like, to remove alternative comfomations, ANISOU,etc.. Please read the CCP4 manual for PDBCUR.
# remove_Hydrogen.sh
pdbcur XYZIN $1 XYZOUT $1_noH.pdb<<EOF

Save the part between the two ### as a text file with name “remove_Hydrogen.sh”, then turn it into an excutable:
>chmod 755 remove_Hydrogen.sh

To use it:
>./remove_Hydrogen.sh xxxx.pdb


From: Afshan Begum 
Sent: Thursday, February 06, 2014 12:12 PM
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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