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<DIV>Hi Afshan，</DIV>
<DIV> </DIV>
<DIV>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.</DIV>
<DIV>###</DIV>
<DIV># remove_Hydrogen.sh</DIV>
<DIV>pdbcur XYZIN $1 XYZOUT $1_noH.pdb<<EOF</DIV>
<DIV>DELHYD</DIV>
<DIV>END</DIV>
<DIV>EOF</DIV>
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<DIV><FONT face=Arial>###</FONT></DIV>
<DIV><FONT face=Arial></FONT> </DIV>
<DIV><FONT face=Arial>Save the part between the two ### as a text file with name
“remove_Hydrogen.sh”, then turn it into an excutable:</FONT></DIV>
<DIV><FONT face=Arial>>chmod 755 remove_Hydrogen.sh</FONT></DIV>
<DIV><FONT face=Arial></FONT> </DIV>
<DIV><FONT face=Arial>To use it:</FONT></DIV>
<DIV><FONT face=Arial>>./remove_Hydrogen.sh xxxx.pdb</FONT></DIV>
<DIV><FONT face=Arial></FONT> </DIV>
<DIV><FONT face=Arial>Zhijie</FONT></DIV>
<DIV><FONT face=Arial></FONT> </DIV>
<DIV><FONT face=Arial></FONT> </DIV>
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<DIV style="font-color: black"><B>From:</B> <A title=afshan490@yahoo.com
href="mailto:afshan490@yahoo.com">Afshan Begum</A> </DIV>
<DIV><B>Sent:</B> Thursday, February 06, 2014 12:12 PM</DIV>
<DIV><B>To:</B> <A title=phenixbb@phenix-online.org
href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</A> </DIV>
<DIV><B>Subject:</B> [phenixbb] how to remove hydrogen from
pdb</DIV></DIV></DIV>
<DIV> </DIV></DIV>
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<DIV>Dear Experts,<BR><BR>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<FONT color=#40007f><BR><SPAN
style="COLOR: rgb(0,0,0)"><SPAN style="FONT-WEIGHT: bold"><BR><BR>Best
Regards</SPAN></SPAN><BR><BR style="COLOR: rgb(0,0,0); FONT-WEIGHT: bold"><SPAN
style="COLOR: rgb(0,0,0); FONT-WEIGHT: bold">AFSHAN</SPAN><BR></FONT></DIV>
<DIV><FONT color=#40007f></FONT></DIV>
<DIV><FONT color=#40007f>===========================================<BR><SPAN
style="COLOR: rgb(0,0,127); FONT-WEIGHT: bold">Dr. Afshan Begum
</SPAN><BR></FONT><A
href="http://de.mc517.mail.yahoo.com/mc/compose?to=Betzel@unisgi1.desy.de"
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<DIV><FONT color=#40007f><SPAN style="BORDER-BOTTOM: rgb(0,102,204) 1px dashed"
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<DIV><FONT color=#40007f></FONT></DIV></DIV>
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