Subject: Re: CCL: Removing all Hydrogens in InsightII

From: Ken Butenhof <kenb-.at.-accelrys.com>
Date: Fri, 19 Sep 2003 15:44:33 -0400

Francois:

The best procedure is to first display ONLY hydrogens (Molecule/Display, 
with Display_Only option on),  select the displayed atom (by dragging a 
selection box around the displayed atoms you wish to delete) then hit the 
delete key.   You can then display all atoms and save.

Ken
_______________________________________________
Kenneth Butenhof          phone:  800 756-4674
Principal Scientist          email:    kenb-.at.-accelrys.com
Accelrys Inc.                   web:     www.accelrys.com

"Peter Gannett" <pgannett-.at.-hsc.wvu.edu> 
Sent by: "Computational Chemistry List" <chemistry-request-.at.-ccl.net>
09/19/2003 07:49 AM

To
<chemistry-.at.-ccl.net>, <fyd-.at.-u-picardie.fr>
cc

Subject
CCL:Hydrogens in InsightII

Francois:

It would probably be easier to write the pdb file and then use the egrep 
command with the -v option, which can be used to exclude all lines 
containing hydrogens, and then dump it to a new file. 

Pete Gannett

>>> FyD <fyd-.at.-u-picardie.fr> 09/18/03 08:24PM >>>
Dear All,

I would interested in knowing 'the command' in insightII which allows to
automatically REMOVE all the hydrogens (of an oligonucleotide) in order to 
save
the structure (to the PDB format) without these hydrogens, keeping only 
the
heavy atoms.

Thanks, regards, Francois

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