Subject: Re: CCL:Hydrogens in InsightII

From: Jeff Nauss <jnauss.-at-.accelrys.com>
Date: Fri, 19 Sep 2003 13:29:04 -0700

I think the simplest way would be to use in InsightII Molecule | Display 
and turn off the display of the hydrogens.  Then go to Molecule | Put with 
the Displayed toggle on.  Only the visible atoms are written to the file 
and you retain your original structure.

Though your suggestion will certainly work if the file is already created.

Jeff
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Jeffrey L. Nauss, Ph.D.
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"Peter Gannett" <pgannett.-at-.hsc.wvu.edu> 
Sent by: "Computational Chemistry List" <chemistry-request.-at-.ccl.net>
09/19/2003 04:49 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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