[MMTK] MMTK and missing atoms

Sabine Beraud Sabine Beraud <sabine@nmr.clarku.edu>
Mon, 21 Oct 2002 14:58:33 -0400 (EDT)

Hi Konrad,

Thanks for your reply. I would still need your help to develop one point:  

>If you can then somehow fix the missing atom positions for non-hydrogens,
>you can also call the hydrogen construction explicitly:

In fact "how to fix those missing atom positions" was my intial question, since 
I need to have hydrogen positions (at least HN positions on the backbone). As I 
need to scan a large number of proteins files (and about 1 file on 7 has missing 
atom(s)) fixing those missing atoms by hand (the only solution that I found 
untill now) will not be very efficient. Do you know a best solution?

If not, is it possible to add only HN hydrogen atoms (most of missing atoms are 
side-chain carbons) for exemple with the command:
>  monomer.findHydrogenPositions()

Thanks again,


Sabine Beraud
Carlson School of Chemistry                          
Clark University                                     
950 Main Street
Worcester, MA 01610-1477
Tel: +1-508-793-7112            Fax: +1-508-793-8861 
E-mail: sabine@nmr.clarku.edu