Subject: Re: CCL:Adding H-atoms??

From: <[email-masked]>
Date: Tue, 7 May 96 21:36:02 EDT

>  I need to know how to add hydrogen atoms to a large crystallographic
>structure that does not report the hydrogen atom positions.
>  Programs like ALCHEMY have an "add H" option that is useful in
>drawing structures, but I can't find a good way to get the coordinates
>into ALCHEMY.
>  For example, one can convert crystallographic xyz coordinates into
>ALCHEMY input with BABEL.  But this conversion involves looking at
>the "bonding nature" of the atoms and doesn't seem to work if the
>hydrogen atoms are missing.

This is a deficiency of Babel, not Alchemy.

>  Am I doing something wrong?  If not, then is there a way to "fool"
>ALCHEMY into accepting the input coordinates so that I can use the
>"add H" option?

I would look for a way to import the coordinates into Alchemy without
using Babel as an intermediary.  That sort of approach would definitely
work with Chem3D; I have to assume the same sort of thing would would
for Alchemy.

If all you want is to see the hydrogens there, you could even use the 
freely-available Chem3D Net, which is capable of adding the hydrogens
(but not of saving the modified files).  Information about Chem3D and Chem3D
Net is available from http://www.camsoft.com

Jonathan Brecher
CambridgeSoft Corporation
[email-masked]