Re: [Jmol-users] Calculate hydrogens bound to specific atoms

[Robert H. <ha...@st...>]

The calculate command accepts a parameter for which ones:

calculate hydrogens {*:A}

"delete" is a command like "select" and "display"

delete hydrogens

just says what atoms to delete.  "delete carbons" would do that. So be
specific:

delete *:A and hydrogens

HOWEVER -- be aware that "calculate hydrogens" is a relatively crude
command. If this is a PDB file, the better option is:

set pdbAddHydrogens
load xxxx.pdb

The difference is that "calculate hydrogens" can only handle the standard
amino acids and nucleic acids. It won't properly add hydrogens to HETATM
groups the way set pdbAddHydrogens will.

Bob




On Sat, Aug 13, 2011 at 9:40 AM, Pascal Auffinger <
p.a...@ib...> wrote:

> Hello,
>
> Didn't found any information related to this action,
> Is it possible by using the command "Calculate/Delete hydrogens" to add an
> hydrogen only to a specific atom ?
>
> Thanks for the reply
>
> Pascal
>
>
>
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-- 
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107


If nature does not answer first what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900