Re: [Jmol-users] Why aren't the implicit hydrogens showing in my model?

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

Brenton,

"showHydrogens" are for *explicit* hydrogens. If you want Jmol to attempt
to calculate implicit hydrogens you can try from the console:

calculate hydrogen

A better alternative, if this is a PDB file is:

set pdbAddHydrogens TRUE

which will automatically add hydrogen atoms and multiple bonding when a PDB
file is loaded, fetching the necessary ligand files to determine bonding in
ligands.

Bob Hanson






On Mon, Apr 8, 2013 at 7:56 AM, Brenton Horne <bre...@gm...>wrote:

> I have installed Jmol from the sh file, but for some reason the implicit
> hydrogens are hidden in my models. I have "Show Hydrogens" enabled (i.e.
> the box ticked) under Style->Atoms menu that appears on right clicking the
> molecule. How do I overcome this problem? I am running Ubuntu 12.10 32 bit,
> with OpenJDK Java 6 as my Java platform.
>
>
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-- 
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


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