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 <[email protected]>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.
>
>
> ------------------------------------------------------------------------------
> Minimize network downtime and maximize team effectiveness.
> Reduce network management and security costs.Learn how to hire
> the most talented Cisco Certified professionals. Visit the
> Employer Resources Portal
> http://www.cisco.com/web/learning/employer_resources/index.html
> _______________________________________________
> Jmol-users mailing list
> [email protected]
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
--
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
------------------------------------------------------------------------------
Minimize network downtime and maximize team effectiveness.
Reduce network management and security costs.Learn how to hire
the most talented Cisco Certified professionals. Visit the
Employer Resources Portal
http://www.cisco.com/web/learning/employer_resources/index.html
_______________________________________________
Jmol-users mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/jmol-users
