Is there a way to selectively show implicit hydrogens in just one or
a few amino acids?
Michael Patrick
UW-Madison
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
<<mailto:[email protected]>[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>http://www.cisco.com/web/learning/employer_resources/index.html
_______________________________________________
Jmol-users mailing list
<mailto:[email protected]>[email protected]
<https://lists.sourceforge.net/lists/listinfo/jmol-users>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>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
------------------------------------------------------------------------------
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
