How do I place these commands into the console? I opened the console via
going to the help menu but when I type what you have said and click "Enter"
nothing happens.
On Tue, Apr 9, 2013 at 12:32 AM, Robert Hanson <[email protected]> wrote:
> 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.
>>
>>
>> ------------------------------------------------------------------------------
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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
>
>
>
> ------------------------------------------------------------------------------
> 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
>
>
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Reduce network management and security costs.Learn how to hire
the most talented Cisco Certified professionals. Visit the
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http://www.cisco.com/web/learning/employer_resources/index.html
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