Two things about that.
1) yes.
select *; delete hydrogens;calculate hydrogens
2) in the first draft of this Jmol wouldn't add hydrogens where hydrogens
already were. Now it does that IF you just say
calculate hydrogens
but if you add a set of atoms
calculate hydrogens {atomno =3}
for instance, then it fills out the valence for that set of atoms.
Bob
On Fri, Feb 12, 2010 at 1:13 PM, Otis Rothenberger <[email protected]>wrote:
> Man. Talk about someone anticipating your question. I sent my query on this
> 30 seconds before I received your answer related note. Talk about service!
>
> Actually, my question is a bit more extensive. Can you delete all the
> hydrogens so that you can make them come back correctly with addHydrogens?
>
> Otis
>
>
> On Fri, Feb 12, 2010 at 1:43 PM, Robert Hanson <[email protected]> wrote:
>
>> Yeah, I threw that bug in just to make sure people were actually using
>> this.... ;)
>>
>> OK, that's fixed for 11.9.29. There was also a problem with deleting
>> atoms. Because I know Otis will ask me for it anyway, I also added:
>>
>> set picking deleteAtom
>>
>> See http://chemapps.stolaf.edu/jmol/docs/examples-11/Jmol-11.zip
>>
>> Bob
>>
>>
>> 2010/2/12 Angel Herráez <[email protected]>
>>
>> Jmol 11.9.28 app
>>>
>>> After "calculate hydrogens", "minimize" does nothing and locks any
>>> further commands (even zap doesn't do anything)
>>>
>>> "minimize addhydrogens" produces the same lock
>>>
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> SOLARIS 10 is the OS for Data Centers - provides features such as DTrace,
>>> Predictive Self Healing and Award Winning ZFS. Get Solaris 10 NOW
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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
>>
>>
>> ------------------------------------------------------------------------------
>> SOLARIS 10 is the OS for Data Centers - provides features such as DTrace,
>> Predictive Self Healing and Award Winning ZFS. Get Solaris 10 NOW
>> http://p.sf.net/sfu/solaris-dev2dev
>>
>> _______________________________________________
>> Jmol-users mailing list
>> [email protected]
>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>
>>
>
>
> --
> Otis Rothenberger
> http://chemagic.org
>
>
> ------------------------------------------------------------------------------
> SOLARIS 10 is the OS for Data Centers - provides features such as DTrace,
> Predictive Self Healing and Award Winning ZFS. Get Solaris 10 NOW
> http://p.sf.net/sfu/solaris-dev2dev
> _______________________________________________
> Jmol-users mailing list
> [email protected]
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
--
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
------------------------------------------------------------------------------
SOLARIS 10 is the OS for Data Centers - provides features such as DTrace,
Predictive Self Healing and Award Winning ZFS. Get Solaris 10 NOW
http://p.sf.net/sfu/solaris-dev2dev
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