No real way around the fact that both cadmium and delta carbon are selected
using *.CD. So just make sure to specify carbon if that is what you want,
and use _Cd for cadmium:
select *.CD &_C
select _Cd
You can also use
select CD
for cadmium, because CD is also its residue name. So you could use
select *.CD and not CD
Bob
On Sat, Sep 13, 2014 at 1:27 PM, Eric Martz <[email protected]>
wrote:
> Dear Bob,
>
> Atom CA can mean calcium or carbon-alpha.
> Atom CD can mean cadmium or carbon-delta.
> (*Are there other such ambiguities?*)
>
> For both Jmol 14.2.4 and 14.0.17:
>
> 'select *.cd' selects both carbons delta and cadmium (1d66).
> 'select *.ca' selects carbons alpha but NOT calcium (4aqr).
>
> What I am using in FirstGlance that fails to select calcium is
> 'select *:A.ca&&hetero'
> (Well, this is not optimal anyway since it would also select alpha carbons
> in non-standard residues)
>
> I am now setting about to change my code to
> 'select [ca]:A'
> (special case when the atom clicked is either calcium or cadmium)
>
> However, I suspect that this inconsistency should be remedied.
>
> Best regards, Eric
>
>
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--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Department of Chemistry
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
------------------------------------------------------------------------------
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