Re: [Jmol-users] Atom specification behavior

[Miguel H. <mt...@mt...>]

> As an inorganic chemist using pdb, I always regarded 'ca' in
> chime/rasmol as a reserved word for use as in the series ca, cb, cg (fo=
r
> describing amino acids) rather the series mg, ca, sr, ba (elements,
> etc.), and this wasn't bothersome or worrisome as long as I could
> specify 'select calcium' or 'select *.calcium' and get by. (In fact, it=

> makes the script just a bit more readable.)
Since you are the inorganic chemist ... if it the behavior doesn't matter=

much to you then there is a good chance it is not going to matter to
anybody else :-)

> On the other hand, I do have occasion to work with iron atoms of
> different oxidation states within the same mineral, for example Fe2+ an=
d
> Fe3+ in magnetite, and I'd like to be able to easily specify, color, an=
d
> size them differently in the visualization.

How do these different states get stored in the .pdb file?

Do the 4 characters in the file actually say =22FE2+=22 ?


Miguel


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