From: Michael Sternberg <sternberg@an...> - 2008-06-16 15:47:38
I just re-discovered Jmol and the amazing progress made by the
developers since v10.
Coming from Rasmol, I ran into a Jmol peculiarity reading partial
charges from XYZ files. I like the XYZ format for its simplicity and
flexibility in optionally conveying auxiliary scalars and vectors.
In Jmol, however, only integers are recognized (as formal charges),
whereas Rasmol (and, I do believe Xmol) is fine with pretty much any
I am attempting to use charges (or temperature) purely to discriminate
atoms of the same element by coordination (here: sp2, sp2+x, sp3), as
in e.g. "select CARBON and charge > 0.2". As a workaround, given the
handful of classes, I created an auxiliary script:
define SP1 none
define SP2 none
define SP3 none
define SP2X none
define SP2 SP2 or atomno==1
define SP2 SP2 or atomno==2
define SP2X SP2X or atomno==3
define SP3 SP3 or atomno==4
Is there a recommended way to convey a general scalar on an atom?
My conundrum with XYZ is that setting formal charges seriously alters
connectivity, and partial charges are not recognized; the latter
appears arbitrary - any way/plans to remove this limitation?
[pardon the crosspost - I wasn't sure where this belongs properly.]
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