Bob,
I think the point is that there is a role for a bond type that looks
like a single, thick, dotted line, not solid+dotted as in aromatic;
not thin and dotted like typical "hbonds".
The fact that there is a file type that registers this suggests that
it is warranted.
Hens, for the life of me I can't find support for "partial01" in the
history of CML file readers. That was in there? Miguel will have to
look into this when he gets back. In the mean time, you can certainly
use connect. Are these animations? Connect can do a nice job of
displaying such bonds.
Example:
http://cheminf.cmbi.ru.nl/wetche/organic/carbonyl/chime2/nucleoj.html
[Excuse for the chime2, still there for historical reasons ;<)]
An animation indeed, with bonds being formed and broken.
This uses Jmol 10.00.11. The mCML file contains several partial01 bonds,
displayed as dotted.
(Angel: note that we use type A for not really aromatic, but "partial12"
bonds. )
Currently I use a Perl script that calculates the bond order -based on
distances- and writes the multipleCML file.
It is for this particular reason that I use the CML format.
Using the same distance information I could rewrite this to a series of
Jmol commands, as in your example below, and stick to multipleXYZ files.
I'll experiment with that anyway.
However, as the partial01 support used to be there, and these type of
bonds can still be drawn by Jmol, is it really so difficult to
re-implement it? Haven't I seen you doing things much more complicated
the past couple of weeks?
For example, here would be a trick to assign all "long" bonds between
specific atoms as normal-width dashed bonds, assuming there were
several frames with animation:
connect 1.6 3.0 (atomno=1) (atomno=2) create single
connect 1.6 3.0 (atomno=1) (atomno=2) modify hbond
The first creates a standard-diameter single bond. The second turns
into a dashed line. This, I think, might be even better than the
partial01 bond idea, because you would have full flexibility over what
is going to be indicated and what isn't, and you could decide exactly
what distances would be displayed as dashed lines. What isn't possible
at this time (but we have discussed it as a possibility) would be
something like:
connect 1.6 3.0 (atomno=1) (atomno=2) create hbond RADIUS 0.05
(SOMETHING like that, anyway), where the bond radius would be created
at the time of connection. Would you have use for that?
Not if we are talking about real hbonds here. I brought up the hbond
only because it is dotted.
On the other hand, I can imagine that some people find the hbond a bit
too thin.
Hens
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