Re: [Jmol-users] partial bond

[Hens B. <h.b...@cm...>]

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