Re: [Jmol-developers] unitcell issues

[E.L. W. <eg...@sc...>]

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On Wednesday 18 February 2004 13:04, Miguel Howard wrote:
> Two items we need to discuss.
>
> 1. connected sets
> I now understand that I need to determine connected sets prior to shifting
> to the unit cell.
> This means that, in cases where the file does not contain bonding
> information, I need to apply the auto-bonding prior to doing the shift.
> However, shelx files are in fractional coordinates. That means that I have
> an extra step with these.
>  - if the input data is in fractional coordinates then conver to euclidean
> space
>
> After that, it will run the same as usual
>  - if there is no bonding information then auto-bond
>  - if it is a crystal, then putAtomsInsideTheUnitcell
>  - if weMovedAnyAtomsInsideTheUnitcell then rebond
>
> Where
>   putAtomsInsideUnitcell will use the connectivity data to determine how
> to do the shifts.
>
> Please confirm that this looks right to you.

Yes, that looks right.

> 2. IxJxK crystal matrix
>
> I think this is a good task and I am glad that you are interested in
> working on it.
> However, I do not think it is simple and I think we need to work on it
> together ... at least to get started.

Ack.

> I believe that it will take several weeks to implement this. But the end
> result will be good. Some of the architectural issues we will face will
> directly apply to animations and vibrations, so it will have good payoff.

Ok.=20

> I think that there are some significant issues involved. Some of them are
> 'crystalography' in nature ... like bonding between the cells. Others are
> implementation dependent ... like the way that the graphics engine works.
>
> First, we need to *really* think about whether we want to try to duplicate
> the atoms, or whether we want to try to handle everything by translating
> the one unitcell to new positions.
>
> Let's start this discussion and we will go from there.

Ok.

We'll discuss this on the IRC chat channel (#cdk at irc.freenode.net for=20
others who are interested... planned at 2pm CET today).

Egon

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eg...@sc...
PhD on Molecular Representation in Chemometrics
Nijmegen University
http://www.cac.sci.kun.nl/people/egonw/
GPG: 1024D/D6336BA6

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