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Re: [gdiscuss] Creating molecules
Felipe Bergo wrote:
> packaging is finished, the only thing missing is the man page, to be
> written today. Until this weekend all I had done with GDIS was opening the
> models that come with it and saying "ooh", but now I tried to create
> 2 issues:
> 1) How do I create bonds between atoms ? I tried to create an Ethane
> (C2H6) molecule in the usual position
Bonds are automatically calculated & will appear only when the two atoms
in question are close enough. The cutoff distance is just the sum of
covalent radii - plus a tolerance of (I think) about 10%. So, the grid
spacing distance is the key thing to watch out for here in order to get
atom distances close enough to bond. NB: you will have to press 'update'
trigger a recalculation of bonding. In the future, I might make the
calculation automatic when the user is moving atoms/molecules around.
Btw, the single/double bond thingy is for modifying *existing* bonds; it
won't actually create a bond for you. This might be a nice feature but
probably require a fairly substantial rewrite - ie don't expect it in
immediate future :-)
> 2) I believe there should be a button in the toolbar to pop up the
> "Creator" dialog for the current model. Once it's closed, looks like
> the only way to get it back is creating a new model then selecting the
> old one.
You can actually do this via the menu option (Edit->coordinates).
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