Re: [gdiscuss] Creating molecules

[Sean Fleming <sean@power.curtin.edu.au>]

Hi Felipe,

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
> models.
> 
> 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
their
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
the
atom distances close enough to bond. NB: you will have to press 'update'
to
trigger a recalculation of bonding. In the future, I might make the
bonding
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
it'd
probably require a fairly substantial rewrite - ie don't expect it in
the
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). 


-- 
Sean Fleming
Department of Applied Chemistry
Curtin University of Technology                     
PO Box U 1987, Perth, 6845, Western Australia
Phone: +61 8 9266 7534    FAX:   +61 8 9266 2300