[xcrysden] Re: Xcrysden bond drawing criteria

[Tone Kokalj]

On Wed, 2006-04-26 at 13:24 -0400, Ling Miao wrote:
>  I have a question regarding the criteria
> of drawing a bond between two atoms. I noticed that in my system, 
> some bonds are drawn between Pd and C
> atoms, some are not, although the bond length difference is only about
> 0.1A between those drawn and not drawn.

There are two parameters that determine the bond drawing.
One is chemical connectivity factor, the other is the covalent radius.
The former is a general parameter, while the latter is set to each
individual atomic type (not atom). Both can be set via the
"Modify-->Atomic radii" menu entry.

The bond between two atoms is drawn, when their distance is smaller than
the sum of their covalent radius times the connectivity factor.

If this is not sufficient to draw (or delete) given set of bonds, then
you can substitute some atoms by different atomic types manually in the
structure file. When displaying the structure assign to them different
covalent radii yet use (set) the same atomic color....

Regards, Tone