[xcrysden] centering plots

[Tone Kokalj]

On Wed, 2013-05-15 at 11:06 +0200, Yves Limoge wrote:
> Y. Limoge						Xcrysden community
> 
> 		Plotting structures and isosurfaces relatives to defects in solids, I would like  i) to 
> center xcysden plots on a given atom (defect), ii) to enlight the defect and surounding 
> atoms but shadowing the others, bot for a better visibility of the structure.
> Is this possible, and how ?

There is no automatic way of doing these, but they can be done more or
less manually.

As for the item-(ii), it can be achieved manually by a trick, which goes
as follows:

i) identify which atoms you would like to enhance visually
ii) substitute all the other atoms in the XSF file by other atom types;
For example: say that we have ZnS, and you want to stress only a few of
Zn and S atoms; substitute all the others, say, by Se an Ga
iii) modify/reduce the display radii of Se and Ga (menu: Modify->Atomic
Radius) and modify their colors (Modify->Atomic color);  by using a
"smart" radii/color modification you can achieve rather good
"enhancement";

In addition to that you can also do some post-processing image
manipulation, e.g., with gimp.

Regards,
-- 
Anton Kokalj
J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia 
(tel: +386-1-477-3523 // fax:+386-1-477-3822)

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