[xcrysden] centering plots

[Yves Limoge]

Le 21/05/2013 12:28, Tone Kokalj a écrit :
> 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,


Y. Limoge						M. T. KOKALJ

				Saclay ce 21 mais 2013

		Dear Sir

	I will try the solution you propose for the enlightment of the defect ans surrounding. 
Thanks for the solution.
	As concern the centering on a given atom of the plot, I already did this operation with a 
small fortan program working on simple data giving the position of the atoms coming from pw 
and producing an input file for xbs, a much simple visualization tools. I wonder if I could 
do the job on the much elaborated xsf files xcrysden uses ? Do you think it is possible ?

	Sincerely yours.

					Y. Limoge