[xcrysden] How to display a whole molecule in unit cell with good connection?

[Matic Poberznik]

Dear Yin,

If I understood your problem correctly, I think the best solution is to 
open the Modify menu and choose the Atomic Radius (Shift+R) option. Once 
there you can modify the Covalent Radius and Connectivity Factor for 
each atom type to suit your needs.

In order to load your custom parameters when xcrysden starts you should 
add a line in $HOME/.xcrysden/custom-definitions file, an example:

#
# this line changes the default atomic radius for aluminum to 1.6
#

set atmRad(13) 1.6

The custom definitions file is described on this link: 
http://www.xcrysden.org/doc/custom.html

If the problem stems from the periodic boundary conditions then first 
try the different display modes of unit cells, i. e. click the button 
for the display of the translational asymmetric unit (bottom center of 
the screen).  Then try Modify => Number of units drawn (Shift+N), if the 
covalent radius is correct at least some molecules should be displayed 
correctly. If that is not enough let me know, there is one more 
workaround but it is a bit more complicated.

Best regards,

Matic



On 10/27/2015 09:19 AM, liyincumt at gmail.com wrote:
> Dear Xcrysden developers,
>
> Thanks for sharing this excellent visualization software for free!
> I am using xcrysden to visualize the input and output files of quantum 
> espresso. I have a problem with visualization of crystals. Due to the 
> presence of periodic boundary condition, some of atoms which are 
> outside of the boundary look like being non-covalently connected. Is 
> it possible to display a whole molecule with good covalent connections 
> in Xcrysden.
>
> Thank you very much!
>
> Best Regards,
> Yin
>
> ------------------------------------------------------------------------
> Dr. Yin Li
> Department of Biophysics,Medical School, University of Pecs,
> No.12 Szigeti Street, Pecs, H-7624, HUNGARY
> Phone: +36-72-535271/36271
>
>
> _______________________________________________
> XCrySDen mailing list
> XCrySDen at democritos.it
> http://www.democritos.it/mailman/listinfo/xcrysden

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