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

[liyincumt at gmail.com]

Dear Matic,

Thanks for your kind help! 
After setting the number of units drawn, some molecules inside the supercell are displayed correctly. But there are too many molecules inside the supercell. The figure would be hardly accepted by journal.
Is it possible to just display the molecules correctly in one unit cell? I have tried buttons of the display which are located in the bottom center of the screen, none of them can work properly. 

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
 
From: Matic Poberznik
Date: 2015-10-27 12:14
To: XCrySDen mailing list
Subject: Re: [xcrysden] How to display a whole molecule in unit cell with good connection?
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

-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://www.democritos.it/pipermail/xcrysden/attachments/20151027/463edd29/attachment.htm