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Dear Yin,<br>
<br>
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. <br>
<br>
In order to load your custom parameters when xcrysden starts you
should add a line in $HOME/.xcrysden/custom-definitions file, an
example:<br>
<br>
#<br>
# this line changes the default atomic radius for aluminum to 1.6<br>
#<br>
<br>
set atmRad(13) 1.6<br>
<br>
The custom definitions file is described on this link:
<a class="moz-txt-link-freetext" href="http://www.xcrysden.org/doc/custom.html">http://www.xcrysden.org/doc/custom.html</a><br>
<br>
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.<br>
<br>
Best regards,<br>
<br>
Matic<br>
<br>
<br>
<br>
<div class="moz-cite-prefix">On 10/27/2015 09:19 AM,
<a class="moz-txt-link-abbreviated" href="mailto:liyincumt@gmail.com">liyincumt@gmail.com</a> wrote:<br>
</div>
<blockquote cite="mid:2015102710192009085257@gmail.com" type="cite">
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<div><span style="line-height: 1.5; background-color: window;">Dear
Xcrysden developers,</span></div>
<div><br>
</div>
<div>Thanks for sharing this excellent visualization software for
free! </div>
<div><span style="line-height: 1.5; background-color: window;">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.</span></div>
<div><span style="line-height: 1.5; background-color: window;"><br>
</span></div>
<div><span style="line-height: 1.5; background-color: window;">Thank
you very much!</span></div>
<div><span style="line-height: 1.5; background-color: window;"><br>
</span></div>
<div><span style="line-height: 1.5; background-color: window;">Best
Regards,</span></div>
<div><span style="line-height: 1.5; background-color: window;">Yin</span></div>
<div><br>
</div>
<hr style="width: 210px; height: 1px;" align="left" size="1"
color="#b5c4df">
<div><span>
<div style="margin: 10px; font-family: verdana; font-size:
15px;"><span style="color: rgb(0, 0, 0); background-color:
rgba(0, 0, 0, 0);">Dr. Yin Li <br>
Department of Biophysics,Medical School, University of Pecs,<br>
No.12 Szigeti Street, Pecs, H-7624, HUNGARY<br>
Phone: +36-72-535271/36271</span></div>
</span></div>
<br>
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<br>
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