<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:times new roman,new york,times,serif;font-size:10pt"><div>dear Tone,<br><br>I have put time to add h-bonds to a nanowire to saturate the dangling bonds, but after all I didn't get to good results.<br><br>I wanted to know if there's a way that I add the h-bonds via xcrysden and get the coordinates from xcrysden, then, I optimize the system!!!<br><br>I have gone through doing it via hyperchem, I got to awful results.<br><br>Any suggestions????<br></div><div style="font-family: times new roman,new york,times,serif; font-size: 10pt;"><br><div style="font-family: arial,helvetica,sans-serif; font-size: 13px;"><font face="Tahoma" size="2"><hr size="1"><b><span style="font-weight: bold;">From:</span></b> "xcrysden-request@democritos.it" <xcrysden-request@democritos.it><br><b><span style="font-weight: bold;">To:</span></b>
xcrysden@democritos.it<br><b><span style="font-weight: bold;">Sent:</span></b> Tuesday, December 23, 2008 4:56:27 PM<br><b><span style="font-weight: bold;">Subject:</span></b> XCrySDen Digest, Vol 12, Issue 13<br></font><br>
Send XCrySDen mailing list submissions to<br> <a ymailto="mailto:xcrysden@democritos.it" href="mailto:xcrysden@democritos.it">xcrysden@democritos.it</a><br><br>To subscribe or unsubscribe via the World Wide Web, visit<br> <a href="http://www.democritos.it/mailman/listinfo/xcrysden" target="_blank">http://www.democritos.it/mailman/listinfo/xcrysden</a><br>or, via email, send a message with subject or body 'help' to<br> <a ymailto="mailto:xcrysden-request@democritos.it" href="mailto:xcrysden-request@democritos.it">xcrysden-request@democritos.it</a><br><br>You can reach the person managing the list at<br> <a ymailto="mailto:xcrysden-owner@democritos.it" href="mailto:xcrysden-owner@democritos.it">xcrysden-owner@democritos.it</a><br><br>When replying, please edit your Subject line so it is more specific<br>than "Re: Contents of XCrySDen digest..."<br><br><br>Today's Topics:<br><br>
1. xcrysden for Siesta (pradeep bisht)<br> 2. Re: H-passivation (Tone Kokalj)<br> 3. Re: xcrysden for Siesta (Tone Kokalj)<br> 4. two iso-surfaces (Rodrigo Oeiras)<br> 5. Re: two iso-surfaces (lan haiping)<br> 6. Re: two iso-surfaces (Robert Hanson)<br> 7. Re: two iso-surfaces (Tone Kokalj)<br> 8. Re: xcrysden for Siesta (Ricardo Faccio)<br><br><br>----------------------------------------------------------------------<br><br>Message: 1<br>Date: Tue, 23 Dec 2008 12:58:25 +0530 (IST)<br>From: pradeep bisht <<a ymailto="mailto:psbishtphyjiwaji@yahoo.co.in" href="mailto:psbishtphyjiwaji@yahoo.co.in">psbishtphyjiwaji@yahoo.co.in</a>><br>Subject: [xcrysden] xcrysden for Siesta<br>To: <a ymailto="mailto:xcrysden@democritos.it" href="mailto:xcrysden@democritos.it">xcrysden@democritos.it</a><br>Message-ID: <<a ymailto="mailto:306790.1298.qm@web94202.mail.in2.yahoo.com"
href="mailto:306790.1298.qm@web94202.mail.in2.yahoo.com">306790.1298.qm@web94202.mail.in2.yahoo.com</a>><br>Content-Type: text/plain; charset="utf-8"<br><br>Respected Xcrysden users,<br>Can we use the xcrysden to visulize the structure in Siesta if yes please help me.<br><br>Thanking you<br>Pradeep<br><br><br><br> Add more friends to your messenger and enjoy! Go to <a href="http://messenger.yahoo.com/invite/" target="_blank">http://messenger.yahoo.com/invite/</a><br>-------------- next part --------------<br>An HTML attachment was scrubbed...<br>URL: <a href="http://www.democritos.it/pipermail/xcrysden/attachments/20081223/3edf4abf/attachment-0001.htm" target="_blank">http://www.democritos.it/pipermail/xcrysden/attachments/20081223/3edf4abf/attachment-0001.htm</a> <br><br>------------------------------<br><br>Message: 2<br>Date: Tue, 23 Dec 2008 08:59:53 +0100<br>From: Tone Kokalj <<a ymailto="mailto:tone.kokalj@ijs.si"
href="mailto:tone.kokalj@ijs.si">tone.kokalj@ijs.si</a>><br>Subject: Re: [xcrysden] H-passivation<br>To: XCrySDen mailing list <<a ymailto="mailto:xcrysden@democritos.it" href="mailto:xcrysden@democritos.it">xcrysden@democritos.it</a>><br>Message-ID: <<a ymailto="mailto:1230019193.18465.14.camel@walk.ijs.si" href="mailto:1230019193.18465.14.camel@walk.ijs.si">1230019193.18465.14.camel@walk.ijs.si</a>><br>Content-Type: text/plain<br><br>On Sun, 2008-12-21 at 22:13 -0800, Hana Milani wrote:<br>> hello,<br>> <br>> I would like to know if there's a way to find the "h" coordinates via<br>> xcrysden in passivated nanostructures.<br><br>What do you mean by H-coordinates? xcrysden can visualize H bonds, and <br>that's more or less all it can do in this respect (menus: Display->H-bonds, <br>and Modify->H-bonds Settings).<br><br>Regards, Tone<br>-- <br>J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia <br>(tel:
+386-1-477-3523 // fax:+386-1-477-3822)<br><br>Please, if possible, avoid sending me Word or PowerPoint attachments.<br>See: <a href="http://www.gnu.org/philosophy/no-word-attachments.html" target="_blank">http://www.gnu.org/philosophy/no-word-attachments.html</a><br><br><br><br>------------------------------<br><br>Message: 3<br>Date: Tue, 23 Dec 2008 09:09:19 +0100<br>From: Tone Kokalj <<a ymailto="mailto:tone.kokalj@ijs.si" href="mailto:tone.kokalj@ijs.si">tone.kokalj@ijs.si</a>><br>Subject: Re: [xcrysden] xcrysden for Siesta<br>To: <a ymailto="mailto:psbishtphyjiwaji@yahoo.co.in" href="mailto:psbishtphyjiwaji@yahoo.co.in">psbishtphyjiwaji@yahoo.co.in</a>, XCrySDen mailing list<br> <<a ymailto="mailto:xcrysden@democritos.it" href="mailto:xcrysden@democritos.it">xcrysden@democritos.it</a>><br>Message-ID: <<a ymailto="mailto:1230019759.18465.20.camel@walk.ijs.si"
href="mailto:1230019759.18465.20.camel@walk.ijs.si">1230019759.18465.20.camel@walk.ijs.si</a>><br>Content-Type: text/plain<br><br>On Tue, 2008-12-23 at 12:58 +0530, pradeep bisht wrote:<br>> Respected Xcrysden users,<br>> Can we use the xcrysden to visulize the structure in Siesta if yes please help me.<br><br><br>Well, I don't know Siesta, but googling "siesta xsf" will give you<br>useful info. The first hit is this one:<br><br><a href="http://www.uam.es/departamentos/ciencias/fismateriac/siesta/Tutorials/Barcelona-2007/Postnikov-visual.pdf" target="_blank">http://www.uam.es/departamentos/ciencias/fismateriac/siesta/Tutorials/Barcelona-2007/Postnikov-visual.pdf</a><br><br>Regards, Tone<br>-- <br>J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia <br>(tel: +386-1-477-3523 // fax:+386-1-477-3822)<br><br>Please, if possible, avoid sending me Word or PowerPoint attachments.<br>See: <a
href="http://www.gnu.org/philosophy/no-word-attachments.html" target="_blank">http://www.gnu.org/philosophy/no-word-attachments.html</a><br><br><br><br>------------------------------<br><br>Message: 4<br>Date: Tue, 23 Dec 2008 01:58:51 -0800 (PST)<br>From: Rodrigo Oeiras <<a ymailto="mailto:rodrigo_oeiras@yahoo.com.br" href="mailto:rodrigo_oeiras@yahoo.com.br">rodrigo_oeiras@yahoo.com.br</a>><br>Subject: [xcrysden] two iso-surfaces<br>To: <a ymailto="mailto:xcrysden@democritos.it" href="mailto:xcrysden@democritos.it">xcrysden@democritos.it</a><br>Message-ID: <<a ymailto="mailto:928799.6288.qm@web55606.mail.re4.yahoo.com" href="mailto:928799.6288.qm@web55606.mail.re4.yahoo.com">928799.6288.qm@web55606.mail.re4.yahoo.com</a>><br>Content-Type: text/plain; charset="utf-8"<br><br>Hi, <br>I can plot two iso-surfaces (with different values) at same molecule?<br>regards<br>oeiras<br><br><br><br> Veja quais s?o os assuntos do
momento no Yahoo! +Buscados<br><a href="http://br.maisbuscados.yahoo.com" target="_blank">http://br.maisbuscados.yahoo.com</a><br>-------------- next part --------------<br>An HTML attachment was scrubbed...<br>URL: <a href="http://www.democritos.it/pipermail/xcrysden/attachments/20081223/679cd122/attachment-0001.htm" target="_blank">http://www.democritos.it/pipermail/xcrysden/attachments/20081223/679cd122/attachment-0001.htm</a> <br><br>------------------------------<br><br>Message: 5<br>Date: Tue, 23 Dec 2008 20:42:31 +0800<br>From: "lan haiping" <<a ymailto="mailto:lanhaiping@gmail.com" href="mailto:lanhaiping@gmail.com">lanhaiping@gmail.com</a>><br>Subject: Re: [xcrysden] two iso-surfaces<br>To: <a ymailto="mailto:rodrigo_oeiras@yahoo.com.br" href="mailto:rodrigo_oeiras@yahoo.com.br">rodrigo_oeiras@yahoo.com.br</a>, "XCrySDen mailing list"<br> <<a ymailto="mailto:xcrysden@democritos.it"
href="mailto:xcrysden@democritos.it">xcrysden@democritos.it</a>><br>Message-ID:<br> <<a ymailto="mailto:c92002fa0812230442x379623fduabe42ba705b8aa6d@mail.gmail.com" href="mailto:c92002fa0812230442x379623fduabe42ba705b8aa6d@mail.gmail.com">c92002fa0812230442x379623fduabe42ba705b8aa6d@mail.gmail.com</a>><br>Content-Type: text/plain; charset="iso-8859-1"<br><br>Hi,<br>As far as i know, xcrysden cannot<br>plot two isosurfaces at the same plot.<br>But you may try to use vmd or other tools.<br>Another way you may try is to write some scripts to combine the data for<br>two iso-surface .<br>regards,<br><br><br><br>2008/12/23 Rodrigo Oeiras <<a ymailto="mailto:rodrigo_oeiras@yahoo.com.br" href="mailto:rodrigo_oeiras@yahoo.com.br">rodrigo_oeiras@yahoo.com.br</a>><br><br>> Hi,<br>> I can plot two iso-surfaces (with different values) at same molecule?<br>> regards<br>> oeiras<br>><br>>
------------------------------<br>> Veja quais s?o os assuntos do momento no Yahoo! + Buscados: Top 10<<a href="http://br.rd.yahoo.com/mail/taglines/mail/*http://br.maisbuscados.yahoo.com/" target="_blank">http://br.rd.yahoo.com/mail/taglines/mail/*http://br.maisbuscados.yahoo.com/</a>>-<br>> Celebridades<<a href="http://br.rd.yahoo.com/mail/taglines/mail/*http://br.maisbuscados.yahoo.com/celebridades/" target="_blank">http://br.rd.yahoo.com/mail/taglines/mail/*http://br.maisbuscados.yahoo.com/celebridades/</a>>-<br>> M?sica<<a href="http://br.rd.yahoo.com/mail/taglines/mail/*http://br.maisbuscados.yahoo.com/m%C3%BAsica/" target="_blank">http://br.rd.yahoo.com/mail/taglines/mail/*http://br.maisbuscados.yahoo.com/m%C3%BAsica/</a>>-<br>> Esportes<<a href="http://br.rd.yahoo.com/mail/taglines/mail/*http://br.maisbuscados.yahoo.com/esportes/"
target="_blank">http://br.rd.yahoo.com/mail/taglines/mail/*http://br.maisbuscados.yahoo.com/esportes/</a>><br>><br>> _______________________________________________<br>> XCrySDen mailing list<br>> <a ymailto="mailto:XCrySDen@democritos.it" href="mailto:XCrySDen@democritos.it">XCrySDen@democritos.it</a><br>> <a href="http://www.democritos.it/mailman/listinfo/xcrysden" target="_blank">http://www.democritos.it/mailman/listinfo/xcrysden</a><br>><br>><br><br><br>-- <br>Hai-Ping Lan<br>Department of Electronics ,<br>Peking University , Bejing, 100871<br><a ymailto="mailto:lanhaiping@gmail.com" href="mailto:lanhaiping@gmail.com">lanhaiping@gmail.com</a>, <a ymailto="mailto:hplan@pku.edu.cn" href="mailto:hplan@pku.edu.cn">hplan@pku.edu.cn</a><br>-------------- next part --------------<br>An HTML attachment was scrubbed...<br>URL: <a href="http://www.democritos.it/pipermail/xcrysden/attachments/20081223/c42ac1c0/attachment-0001.htm"
target="_blank">http://www.democritos.it/pipermail/xcrysden/attachments/20081223/c42ac1c0/attachment-0001.htm</a> <br><br>------------------------------<br><br>Message: 6<br>Date: Tue, 23 Dec 2008 07:14:32 -0600<br>From: "Robert Hanson" <<a ymailto="mailto:hansonr@stolaf.edu" href="mailto:hansonr@stolaf.edu">hansonr@stolaf.edu</a>><br>Subject: Re: [xcrysden] two iso-surfaces<br>To: "XCrySDen mailing list" <<a ymailto="mailto:xcrysden@democritos.it" href="mailto:xcrysden@democritos.it">xcrysden@democritos.it</a>><br>Message-ID:<br> <<a ymailto="mailto:ba9c0bd60812230514k6223c777p1bc45942b199af66@mail.gmail.com" href="mailto:ba9c0bd60812230514k6223c777p1bc45942b199af66@mail.gmail.com">ba9c0bd60812230514k6223c777p1bc45942b199af66@mail.gmail.com</a>><br>Content-Type: text/plain; charset=ISO-8859-1<br><br>Jmol will draw as many isosurfaces as you want.<br><br>On Tue, Dec 23, 2008 at 6:42 AM, lan haiping <<a
ymailto="mailto:lanhaiping@gmail.com" href="mailto:lanhaiping@gmail.com">lanhaiping@gmail.com</a>> wrote:<br>> Hi,<br>> As far as i know, xcrysden cannot<br>> plot two isosurfaces at the same plot.<br>> But you may try to use vmd or other tools.<br>> Another way you may try is to write some scripts to combine the data for<br>> two iso-surface .<br>> regards,<br>><br>><br>><br>> 2008/12/23 Rodrigo Oeiras <<a ymailto="mailto:rodrigo_oeiras@yahoo.com.br" href="mailto:rodrigo_oeiras@yahoo.com.br">rodrigo_oeiras@yahoo.com.br</a>><br>>><br>>> Hi,<br>>> I can plot two iso-surfaces (with different values) at same molecule?<br>>> regards<br>>> oeiras<br>>><br>>> ________________________________<br>>> Veja quais s?o os assuntos do momento no Yahoo! + Buscados: Top 10 -<br>>> Celebridades - M?sica - Esportes<br>>>
_______________________________________________<br>>> XCrySDen mailing list<br>>> <a ymailto="mailto:XCrySDen@democritos.it" href="mailto:XCrySDen@democritos.it">XCrySDen@democritos.it</a><br>>> <a href="http://www.democritos.it/mailman/listinfo/xcrysden" target="_blank">http://www.democritos.it/mailman/listinfo/xcrysden</a><br>>><br>><br>><br>><br>> --<br>> Hai-Ping Lan<br>> Department of Electronics ,<br>> Peking University , Bejing, 100871<br>> <a ymailto="mailto:lanhaiping@gmail.com" href="mailto:lanhaiping@gmail.com">lanhaiping@gmail.com</a>, <a ymailto="mailto:hplan@pku.edu.cn" href="mailto:hplan@pku.edu.cn">hplan@pku.edu.cn</a><br>><br>> _______________________________________________<br>> XCrySDen mailing list<br>> <a ymailto="mailto:XCrySDen@democritos.it" href="mailto:XCrySDen@democritos.it">XCrySDen@democritos.it</a><br>> <a
href="http://www.democritos.it/mailman/listinfo/xcrysden" target="_blank">http://www.democritos.it/mailman/listinfo/xcrysden</a><br>><br>><br><br><br><br>-- <br>Robert M. Hanson<br>Professor of Chemistry<br>St. Olaf College<br>1520 St. Olaf Ave.<br>Northfield, MN 55057<br><a href="http://www.stolaf.edu/people/hansonr" target="_blank">http://www.stolaf.edu/people/hansonr</a><br>phone: 507-786-3107<br><br><br>If nature does not answer first what we want,<br>it is better to take what answer we get.<br><br>-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900<br><br><br>------------------------------<br><br>Message: 7<br>Date: Tue, 23 Dec 2008 14:22:59 +0100<br>From: Tone Kokalj <<a ymailto="mailto:tone.kokalj@ijs.si" href="mailto:tone.kokalj@ijs.si">tone.kokalj@ijs.si</a>><br>Subject: Re: [xcrysden] two iso-surfaces<br>To: <a ymailto="mailto:rodrigo_oeiras@yahoo.com.br"
href="mailto:rodrigo_oeiras@yahoo.com.br">rodrigo_oeiras@yahoo.com.br</a>, XCrySDen mailing list<br> <<a ymailto="mailto:xcrysden@democritos.it" href="mailto:xcrysden@democritos.it">xcrysden@democritos.it</a>><br>Message-ID: <<a ymailto="mailto:1230038579.27591.9.camel@walk.ijs.si" href="mailto:1230038579.27591.9.camel@walk.ijs.si">1230038579.27591.9.camel@walk.ijs.si</a>><br>Content-Type: text/plain<br><br>On Tue, 2008-12-23 at 01:58 -0800, Rodrigo Oeiras wrote:<br>> Hi, <br>> I can plot two iso-surfaces (with different values) at same molecule?<br><br>In general, xcrysden cannot. There is only one exception: you can plot +value and -value <br>isosurface at once (there is a checkbutton Render +/- isovalue). Why? At the time I programmed it, <br>I thought that more than one isosurface at once would be too much info and not very useful. <br>Probably I was wrong.<br><br>Regards, Tone<br>-- <br>J. Stefan Institute,
Jamova 39, 1000 Ljubljana, Slovenia <br>(tel: +386-1-477-3523 // fax:+386-1-477-3822)<br><br>Please, if possible, avoid sending me Word or PowerPoint attachments.<br>See: <a href="http://www.gnu.org/philosophy/no-word-attachments.html" target="_blank">http://www.gnu.org/philosophy/no-word-attachments.html</a><br><br><br><br>------------------------------<br><br>Message: 8<br>Date: Tue, 23 Dec 2008 10:53:21 -0300<br>From: "Ricardo Faccio" <<a ymailto="mailto:rfaccio@fq.edu.uy" href="mailto:rfaccio@fq.edu.uy">rfaccio@fq.edu.uy</a>><br>Subject: Re: [xcrysden] xcrysden for Siesta<br>To: <<a ymailto="mailto:psbishtphyjiwaji@yahoo.co.in" href="mailto:psbishtphyjiwaji@yahoo.co.in">psbishtphyjiwaji@yahoo.co.in</a>>, "XCrySDen mailing list"<br> <<a ymailto="mailto:xcrysden@democritos.it" href="mailto:xcrysden@democritos.it">xcrysden@democritos.it</a>><br>Message-ID:
<004d01c96505$d1f3d6b0$0602a8c0@ricardof><br>Content-Type: text/plain; charset="utf-8"<br><br>Dear Pradeep<br>In the Postnikov's web page you can find a script called xv2xsf for a case.XV file and transforms it into case.XSF, that can easily be read by Xcrysden. This script is found with other tools in a collection called Sies2xsf (<a href="http://www.home.uni-osnabrueck.de/apostnik/download.html" target="_blank">http://www.home.uni-osnabrueck.de/apostnik/download.html</a>)<br>Regards<br>Ricardo<br>-------------------------------------------------------------------------<br>----- Dr. Ricardo Faccio<br> <br> Mail: Cryssmat-Lab., C?tedra de F?sica, DETEMA<br> Facultad de Qu?mica, Universidad de la Rep?blica<br> Av. Gral. Flores 2124, C.C. 1157<br> C.P. 11800, Montevideo, Uruguay.<br> E-mail: <a ymailto="mailto:rfaccio@fq.edu.uy"
href="mailto:rfaccio@fq.edu.uy">rfaccio@fq.edu.uy</a><br> Phone: 598 2 9249859<br> 598 2 9290705<br> Fax: 598 2 9241906<br> Web: <a href="http://cryssmat.fq.edu.uy/ricardo/ricardo.htm" target="_blank">http://cryssmat.fq.edu.uy/ricardo/ricardo.htm</a><br> ----- Original Message ----- <br> From: pradeep bisht <br> To: <a ymailto="mailto:xcrysden@democritos.it" href="mailto:xcrysden@democritos.it">xcrysden@democritos.it</a> <br> Sent: Tuesday, December 23, 2008 4:28 AM<br> Subject: [xcrysden] xcrysden for Siesta<br><br><br> Respected Xcrysden users,<br> Can we use the xcrysden to visulize the structure in Siesta if yes please help me.<br><br> Thanking you<br> Pradeep<br>
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