[xcrysden] XCrySDen Digest, Vol 12, Issue 13
Hana Milani
hana.milani at yahoo.com
Tue Dec 23 16:23:59 CET 2008
dear Tone,
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.
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!!!
I have gone through doing it via hyperchem, I got to awful results.
Any suggestions????
________________________________
From: "xcrysden-request at democritos.it" <xcrysden-request at democritos.it>
To: xcrysden at democritos.it
Sent: Tuesday, December 23, 2008 4:56:27 PM
Subject: XCrySDen Digest, Vol 12, Issue 13
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Today's Topics:
1. xcrysden for Siesta (pradeep bisht)
2. Re: H-passivation (Tone Kokalj)
3. Re: xcrysden for Siesta (Tone Kokalj)
4. two iso-surfaces (Rodrigo Oeiras)
5. Re: two iso-surfaces (lan haiping)
6. Re: two iso-surfaces (Robert Hanson)
7. Re: two iso-surfaces (Tone Kokalj)
8. Re: xcrysden for Siesta (Ricardo Faccio)
----------------------------------------------------------------------
Message: 1
Date: Tue, 23 Dec 2008 12:58:25 +0530 (IST)
From: pradeep bisht <psbishtphyjiwaji at yahoo.co.in>
Subject: [xcrysden] xcrysden for Siesta
To: xcrysden at democritos.it
Message-ID: <306790.1298.qm at web94202.mail.in2.yahoo.com>
Content-Type: text/plain; charset="utf-8"
Respected Xcrysden users,
Can we use the xcrysden to visulize the structure in Siesta if yes please help me.
Thanking you
Pradeep
Add more friends to your messenger and enjoy! Go to http://messenger.yahoo.com/invite/
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Message: 2
Date: Tue, 23 Dec 2008 08:59:53 +0100
From: Tone Kokalj <tone.kokalj at ijs.si>
Subject: Re: [xcrysden] H-passivation
To: XCrySDen mailing list <xcrysden at democritos.it>
Message-ID: <1230019193.18465.14.camel at walk.ijs.si>
Content-Type: text/plain
On Sun, 2008-12-21 at 22:13 -0800, Hana Milani wrote:
> hello,
>
> I would like to know if there's a way to find the "h" coordinates via
> xcrysden in passivated nanostructures.
What do you mean by H-coordinates? xcrysden can visualize H bonds, and
that's more or less all it can do in this respect (menus: Display->H-bonds,
and Modify->H-bonds Settings).
Regards, Tone
--
J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
(tel: +386-1-477-3523 // fax:+386-1-477-3822)
Please, if possible, avoid sending me Word or PowerPoint attachments.
See: http://www.gnu.org/philosophy/no-word-attachments.html
------------------------------
Message: 3
Date: Tue, 23 Dec 2008 09:09:19 +0100
From: Tone Kokalj <tone.kokalj at ijs.si>
Subject: Re: [xcrysden] xcrysden for Siesta
To: psbishtphyjiwaji at yahoo.co.in, XCrySDen mailing list
<xcrysden at democritos.it>
Message-ID: <1230019759.18465.20.camel at walk.ijs.si>
Content-Type: text/plain
On Tue, 2008-12-23 at 12:58 +0530, pradeep bisht wrote:
> Respected Xcrysden users,
> Can we use the xcrysden to visulize the structure in Siesta if yes please help me.
Well, I don't know Siesta, but googling "siesta xsf" will give you
useful info. The first hit is this one:
http://www.uam.es/departamentos/ciencias/fismateriac/siesta/Tutorials/Barcelona-2007/Postnikov-visual.pdf
Regards, Tone
--
J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
(tel: +386-1-477-3523 // fax:+386-1-477-3822)
Please, if possible, avoid sending me Word or PowerPoint attachments.
See: http://www.gnu.org/philosophy/no-word-attachments.html
------------------------------
Message: 4
Date: Tue, 23 Dec 2008 01:58:51 -0800 (PST)
From: Rodrigo Oeiras <rodrigo_oeiras at yahoo.com.br>
Subject: [xcrysden] two iso-surfaces
To: xcrysden at democritos.it
Message-ID: <928799.6288.qm at web55606.mail.re4.yahoo.com>
Content-Type: text/plain; charset="utf-8"
Hi,
I can plot two iso-surfaces (with different values) at same molecule?
regards
oeiras
Veja quais s?o os assuntos do momento no Yahoo! +Buscados
http://br.maisbuscados.yahoo.com
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Message: 5
Date: Tue, 23 Dec 2008 20:42:31 +0800
From: "lan haiping" <lanhaiping at gmail.com>
Subject: Re: [xcrysden] two iso-surfaces
To: rodrigo_oeiras at yahoo.com.br, "XCrySDen mailing list"
<xcrysden at democritos.it>
Message-ID:
<c92002fa0812230442x379623fduabe42ba705b8aa6d at mail.gmail.com>
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Hi,
As far as i know, xcrysden cannot
plot two isosurfaces at the same plot.
But you may try to use vmd or other tools.
Another way you may try is to write some scripts to combine the data for
two iso-surface .
regards,
2008/12/23 Rodrigo Oeiras <rodrigo_oeiras at yahoo.com.br>
> Hi,
> I can plot two iso-surfaces (with different values) at same molecule?
> regards
> oeiras
>
> ------------------------------
> Veja quais s?o os assuntos do momento no Yahoo! + Buscados: Top 10<http://br.rd.yahoo.com/mail/taglines/mail/*http://br.maisbuscados.yahoo.com/>-
> Celebridades<http://br.rd.yahoo.com/mail/taglines/mail/*http://br.maisbuscados.yahoo.com/celebridades/>-
> M?sica<http://br.rd.yahoo.com/mail/taglines/mail/*http://br.maisbuscados.yahoo.com/m%C3%BAsica/>-
> Esportes<http://br.rd.yahoo.com/mail/taglines/mail/*http://br.maisbuscados.yahoo.com/esportes/>
>
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>
--
Hai-Ping Lan
Department of Electronics ,
Peking University , Bejing, 100871
lanhaiping at gmail.com, hplan at pku.edu.cn
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Message: 6
Date: Tue, 23 Dec 2008 07:14:32 -0600
From: "Robert Hanson" <hansonr at stolaf.edu>
Subject: Re: [xcrysden] two iso-surfaces
To: "XCrySDen mailing list" <xcrysden at democritos.it>
Message-ID:
<ba9c0bd60812230514k6223c777p1bc45942b199af66 at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
Jmol will draw as many isosurfaces as you want.
On Tue, Dec 23, 2008 at 6:42 AM, lan haiping <lanhaiping at gmail.com> wrote:
> Hi,
> As far as i know, xcrysden cannot
> plot two isosurfaces at the same plot.
> But you may try to use vmd or other tools.
> Another way you may try is to write some scripts to combine the data for
> two iso-surface .
> regards,
>
>
>
> 2008/12/23 Rodrigo Oeiras <rodrigo_oeiras at yahoo.com.br>
>>
>> Hi,
>> I can plot two iso-surfaces (with different values) at same molecule?
>> regards
>> oeiras
>>
>> ________________________________
>> Veja quais s?o os assuntos do momento no Yahoo! + Buscados: Top 10 -
>> Celebridades - M?sica - Esportes
>> _______________________________________________
>> XCrySDen mailing list
>> XCrySDen at democritos.it
>> http://www.democritos.it/mailman/listinfo/xcrysden
>>
>
>
>
> --
> Hai-Ping Lan
> Department of Electronics ,
> Peking University , Bejing, 100871
> lanhaiping at gmail.com, hplan at pku.edu.cn
>
> _______________________________________________
> XCrySDen mailing list
> XCrySDen at democritos.it
> http://www.democritos.it/mailman/listinfo/xcrysden
>
>
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
------------------------------
Message: 7
Date: Tue, 23 Dec 2008 14:22:59 +0100
From: Tone Kokalj <tone.kokalj at ijs.si>
Subject: Re: [xcrysden] two iso-surfaces
To: rodrigo_oeiras at yahoo.com.br, XCrySDen mailing list
<xcrysden at democritos.it>
Message-ID: <1230038579.27591.9.camel at walk.ijs.si>
Content-Type: text/plain
On Tue, 2008-12-23 at 01:58 -0800, Rodrigo Oeiras wrote:
> Hi,
> I can plot two iso-surfaces (with different values) at same molecule?
In general, xcrysden cannot. There is only one exception: you can plot +value and -value
isosurface at once (there is a checkbutton Render +/- isovalue). Why? At the time I programmed it,
I thought that more than one isosurface at once would be too much info and not very useful.
Probably I was wrong.
Regards, Tone
--
J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
(tel: +386-1-477-3523 // fax:+386-1-477-3822)
Please, if possible, avoid sending me Word or PowerPoint attachments.
See: http://www.gnu.org/philosophy/no-word-attachments.html
------------------------------
Message: 8
Date: Tue, 23 Dec 2008 10:53:21 -0300
From: "Ricardo Faccio" <rfaccio at fq.edu.uy>
Subject: Re: [xcrysden] xcrysden for Siesta
To: <psbishtphyjiwaji at yahoo.co.in>, "XCrySDen mailing list"
<xcrysden at democritos.it>
Message-ID: <004d01c96505$d1f3d6b0$0602a8c0 at ricardof>
Content-Type: text/plain; charset="utf-8"
Dear Pradeep
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 (http://www.home.uni-osnabrueck.de/apostnik/download.html)
Regards
Ricardo
-------------------------------------------------------------------------
----- Dr. Ricardo Faccio
Mail: Cryssmat-Lab., C?tedra de F?sica, DETEMA
Facultad de Qu?mica, Universidad de la Rep?blica
Av. Gral. Flores 2124, C.C. 1157
C.P. 11800, Montevideo, Uruguay.
E-mail: rfaccio at fq.edu.uy
Phone: 598 2 9249859
598 2 9290705
Fax: 598 2 9241906
Web: http://cryssmat.fq.edu.uy/ricardo/ricardo.htm
----- Original Message -----
From: pradeep bisht
To: xcrysden at democritos.it
Sent: Tuesday, December 23, 2008 4:28 AM
Subject: [xcrysden] xcrysden for Siesta
Respected Xcrysden users,
Can we use the xcrysden to visulize the structure in Siesta if yes please help me.
Thanking you
Pradeep
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