From owner-chemistry@ccl.net Wed Jul 14 04:46:01 2010
From: "Visvaldas K. coyote_v2002^_^yahoo.com" <owner-chemistry_._server.ccl.net>
To: CCL
Subject: CCL: Generating image for small molecules:
Message-Id: <-42274-100714044442-19721-WaVp+qXFl8iENqxW61+LEw_._server.ccl.net>
X-Original-From: "Visvaldas K." <coyote_v2002:+:yahoo.com>
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Sent to CCL by: "Visvaldas K." [coyote_v2002|,|yahoo.com]
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Qutemol http://qutemol.sourceforge.net/ looks very interesting, with different visual effects.
Vis





      
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<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;">Qutemol http://qutemol.sourceforge.net/ looks very interesting, with different visual effects.<br>Vis<div id="yiv376727407"><br>
</div><br><div style="visibility: hidden;" title="1279097016645" id="_booktextmark_tab_id_"></div></td></tr></table><br>

      
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From owner-chemistry@ccl.net Wed Jul 14 08:08:00 2010
From: "Matthew Clark mclark%a%pharmatrope.com" <owner-chemistry:server.ccl.net>
To: CCL
Subject: CCL:G: Generating image for small molecules:
Message-Id: <-42275-100714065445-19009-4GyjGPRYmQSs2J3RR2gdPQ:server.ccl.net>
X-Original-From: Matthew Clark <mclark-.-pharmatrope.com>
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Sent to CCL by: Matthew Clark [mclark * pharmatrope.com]

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Also,  pymol is very easy to use and has a lot of rendering options,
including a built-in ray tracing for shiny surfaces.

Matt


On Tue, 2010-07-13 at 09:07 -0700, Jamin Krinsky jamink:_:berkeley.edu
wrote:

> I would recommend VMD, it's free for all operating systems and while
> it is made for protein work you can do almost anything graphically. It
> accepts many coordinate file types (and cube files from Gaussian, for
> generating MO pictures). It also has an interface with POVRay (install
> that separately) although I've never used it.
> Regards,
> Jamin
> 
> 2010/7/12 Vlad vvv900##anusf.anu.edu.au <owner-chemistry|a|ccl.net>
> 
>         
>         Sent to CCL by: Vlad [vvv900,+,anusf.anu.edu.au]
>         Dear Sangi,
>         
>         
>                  Can someone suggest me freeware for generating good
>                 image files for
>                  small molecules.
>         
>         
>         You can use Jamberoo
>         (http://sf.anu.edu.au/~vvv900/cct/appl/jmoleditor/index.html
>         <http://sf.anu.edu.au/%
>         7Evvv900/cct/appl/jmoleditor/index.html>)
>         
>         You have several options.
>         
>         1) Save a picture in jpg or png format
>         
>         2) For publication quality save your scene as a Povray input
>         file and then use Povray (multi platform freeware) to generate
>         high quality ray-traced image.
>         
>         3) Save your molecular scene as a VRML file. You'll be able to
>         embed it into the pdf document to obtain interactive 3d pdf
>         document (some 3d pdf sample files are here:
>         http://sf.anu.edu.au/~vvv900/cct/appl/jmoleditor/manual/tutorials/3d-pdf/index.html <http://sf.anu.edu.au/%7Evvv900/cct/appl/jmoleditor/manual/tutorials/3d-pdf/index.html>).
>         
>         Regards,
>         Vlad
>         
>         
>         
>         -= This is automatically added to each message by the mailing
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>         E-mail to subscribers: CHEMISTRY|a|ccl.net or use:>         
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> 
> 
> 
> 
> -- 
> Jamin L Krinsky, Ph.D.
> Molecular Graphics and Computation Facility
> 175 Tan Hall, University of California, Berkeley, CA 94720
> jamink|a|berkeley.edu, 510-643-0616
> http://glab.cchem.berkeley.edu
> 

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<BR>
Also,&nbsp; pymol is very easy to use and has a lot of rendering options, including a built-in ray tracing for shiny surfaces.<BR>
<BR>
Matt<BR>
<BR>
<BR>
On Tue, 2010-07-13 at 09:07 -0700, Jamin Krinsky jamink:_:berkeley.edu wrote:<BR>
<BLOCKQUOTE TYPE=CITE>
    I would recommend VMD, it's free for all operating systems and while it is made for protein work you can do almost anything graphically. It accepts many coordinate file types (and cube files from Gaussian, for generating MO pictures). It also has an interface with POVRay (install that separately) although I've never used it.<BR>
    Regards,<BR>
    Jamin<BR>
    <BR>
    2010/7/12 Vlad vvv900##<A HREF="http://anusf.anu.edu.au">anusf.anu.edu.au</A> &lt;<A HREF="mailto:owner-chemistry%7Ca%7Cccl.net">owner-chemistry|a|ccl.net</A>&gt;<BR>
    <BLOCKQUOTE>
        <BR>
        Sent to CCL by: Vlad [vvv900,+,<A HREF="http://anusf.anu.edu.au">anusf.anu.edu.au</A>]<BR>
        Dear Sangi,<BR>
        <BR>
        <BLOCKQUOTE>
            &nbsp;Can someone suggest me freeware for generating good image files for<BR>
            &nbsp;small molecules.<BR>
        </BLOCKQUOTE>
        <BR>
        You can use Jamberoo (<A HREF="http://sf.anu.edu.au/%7Evvv900/cct/appl/jmoleditor/index.html">http://sf.anu.edu.au/~vvv900/cct/appl/jmoleditor/index.html</A> &lt;<A HREF="http://sf.anu.edu.au/%7Evvv900/cct/appl/jmoleditor/index.html">http://sf.anu.edu.au/%7Evvv900/cct/appl/jmoleditor/index.html</A>&gt;)<BR>
        <BR>
        You have several options.<BR>
        <BR>
        1) Save a picture in jpg or png format<BR>
        <BR>
        2) For publication quality save your scene as a Povray input file and then use Povray (multi platform freeware) to generate high quality ray-traced image.<BR>
        <BR>
        3) Save your molecular scene as a VRML file. You'll be able to embed it into the pdf document to obtain interactive 3d pdf document (some 3d pdf sample files are here: <A HREF="http://sf.anu.edu.au/%7Evvv900/cct/appl/jmoleditor/manual/tutorials/3d-pdf/index.html">http://sf.anu.edu.au/~vvv900/cct/appl/jmoleditor/manual/tutorials/3d-pdf/index.html</A> &lt;<A HREF="http://sf.anu.edu.au/%7Evvv900/cct/appl/jmoleditor/manual/tutorials/3d-pdf/index.html">http://sf.anu.edu.au/%7Evvv900/cct/appl/jmoleditor/manual/tutorials/3d-pdf/index.html</A>&gt;).<BR>
        <BR>
        Regards,<BR>
        Vlad<BR>
        <BR>
        <BR>
        <BR<BR>
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    </BLOCKQUOTE>
    <BR>
    <BR>
    <BR>
    -- <BR>
    Jamin L Krinsky, Ph.D.<BR>
    Molecular Graphics and Computation Facility<BR>
    175 Tan Hall, University of California, Berkeley, CA 94720<BR>
    <A HREF="mailto:jamink%7Ca%7Cberkeley.edu">jamink|a|berkeley.edu</A>, 510-643-0616<BR>
    <A HREF="http://glab.cchem.berkeley.edu">http://glab.cchem.berkeley.edu</A><BR>
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From owner-chemistry@ccl.net Wed Jul 14 10:26:00 2010
From: "zouzou adnani zinebeladnani ~ hotmail.com" <owner-chemistry+*+server.ccl.net>
To: CCL
Subject: CCL:G: HCl effect in G03
Message-Id: <-42276-100714102320-29546-EcPAruBmMLVdpObB+93CAA+*+server.ccl.net>
X-Original-From: "zouzou  adnani" <zinebeladnani_._hotmail.com>
Date: Wed, 14 Jul 2010 10:23:11 -0400


Sent to CCL by: "zouzou  adnani" [zinebeladnani~~hotmail.com]
I want to simulate hydrochloric acid HCl solvent effects, with the G03 but I do not know how to do it; Any form of information will be greatly appreciated.
please help me.

Zineb EL ADNANI


From owner-chemistry@ccl.net Wed Jul 14 15:11:00 2010
From: "Damian Bikiel dbikiel]~[qi.fcen.uba.ar" <owner-chemistry!=!server.ccl.net>
To: CCL
Subject: CCL:G: HCl effect in G03
Message-Id: <-42277-100714130551-11968-wVyHGiFQEfUrpTWJ8TpocA!=!server.ccl.net>
X-Original-From: Damian Bikiel <dbikiel.!=!.qi.fcen.uba.ar>
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Sent to CCL by: Damian Bikiel [dbikiel]|[qi.fcen.uba.ar]
It depends on the level of detail that you want to use to describe the 
solvent. If you only need an implicit solvent, check the SCRF keyword:

http://www.gaussian.com/g_tech/g_ur/k_scrf.htm

Damian Bikiel

On Miércoles 14 Julio 2010 11:23:11 zouzou adnani zinebeladnani ~ hotmail.com 
wrote:
> Sent to CCL by: "zouzou  adnani" [zinebeladnani~~hotmail.com]
> I want to simulate hydrochloric acid HCl solvent effects, with the G03 but
> I do not know how to do it; Any form of information will be greatly
> appreciated. please help me.
>
> Zineb EL ADNANI-- 
Dr. Damian Bikiel
Grupo de Modelado Molecular
Laboratorio de Química Organometálica
DQIAQyF-INQUIMAE, FCEyN, UBA


From owner-chemistry@ccl.net Wed Jul 14 17:21:00 2010
From: "errol lewars elewars[-]trentu.ca" <owner-chemistry-$-server.ccl.net>
To: CCL
Subject: CCL:G: HCl effect in G03
Message-Id: <-42278-100714160518-17750-7Z8Unu67elR0eX/wrmpP6w-$-server.ccl.net>
X-Original-From: errol lewars <elewars a trentu.ca>
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Sent to CCL by: errol lewars [elewars : trentu.ca]
2010 July 14

Hello, these may be of help:

"Squeezing the water out of HCl(aq)" (smallest number of H2O needed to 
fully ionize HCl)
(1) T. S. Zwier, Science, 2009, 324 [19 June], 1522

(2) Solvolysis of CH3Cl in H2O (H+ and Cl- are formed)
H. Yamataka, M. Aida, Chem Phys. Lett., 1998, 289, 105.

You may also look at the literature on calculations on solvated H+ and 
Cl- and the behavior of covalent HCl in sovents. Molecular dynamics may 
be useful for the latter.

E. Lewars
==





zouzou adnani zinebeladnani ~ hotmail.com wrote:
> Sent to CCL by: "zouzou  adnani" [zinebeladnani~~hotmail.com]
> I want to simulate hydrochloric acid HCl solvent effects, with the G03 but I do not know how to do it; Any form of information will be greatly appreciated.
> please help me.
>
> Zineb EL ADNANI>
>
>


From owner-chemistry@ccl.net Wed Jul 14 22:26:00 2010
From: "Will James McDonald mcdonald*_*chemistry.ucsc.edu" <owner-chemistry|a|server.ccl.net>
To: CCL
Subject: CCL: G03: How to generate a beta spin-orbital cube file using cubegen?
Message-Id: <-42279-100714202822-27865-bZ0GTgPS6RYYDKHqMjSz1A|a|server.ccl.net>
X-Original-From: "Will James McDonald" <mcdonald]-[chemistry.ucsc.edu>
Date: Wed, 14 Jul 2010 20:28:14 -0400


Sent to CCL by: "Will James McDonald" [mcdonald.:.chemistry.ucsc.edu]
Dear all,

I have a spin-unrestricted PBE0 density and I would like to visualize a few of the beta spin-orbitals. However, if I use the cubegen utility and the MO=n keyword, only the n-th alpha spin-orbital is generated. Am I missing something obvious? How can one generate a cube file for a beta spin orbital without generating files for all beta spin-orbitals using the OccB keyword (there are 100 occupied beta orbitals)?
Your help is greatly appreciated.

Will McDonald
mcdonald:_:chemistry.ucsc.edu
Dept. Chem. and Biochem.
University of CA, Santa Cruz