From owner-chemistry@ccl.net Wed Mar 3 13:43:01 2010 From: "Jamin Krinsky jamink(0)berkeley.edu" To: CCL Subject: CCL: Visualizing Software Message-Id: <-41366-100303130547-24284-9PGASXBTRy3W0blhPcqplA~~server.ccl.net> X-Original-From: Jamin Krinsky Content-Type: multipart/alternative; boundary=00163630f673428ba10480e95452 Date: Wed, 3 Mar 2010 10:05:36 -0800 MIME-Version: 1.0 Sent to CCL by: Jamin Krinsky [jamink]![berkeley.edu] --00163630f673428ba10480e95452 Content-Type: text/plain; charset=ISO-8859-1 Dear Anthony, I see you got the needed info about ORTEP, but keep in mind that the graphic you indicated is a drawing from an X-ray diffraction experiment, so the ellipsoids represent thermal motion (and sometimes disorder), which you obviously don't have in a normal computational output. So, your atoms will just come out as banded spheres, in which case you may be better off using VMD and setting everything to grey and black. Regards, Jamin On Tue, Mar 2, 2010 at 12:55 PM, Anthony F kwyjib09[-]gmail.com < owner-chemistry/a\ccl.net> wrote: > > Sent to CCL by: "Anthony F" [kwyjib09|*|gmail.com] > Thanks for everyone previous help on visualizing NBOS. > > My next question is on visualizing my XYZ files. I have used Avogadro, VMD, > and Gabedit. But I want to make diagrams like these: > > http://bhgroup.lsa.umich.edu/files/u1/ge-prop-ortep.gif > > I prefer how the ellipsoids have the 3D effect and that everything is in > black and white. I don't like how bonds have two different colors in > Avogadro and VMD. > > Can you guys suggest a program that can visualize those clusters? > > Thanks > > Anthony> > > -- 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 --00163630f673428ba10480e95452 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear Anthony,
I see you got the needed info about ORTEP, but keep in min= d that the graphic you indicated is a drawing from an X-ray diffraction exp= eriment, so the ellipsoids represent thermal motion (and sometimes disorder= ), which you obviously don't have in a normal computational output. So,= your atoms will just come out as banded spheres, in which case you may be = better off using VMD and setting everything to grey and black.
Regards,
Jamin

On Tue, Mar 2, 2010 at = 12:55 PM, Anthony F kwyjib09[-]gmail.com <owner-chemistry/a\ccl.net> wrote:

Sent to CCL by: "Anthony =A0F" [kwyjib09|*|gmail.com]
Thanks for everyone previous help on visualizing NBOS.

My next question is on visualizing my XYZ files. I have used Avogadro, VMD,= and Gabedit. But I want to make diagrams like these:

http://bhgroup.lsa.umich.edu/files/u1/ge-prop-ortep.gif

I prefer how the ellipsoids have the 3D effect and that everything is in bl= ack and white. I don't like how bonds have two different colors in Avog= adro and VMD.

Can you guys suggest a program that can visualize those clusters?

Thanks

Anthony



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--
Jamin L Krinsky, Ph.D.<= br>Molecular Graphics and Computation Facility
175 Tan Hall, University = of California, Berkeley, CA 94720
jamink/a\berkeley.edu, 510-643-0616
http://glab.cc= hem.berkeley.edu

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