From owner-chemistry@ccl.net Mon Jun 20 09:58:01 2022 From: "Zhong, Xiang xxz385##miami.edu" To: CCL Subject: CCL:G: [EXTERNAL] CCL:G: How to add point markers in a molecular visualization Message-Id: <-54730-220620040151-8568-PCFf1l9MLlz1wLVHiHpC2Q(-)server.ccl.net> X-Original-From: "Zhong, Xiang" Content-Language: en-US Content-Type: multipart/alternative; boundary="_000_BN6PR07MB29156320FD28A9C24DBEEB4985B09BN6PR07MB2915namp_" Date: Mon, 20 Jun 2022 08:01:42 +0000 MIME-Version: 1.0 Sent to CCL by: "Zhong, Xiang" [xxz385++miami.edu] --_000_BN6PR07MB29156320FD28A9C24DBEEB4985B09BN6PR07MB2915namp_ Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Hello, I do not think GaussView has the functions that you want. Instead, VMD meet= s all your needs, except the adding of "Dummy Atoms", but it is fairly easy= by the help of an additional XYZ file(simplest one, also, you can use the = supported form that you feel comfortable with). Best, Xiang Xiang Zhong, PhD Department of Chemistry University of Miami ________________________________ > From: owner-chemistry+xxz385=3D=3Dmiami.edu**ccl.net on behalf of Andrew DeYoung andrewdaviddeyoung^^gm= ail.com Sent: Sunday, June 19, 2022 9:57 PM To: Zhong, Xiang Subject: [EXTERNAL] CCL:G: How to add point markers in a molecular visualiz= ation CAUTION: This email originated from outside the organization. DO NOT CLICK = ON LINKS or OPEN ATTACHMENTS unless you know and trust the sender. Hi, I'm running GaussView, which my institution purchased with Gaussian 16. I'= ve used Gaussian to find an optimized geometry -- a local minimum on the po= tential energy surface -- of a pair of ions. GaussView can open the final = geometry from the .log output file and print a list of the (x, y, z) Cartes= ian coordinates of the atoms in that configuration. From those Cartesian c= oordinates, I can manually calculate, for example, the Cartesian coordinate= s of the center of mass of the ion pair. How can I then plot the center of mass of the ion pair -- or any other Cart= esian coordinates -- as points, dots, or small spheres in the visualization= ? Does anyone know if this is possible directly in GaussView? Or should I= instead look into visualizing the Gaussian .log file in another visualizat= ion software, such as VMD or Avogadro? I do see that in GaussView, the Cartesian axes can be visualized by selecti= ng "View" -> "Cartesian Axes", but I'm not seeing how to add points, dots, = or spheres to the visualization. In principle, I could probably convert the configuration to an xyz file and= then add some sort of dummy atom having the coordinates of the system's ce= nter of mass (or other coordinates I'm interested in), and then visualize t= he file with GaussView. But for publication I may not want the marker to b= e as large of a sphere as a typical atom, and offhand I'm not sure how to c= hange atomic radii or atom colors in GaussView... What are some favorite t= ools of yours for making publication-quality chemical visualizations? The = visualization doesn't need to be super fancy or even rendered; it just need= s to be functional and readable. Thank you for your time! Andrew Andrew DeYoung, PhD Department of Chemistry Carnegie Mellon University --_000_BN6PR07MB29156320FD28A9C24DBEEB4985B09BN6PR07MB2915namp_ Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable
Hello,

I do not think GaussView has the functions that you want. Instead, VMD meet= s all your needs, except the adding of "Dummy Atoms", but it is f= airly easy by the help of an additional XYZ file(simplest one, also, you ca= n use the supported form that you feel comfortable with).

Best,
Xiang

Xiang Zhong, PhD
Department of Chemistry
University of Miami
From: owner-chemistry+xxz38= 5=3D=3Dmiami.edu**ccl.net <owner-chemistry+xxz385=3D=3Dmiami.edu**ccl.net&= gt; on behalf of Andrew DeYoung andrewdaviddeyoung^^gmail.com <owner-chemistry**ccl.net>
Sent: Sunday, June 19, 2022 9:57 PM
To: Zhong, Xiang <xxz385**miami.edu>
Subject: [EXTERNAL] CCL:G: How to add point markers in a molecular v= isualization
 
CA= UTION: This email originated from outside the organization. DO= NOT CLICK ON LINKS or OPEN ATTACHMENTS unless you know and trust the sender.

Hi,

I'm running GaussView, which my institution purchased with Gaussian 16= .  I've used Gaussian to find an optimized geometry -- a local minimum= on the potential energy surface -- of a pair of ions.  GaussView can = open the final geometry from the .log output file and print a list of the (x, y, z) Cartesian coordinates of the atoms = in that configuration.  From those Cartesian coordinates, I can manual= ly calculate, for example, the Cartesian coordinates of the center of mass = of the ion pair.

How can I then plot the center of mass of the ion pair -- or any other= Cartesian coordinates -- as points, dots, or small spheres in the visualiz= ation?  Does anyone know if this is possible directly in GaussView?&nb= sp; Or should I instead look into visualizing the Gaussian .log file in another visualization software, such as VMD or A= vogadro?  

I do see that in GaussView, the Cartesian axes can be visualized by se= lecting "View" -> "Cartesian Axes", but I'm not seei= ng how to add points, dots, or spheres to the visualization.

In principle, I could probably convert the configuration to an xyz fil= e and then add some sort of dummy atom having the coordinates of the system= 's center of mass (or other coordinates I'm interested in), and then visual= ize the file with GaussView.  But for publication I may not want the marker to be as large of a sphere as a = typical atom, and offhand I'm not sure how to change atomic radii or atom&n= bsp;colors in GaussView...  What are some favorite tools of yours for = making publication-quality chemical visualizations?  The visualization doesn't need to be super fancy or even rendered; it just=  needs to be functional and readable.

Thank you for your time! 
Andrew

Andrew DeYoung, PhD
Department of Chemistry 
Carnegie Mellon University
--_000_BN6PR07MB29156320FD28A9C24DBEEB4985B09BN6PR07MB2915namp_-- From owner-chemistry@ccl.net Mon Jun 20 12:07:00 2022 From: "Geoffrey Hutchison geoff.hutchison.:.gmail.com" To: CCL Subject: CCL:G: How to add point markers in a molecular visualization Message-Id: <-54731-220620114426-3956-fQmNBbjgscI5sn5y3jNoYw/a\server.ccl.net> X-Original-From: Geoffrey Hutchison Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=us-ascii Date: Mon, 20 Jun 2022 11:44:19 -0400 Mime-Version: 1.0 (Mac OS X Mail 16.0 \(3696.100.31\)) Sent to CCL by: Geoffrey Hutchison [geoff.hutchison(-)gmail.com] Hi Andrew, This is really easy to do in Avogadro. If you select some atoms, you can add a center of mass or center of geometry of the selection as a dummy atom. It shows up as a smaller dark grey "atom." The coordinates can be retrieved from the Cartesian Editor .. it's the "Xx" atom (atomic number 0). Not surprisingly, I'm somewhat biased towards using Avogadro for "publication quality visualizations." Best regards, -Geoff --- Prof. Geoffrey Hutchison Department of Chemistry University of Pittsburgh tel: (412) 648-0492 email: geoffh(0)pitt.edu twitter: (0)ghutchis web: https://hutchisonlab.org/ > On Jun 19, 2022, at 9:57 PM, Andrew DeYoung andrewdaviddeyoung^^gmail.com wrote: > > Hi, > > I'm running GaussView, which my institution purchased with Gaussian 16. I've used Gaussian to find an optimized geometry -- a local minimum on the potential energy surface -- of a pair of ions. GaussView can open the final geometry from the .log output file and print a list of the (x, y, z) Cartesian coordinates of the atoms in that configuration. From those Cartesian coordinates, I can manually calculate, for example, the Cartesian coordinates of the center of mass of the ion pair. > > How can I then plot the center of mass of the ion pair -- or any other Cartesian coordinates -- as points, dots, or small spheres in the visualization? Does anyone know if this is possible directly in GaussView? Or should I instead look into visualizing the Gaussian .log file in another visualization software, such as VMD or Avogadro? > > I do see that in GaussView, the Cartesian axes can be visualized by selecting "View" -> "Cartesian Axes", but I'm not seeing how to add points, dots, or spheres to the visualization. > > In principle, I could probably convert the configuration to an xyz file and then add some sort of dummy atom having the coordinates of the system's center of mass (or other coordinates I'm interested in), and then visualize the file with GaussView. But for publication I may not want the marker to be as large of a sphere as a typical atom, and offhand I'm not sure how to change atomic radii or atom colors in GaussView... What are some favorite tools of yours for making publication-quality chemical visualizations? The visualization doesn't need to be super fancy or even rendered; it just needs to be functional and readable. > > Thank you for your time! > Andrew > > Andrew DeYoung, PhD > Department of Chemistry > Carnegie Mellon University