From owner-chemistry@ccl.net Sun Jun 19 22:04:01 2022 From: "Andrew DeYoung andrewdaviddeyoung^^gmail.com" To: CCL Subject: CCL:G: How to add point markers in a molecular visualization Message-Id: <-54728-220619215739-7697-JYUq668hFETnr4ZAZGz8bQ%a%server.ccl.net> X-Original-From: Andrew DeYoung Content-Type: multipart/alternative; boundary="00000000000070484d05e1d76db9" Date: Sun, 19 Jun 2022 21:57:22 -0400 MIME-Version: 1.0 Sent to CCL by: Andrew DeYoung [andrewdaviddeyoung-x-gmail.com] --00000000000070484d05e1d76db9 Content-Type: text/plain; charset="UTF-8" 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 --00000000000070484d05e1d76db9 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hi,

I'm running GaussView, which my= institution purchased with Gaussian 16.=C2=A0 I've used Gaussian to fi= nd an optimized geometry -- a local minimum on the potential energy surface= -- of a pair of ions.=C2=A0 GaussView can open the final geometry from the= .log output file and print a list of the (x, y, z) Cartesian coordinates o= f the atoms in that configuration.=C2=A0 From those Cartesian coordinates, = I can manually calculate, for example, the Cartesian coordinates of the cen= ter of mass of the ion pair.

How can I then plot t= he center of mass of the ion pair -- or any other Cartesian coordinates -- = as points, dots, or small spheres in the visualization?=C2=A0 Does anyone k= now if this is possible directly in GaussView?=C2=A0 Or should I instead lo= ok into visualizing the Gaussian .log file in another visualization softwar= e, such as VMD or Avogadro?=C2=A0=C2=A0

I do see that in = GaussView, the Cartesian axes can be visualized by selecting "View&quo= t; -> "Cartesian Axes", but I'm not seeing how to add poin= ts, dots, or spheres to the visualization.

In prin= ciple, I could probably convert the configuration to an xyz file and then a= dd some sort of dummy atom having the coordinates of the system's cente= r of mass (or other coordinates I'm interested in), and then visualize = the file with GaussView.=C2=A0 But for publication I may not want the marke= r to be as large of a sphere as a typical atom, and offhand I'm not sur= e how to change atomic radii or atom=C2=A0colors in GaussView...=C2=A0 What= are some favorite tools of yours for making publication-quality chemical v= isualizations?=C2=A0 The visualization doesn't need to be super fancy o= r even rendered; it just=C2=A0needs to be functional and readable.

<= /div>
Thank you for your time!=C2=A0
Andrew

Andrew DeYoung, PhD
Department of Chemistry=C2=A0
Carnegie Mellon University
--00000000000070484d05e1d76db9-- From owner-chemistry@ccl.net Sun Jun 19 23:29:01 2022 From: "Sumitra Godara (P15CY007) godara.1/./iitj.ac.in" To: CCL Subject: CCL:G: How to add point markers in a molecular visualization Message-Id: <-54729-220619231726-10183-7eLbUZAueechymmo1cTGpA[A]server.ccl.net> X-Original-From: "Sumitra Godara (P15CY007)" Content-Type: multipart/alternative; boundary="000000000000a5bf6305e1d88a73" Date: Mon, 20 Jun 2022 08:47:06 +0530 MIME-Version: 1.0 Sent to CCL by: "Sumitra Godara (P15CY007)" [godara.1-$-iitj.ac.in] --000000000000a5bf6305e1d88a73 Content-Type: text/plain; charset="UTF-8" Hello, Use VMD and molden software for visualisation purpose as well as for images in publication. I also do not have knowledge to use Guess view for the same. On Mon, Jun 20, 2022, 08:28 Andrew DeYoung andrewdaviddeyoung^^gmail.com < owner-chemistry() ccl.net> 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 > --000000000000a5bf6305e1d88a73 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hello,

Use VMD and molden software for visualisation purpose as= well as for images in publication. I also do not have knowledge to use Gue= ss view for the same.=C2=A0

On Mon, Jun 20, 2022, 08:28 Andrew DeYoung= andrewdaviddeyoung^^gmail.com <owner-chemistry() cc= l.net> wrote:
Hi,

I'm running GaussView, which my institution p= urchased with Gaussian 16.=C2=A0 I've used Gaussian to find an optimize= d geometry -- a local minimum on the potential energy surface -- of a pair = of ions.=C2=A0 GaussView can open the final geometry from the .log output f= ile and print a list of the (x, y, z) Cartesian coordinates of the atoms in= that configuration.=C2=A0 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 m= ass of the ion pair -- or any other Cartesian coordinates -- as points, dot= s, or small spheres in the visualization?=C2=A0 Does anyone know if this is= possible directly in GaussView?=C2=A0 Or should I instead look into visual= izing the Gaussian .log file in another visualization software, such as VMD= or Avogadro?=C2=A0=C2=A0

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 s= pheres to the visualization.

In principle, I could= probably convert the configuration to an xyz file and then add some sort o= f 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.=C2=A0 But for publication I may not want the marker to be as lar= ge of a sphere as a typical atom, and offhand I'm not sure how to chang= e atomic radii or atom=C2=A0colors in GaussView...=C2=A0 What are some favo= rite tools of yours for making publication-quality chemical visualizations?= =C2=A0 The visualization doesn't need to be super fancy or even rendere= d; it just=C2=A0needs to be functional and readable.

Than= k you for your time!=C2=A0
Andrew

Andrew= DeYoung, PhD
Department of Chemistry=C2=A0
Carnegie Me= llon University
--000000000000a5bf6305e1d88a73--