Andre= w,

Jmol has a useful =E2=80=9Ccompare=E2=80=9D comm= and. Here is a tutorial on how to use it. This deals with 2 proteins, but i= t could be applied to any 2 conformations.

https://prot= eopedia.org/wiki/index.php/Jmol/superposition

T= he online reference for all Jmol commands is at

https://chemapps.stolaf.edu= /jmol/docs/

John Keller

Department of Chemistry and Bioc= hemistry

University of Alaska Fairbanks

Sent from Mail for Windows

<= /o:p>

From: Andrew DeYoung andrewdaviddeyoung**gmail.com
Sent: Tue= sday, April 26, 2022 7:45 PM
To: Keller, John W
Subject: CCL:G: Overlaying con= formers for visualization

Hi,

I'm a postdoc and quantum chemistry = novice. I've run geometry optimization ("Opt") using Gaussi= an to find several molecular geometries corresponding to local minima on th= e potential energy surface for a single molecule. The geometries are = similar but not exact. I'd like to overlay several geometries in orde= r to visualize, qualitatively, how they differ. In other words I want= to overlay multiple conformers.

&n= bsp;

Could someone please suggest = a relatively simple way to overlay geometries for visualization? = I have access to GaussView, Avogadro, VMD, and any other freeware applicat= ions you can think of. The molecular geometries are in separate .log = files (i.e., output from Gaussian), but of course it is easy to convert the= se to almost any other chemical file format, using Avogadro or the like.

I realize, though, that "overlaying several conformers&qu= ot; is not a unique specification; one would need to specify which atom(s) = to try to overlap exactly. Is there an algorithm in a computational c= hemistry program that does this?

&n= bsp;

Thank you for any guidance yo= u can provide!

Andrew

Andrew DeYoung, PhD

Department of Chemistry

Carnegie Mellon University

= From owner-chemistry@ccl.net Wed Apr 27 11:46:01 2022 From: "marius bouba ousmanou mariusolaar3(~)gmail.com" To: CCL Subject: CCL:G: Overlaying conformers for visualization Message-Id: <-54650-220427012432-532-+j7chJ6BvDaCdGL6LQKV+w!^!server.ccl.net> X-Original-From: marius bouba ousmanou Content-Type: multipart/alternative; boundary="000000000000de162e05dd9c0508" Date: Wed, 27 Apr 2022 06:24:14 +0100 MIME-Version: 1.0 Sent to CCL by: marius bouba ousmanou [mariusolaar3[-]gmail.com] --000000000000de162e05dd9c0508 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable Hello everyone Dear Andrew, As contribution, it is better to use gaussView5.0 rather than 6.0 version. So you Can extract the geometry optimization curve. But basically, you Can manually extract molecular coordinates by searching. "Standard orientation" from your log file. Then all the optimized g=C3=A9om=C3=A9tries Can be respectively edited from these g=C3= =A9om=C3=A9tries. Best regards. Marius Bouba Ousmanou Le mer. 27 avr. 2022 =C3=A0 04:02, Andrew DeYoung andrewdaviddeyoung**gmail= .com < owner-chemistry]|[ccl.net> a =C3=A9crit : > Hi, > > I'm a postdoc and quantum chemistry novice. I've run geometry > optimization ("Opt") using Gaussian to find several molecular geometries > corresponding to local minima on the potential energy surface for a singl= e > molecule. The geometries are similar but not exact. I'd like to overlay > several geometries in order to visualize, qualitatively, how they differ. > In other words I want to overlay multiple conformers. > > Could someone please suggest a relatively simple way to overlay geometrie= s > for visualization? I have access to GaussView, Avogadro, VMD, and any > other freeware applications you can think of. The molecular geometries a= re > in separate .log files (i.e., output from Gaussian), but of course it is > easy to convert these to almost any other chemical file format, using > Avogadro or the like. > > I realize, though, that "overlaying several conformers" is not a unique > specification; one would need to specify which atom(s) to try to overlap > exactly. Is there an algorithm in a computational chemistry program that > does this? > > Thank you for any guidance you can provide! > > Andrew > > Andrew DeYoung, PhD > Department of Chemistry > Carnegie Mellon University > --000000000000de162e05dd9c0508 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable

Hello everyone

<= br>

Dear Andrew,

As contribution, it is better to use gaussView5.0 rather than 6.0 ver= sion. So you Can extract the geometry optimization curve.=C2=A0

But basically, you Can manually extract molecular=C2=A0 coordin= ates by searching. "Standard orientation" from your log file. The= n all the optimized g=C3=A9om=C3=A9tries Can be respectively edited from th= ese g=C3=A9om=C3=A9tries.=C2=A0

Best regards.

Marius Bouba Ousmanou

<= /div>

Le mer. 27 avr. 2022 =C3=A0 04:02, Andrew DeYoung andrewdaviddeyoung**= gmail.com <owner-chemistry]|[ccl.net> a =C3=A9crit=C2=A0:

Hi,

I&#= 39;m a postdoc and quantum chemistry novice.=C2=A0 I've run geometry op= timization ("Opt") using Gaussian to find several molecular geome= tries corresponding to local minima on the potential energy surface for a s= ingle molecule.=C2=A0 The geometries are similar but not exact.=C2=A0 I'= ;d like to overlay several geometries in order to visualize, qualitatively,= how they differ.=C2=A0 In other words I want to overlay multiple conformer= s.

Could someone please suggest a relatively=C2=A0= simple way to overlay geometries for visualization?=C2=A0 I have access to = GaussView, Avogadro, VMD, and any other freeware applications you can think= of.=C2=A0 The molecular geometries are in separate .log files (i.e., outpu= t from Gaussian), but of course it is easy to convert these to almost any o= ther chemical file format, using Avogadro or the like.

=
I realize, though, that "overlaying several conformers" is n= ot a unique specification; one would need to specify which atom(s) to try t= o overlap exactly.=C2=A0 Is there an algorithm in a computational chemistry= program that does this?

Thank you for any guidanc= e you can provide!

Andrew

Andrew DeYoung, PhD
Department of Chemistry
Carnegie M= ellon University

--000000000000de162e05dd9c0508-- From owner-chemistry@ccl.net Wed Apr 27 12:21:00 2022 From: "Michel Petitjean petitjean.chiral[-]gmail.com" To: CCL Subject: CCL:G: Overlaying conformers for visualization Message-Id: <-54651-220427022527-26470-rJvDBhf4ySmkmarjU3clLA[-]server.ccl.net> X-Original-From: Michel Petitjean Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="UTF-8" Date: Wed, 27 Apr 2022 08:30:19 +0200 MIME-Version: 1.0 Sent to CCL by: Michel Petitjean [petitjean.chiral : gmail.com] Dear Andrew, There are two cases: (1) The atom numbering is the same for all conformers. (2) The atom numbering is different. In case (1), there are many softwares which perform an optimal superposition of two conformers (optimal, in the sense of minimizing the RMSD). E.g., ARMS do that and outputs the coordinates of the moved conformer superposed on the reference one. http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html#ARMS In case (2), CSR retrieves the pairwise correspondence and then computes the minimized RMSD, as in ARMS. http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html#CSR Pls be careful: in both cases you must define one of your conformers as the reference one, because, when conformer 2 is optimally superposed on conformer 1 and conformer 3 is also optimally superposed on conformer 1, then in general conformer 3 is not optimally superposed on conformer 2. Best regards, Michel Petitjean Université Paris Cité, BFA, CNRS UMR 8251, INSERM ERL U1133, F-75013 Paris, France Phone: +331 5727 8434; Fax: +331 5727 8372 E-mail: petitjean.chiral.[-].gmail.com (preferred), michel.petitjean.[-].u-paris.fr http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html Le mer. 27 avr. 2022 à 05:09, Andrew DeYoung andrewdaviddeyoung**gmail.com a écrit : > > Hi, > > I'm a postdoc and quantum chemistry novice. I've run geometry optimization ("Opt") using Gaussian to find several molecular geometries corresponding to local minima on the potential energy surface for a single molecule. The geometries are similar but not exact. I'd like to overlay several geometries in order to visualize, qualitatively, how they differ. In other words I want to overlay multiple conformers. > > Could someone please suggest a relatively simple way to overlay geometries for visualization? I have access to GaussView, Avogadro, VMD, and any other freeware applications you can think of. The molecular geometries are in separate .log files (i.e., output from Gaussian), but of course it is easy to convert these to almost any other chemical file format, using Avogadro or the like. > > I realize, though, that "overlaying several conformers" is not a unique specification; one would need to specify which atom(s) to try to overlap exactly. Is there an algorithm in a computational chemistry program that does this? > > Thank you for any guidance you can provide! > > Andrew > > Andrew DeYoung, PhD > Department of Chemistry > Carnegie Mellon University From owner-chemistry@ccl.net Wed Apr 27 12:56:01 2022 From: "=?UTF-8?Q?Jan_G=c3=b6tze?= jgoetze[*]zedat.fu-berlin.de" To: CCL Subject: CCL:G: Overlaying conformers for visualization Message-Id: <-54652-220427024747-1038-3nLX7QiRR61WocKSm1n0gw[*]server.ccl.net> X-Original-From: =?UTF-8?Q?Jan_G=c3=b6tze?= Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8; format=flowed Date: Wed, 27 Apr 2022 08:47:38 +0200 MIME-Version: 1.0 Sent to CCL by: =?UTF-8?Q?Jan_G=c3=b6tze?= [jgoetze---zedat.fu-berlin.de] Dear Andrew, I suggest using the RMSD Tools you will find in VMD in "Extensions"->"Analysis"->"RMSD ...". They allow for atom-selective alignment of your structures, leading to pretty images of your structures and provide the numerical values to quantify your results. Best wishes, Jan Am 26.04.2022 um 19:14 schrieb Andrew DeYoung andrewdaviddeyoung**gmail.com: > Hi, > > I'm a postdoc and quantum chemistry novice. I've run geometry > optimization ("Opt") using Gaussian to find several molecular > geometries corresponding to local minima on the potential energy > surface for a single molecule. The geometries are similar but not > exact. I'd like to overlay several geometries in order to visualize, > qualitatively, how they differ. In other words I want to overlay > multiple conformers. > > Could someone please suggest a relatively simple way to overlay > geometries for visualization? I have access to GaussView, Avogadro, > VMD, and any other freeware applications you can think of. The > molecular geometries are in separate .log files (i.e., output from > Gaussian), but of course it is easy to convert these to almost any > other chemical file format, using Avogadro or the like. > > I realize, though, that "overlaying several conformers" is not a > unique specification; one would need to specify which atom(s) to try > to overlap exactly. Is there an algorithm in a computational > chemistry program that does this? > > Thank you for any guidance you can provide! > > Andrew > > Andrew DeYoung, PhD > Department of Chemistry > Carnegie Mellon University -- ---------------------- Dr. Jan Philipp Götze Quantum Chemistry of Biological Systems Institut für Chemie und Biochemie Freie Universität Berlin https://jgoetze.userpage.fu-berlin.de Currently only home office due to Corona restrictions From owner-chemistry@ccl.net Wed Apr 27 13:31:01 2022 From: "Anson Thomas thomasanson53..@..gmail.com" To: CCL Subject: CCL:G: Overlaying conformers for visualization Message-Id: <-54653-220427025403-3232-Q45XSj9SwFtCSI+U0TYhEQ.@.server.ccl.net> X-Original-From: Anson Thomas Content-Type: multipart/alternative; boundary="000000000000fe49a605dd9d45d0" Date: Wed, 27 Apr 2022 12:23:20 +0530 MIME-Version: 1.0 Sent to CCL by: Anson Thomas [thomasanson53||gmail.com] --000000000000fe49a605dd9d45d0 Content-Type: text/plain; charset="UTF-8" Dear Andrew, there are multiple ways to accomplish this. 1. You may open the structure files separately which you want to overlay (say in the xyz format) in Avogadro. Copy all the atoms of one structure and paste them into the other structure window. This will show both the conformers together. You can adjust the orientation of the pasted structure as per your choice. 2. This can also be done using VMD. After opening up VMD, you can load the two structures by going to Files -> New Molecule. This will show the two conformers together. 3. Importing the two structures into Pymol can also help achieve the same. In case you want to get more quantitative information, such as the RMSD, you may enter this command after importing the two structures (say, 1.xyz and 2.xyz): *align 1, 2, cycles=0, transform=0* This will align the atoms and give you the RMSD value on the terminal. Hope this helps. On Wed, Apr 27, 2022 at 9:20 AM Andrew DeYoung andrewdaviddeyoung**gmail.com wrote: > Hi, > > I'm a postdoc and quantum chemistry novice. I've run geometry > optimization ("Opt") using Gaussian to find several molecular geometries > corresponding to local minima on the potential energy surface for a single > molecule. The geometries are similar but not exact. I'd like to overlay > several geometries in order to visualize, qualitatively, how they differ. > In other words I want to overlay multiple conformers. > > Could someone please suggest a relatively simple way to overlay geometries > for visualization? I have access to GaussView, Avogadro, VMD, and any > other freeware applications you can think of. The molecular geometries are > in separate .log files (i.e., output from Gaussian), but of course it is > easy to convert these to almost any other chemical file format, using > Avogadro or the like. > > I realize, though, that "overlaying several conformers" is not a unique > specification; one would need to specify which atom(s) to try to overlap > exactly. Is there an algorithm in a computational chemistry program that > does this? > > Thank you for any guidance you can provide! > > Andrew > > Andrew DeYoung, PhD > Department of Chemistry > Carnegie Mellon University > -- *Anson Thomas* M.Sc. Chemistry, IIT Roorkee --000000000000fe49a605dd9d45d0 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable

Dear Andrew, there are multiple ways to accompli= sh this.

1. You may open th= e structure files separately which you want to overlay (say in the xyz form= at) in Avogadro. Copy all the atoms of one structure and paste them into th= e other structure window. This will show both the conformers together. You = can adjust the orientation of the pasted structure as per your choice.

2. This can also be done using VMD. After openi= ng up VMD, you can load the two structures by going to Files=C2=A0-> New= Molecule. This will show the two conformers together.

3. Importing the=C2=A0two structures=C2=A0into Pymol can also= help achieve=C2=A0the same. In case you want to get more quantitative info= rmation, such as the RMSD, you may enter this command after importing the t= wo structures (say,=C2=A01.xyz=C2=A0and=C2=A0<= a href=3D"http://2.xyz">2.xyz):

align 1, 2, = cycles=3D0, transform=3D0

<= div dir=3D"ltr">
This will align the atoms and give you the RMSD value on the = terminal.=C2=A0

<= div>

Hope this helps.

On Wed, Apr 27, = 2022 at 9:20 AM Andrew DeYoung andrewdaviddeyoung**gmail.com <owner-che= mistry.:.ccl.net> wrote:

Hi,

I'm a postdoc and= quantum chemistry novice.=C2=A0 I've run geometry optimization ("= Opt") using Gaussian to find several molecular geometries correspondin= g to local minima on the potential energy surface for a single molecule.=C2= =A0 The geometries are similar but not exact.=C2=A0 I'd like to overlay= several geometries in order to visualize, qualitatively, how they differ.= =C2=A0 In other words I want to overlay multiple conformers.

=
Could someone please suggest a relatively=C2=A0simple way to ove= rlay geometries for visualization?=C2=A0 I have access to GaussView, Avogad= ro, VMD, and any other freeware applications you can think of.=C2=A0 The mo= lecular geometries are in separate .log files (i.e., output from Gaussian),= but of course it is easy to convert these to almost any other chemical fil= e format, using Avogadro or the like.

I realize, t= hough, that "overlaying several conformers" is not a unique speci= fication; one would need to specify which atom(s) to try to overlap exactly= .=C2=A0 Is there an algorithm in a computational chemistry program that doe= s this?

Thank you for any guidance you can provide= !

Andrew

Andrew DeYoung, = PhD
Department of Chemistry
Carnegie Mellon University<= /div>

Anson Thomas

M.Sc. C= hemistry, IIT Roorkee

--000000000000fe49a605dd9d45d0-- From owner-chemistry@ccl.net Wed Apr 27 14:06:01 2022 From: "Brian Skinn brian.skinn[A]gmail.com" To: CCL Subject: CCL:G: Overlaying conformers for visualization Message-Id: <-54654-220427073035-18389-IAgnd2A2Q0yBfuQHGnanKQ^_^server.ccl.net> X-Original-From: Brian Skinn Content-Type: multipart/alternative; boundary="000000000000e7137505dda12245" Date: Wed, 27 Apr 2022 07:30:18 -0400 MIME-Version: 1.0 Sent to CCL by: Brian Skinn [brian.skinn]![gmail.com] --000000000000e7137505dda12245 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable Andrew, I'm pretty sure RDKit can do what you want, I was looking into the same sort of tool a while ago. A quick scan of their docs turned up this, which at least seems like it's in the right ballpark: https://www.rdkit.org/docs/source/rdkit.Chem.rdMolAlign.html Good luck! -Brian On Wed, Apr 27, 2022, 02:54 John Keller jwkeller]~[alaska.edu < owner-chemistry:ccl.net> wrote: > Sent to CCL by: John Keller [jwkeller,alaska.edu] > > Andrew, > > Jmol has a useful =E2=80=9Ccompare=E2=80=9D command. Here is a tutorial o= n how to use it. > This deals with 2 proteins, but it could be applied to any 2 conformation= s. > > https://proteopedia.org/wiki/index.php/Jmol/superposition > > The online reference for all Jmol commands is at > > https://chemapps.stolaf.edu/jmol/docs/ > > > > John Keller > > Department of Chemistry and Biochemistry > > University of Alaska Fairbanks > > > > > > Sent from Mail for > Windows > > > > *From: *Andrew DeYoung andrewdaviddeyoung**gmail.com > > *Sent: *Tuesday, April 26, 2022 7:45 PM > *To: *Keller, John W > *Subject: *CCL:G: Overlaying conformers for visualization > > > > Hi, > > > > I'm a postdoc and quantum chemistry novice. I've run geometry > optimization ("Opt") using Gaussian to find several molecular geometries > corresponding to local minima on the potential energy surface for a singl= e > molecule. The geometries are similar but not exact. I'd like to overlay > several geometries in order to visualize, qualitatively, how they differ. > In other words I want to overlay multiple conformers. > > > > Could someone please suggest a relatively simple way to overlay geometrie= s > for visualization? I have access to GaussView, Avogadro, VMD, and any > other freeware applications you can think of. The molecular geometries a= re > in separate .log files (i.e., output from Gaussian), but of course it is > easy to convert these to almost any other chemical file format, using > Avogadro or the like. > > > > I realize, though, that "overlaying several conformers" is not a unique > specification; one would need to specify which atom(s) to try to overlap > exactly. Is there an algorithm in a computational chemistry program that > does this? > > > > Thank you for any guidance you can provide! > > > > Andrew > > > > Andrew DeYoung, PhD > > Department of Chemistry > > Carnegie Mellon University > > > - This is automatically added to each message by the mailing script - To > recover the email address of the author of the message, please change the > strange characters on the top line to the : sign. You can also look up th= e > X-Original-From: line in the mail header. E-mail to subscribers: > CHEMISTRY:ccl.net or use:Before posting, check wait > time at: http://www.ccl.netConferences: > http://server.ccl.net/chemistry/announcements/conferences/ Search > Messages: http://www.ccl.net/chemistry/searchccl/index.shtml If your mail > bounces from CCL with 5.7.1 error, check:--000000000000e7137505dda12245 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable

Andrew,

I= 9;m pretty sure RDKit can do what you want, I was looking into the same sor= t of tool a while ago.

A= quick scan of their docs turned up this, which at least seems like it'= s in the right ballpark:=C2=A0https://www.rdkit.org/docs/source/rdkit.Chem.rd= MolAlign.html

Good luck!

-Brian

On Wed, Apr 27, 2022, 02:54 John Keller jwkeller]~[alaska.edu <owner= -chemistry:ccl.net> wrote:

Sent to CCL by: John Keller [jwkeller,alaska.edu]
Andrew,
Jmol = has a useful =E2=80=9Ccompare=E2=80=9D command. Here is a tutorial on how t= o use it. This deals with 2 proteins, but it could be applied to any 2 conf= ormations.
https://proteopedia.org/wiki/index.php/Jmol/superposition
The online reference for all Jmol commands is at
https://chemapps.stolaf.edu/jm= ol/docs/
=C2=A0
John Keller
Department of Chemistry an= d Biochemistry
University of Alaska Fairbanks
=
=C2=A0
=C2=A0
Sent from Mail for Windows
=C2=A0=
<= b>From: Andrew DeYoung andrewdaviddeyoung**gmail.com<= /a>
Sent: Tuesday, April 26, 2022 7:45 PM
To: Keller, John W
Subject: CCL:G: Overlaying conformers = for visualization
=C2=A0
<= div>
Hi,
=C2=A0=
I'm a postdoc and quantum = chemistry novice.=C2=A0 I've run geometry optimization ("Opt"= ) using Gaussian to find several molecular geometries corresponding to loca= l minima on the potential energy surface for a single molecule.=C2=A0 The g= eometries are similar but not exact.=C2=A0 I'd like to overlay several = geometries in order to visualize, qualitatively, how they differ.=C2=A0 In = other words I want to overlay multiple conformers.
=C2=A0
Co= uld someone please suggest a relatively=C2=A0simple way to overlay geometri= es for visualization?=C2=A0 I have access to GaussView, Avogadro, VMD, and = any other freeware applications you can think of.=C2=A0 The molecular geome= tries are in separate .log files (i.e., output from Gaussian), but of cours= e it is easy to convert these to almost any other chemical file format, usi= ng Avogadro or the like.
=C2=A0=
I realize, though, that "= overlaying several conformers" is not a unique specification; one woul= d need to specify which atom(s) to try to overlap exactly.=C2=A0 Is there a= n algorithm in a computational chemistry program that does this?
<= div>
=C2=A0
Thank you for any guidance you can provide!
=C2=A0
A= ndrew
=C2=A0
Andrew DeYoung, PhD
Department of Chemistry

Carne= gie Mellon University

=C2=A0

- This is automatically added to each message by the mailing script -E-mail to subscribers: CHEMISTRY:ccl.net or use: http://www.ccl.net/cgi-bin/ccl/send_= ccl_message E-mail to administrators: CHEMISTRY-REQUEST:ccl.net = or use http://www.ccl.net/cgi-bin/ccl/send_= ccl_message Subscribe/Unsubscribe:=20 http://www.ccl.net/chemistry/sub_unsub.= shtml Before posting, check wait time at: http://www.ccl.net Job: http://www.ccl.net/jobs=20 Conferences: http://server.ccl.= net/chemistry/announcements/conferences/ Search Messages: http://www.ccl.net/che= mistry/searchccl/index.shtmlhttp://www.ccl.net/spammers.txt RTFI: http://www.ccl.net/chemistry/a= boutccl/instructions/

--000000000000e7137505dda12245-- From owner-chemistry@ccl.net Wed Apr 27 18:38:00 2022 From: "Alan Shusterman alan_+_reed.edu" To: CCL Subject: CCL:G: Overlaying conformers for visualization Message-Id: <-54655-220427134254-20759-ySEQynUUglbh6QmJUjYUrA|a|server.ccl.net> X-Original-From: Alan Shusterman Content-Type: multipart/alternative; boundary="00000000000053262f05dda65673" Date: Wed, 27 Apr 2022 10:42:34 -0700 MIME-Version: 1.0 Sent to CCL by: Alan Shusterman [alan^_^reed.edu] --00000000000053262f05dda65673 Content-Type: text/plain; charset="UTF-8" Hi Andrew, I know that you're looking for free software, but if someone at your location has a copy of Spartan, try that. It contains a simple, easy-to-use Align tool that allows you to overlay conformers very easily, and also perform other useful tasks using a built-in spreadsheet. Briefly, to overlay structures in Spartan... 1. You get all of your structures into a single data file (Spartan calls this a "list" model) 2. You select one structure from the list as your reference structure and choose the Align tool 3. You select the atoms in the reference structure that you want to use as your points of reference (I usually choose the atoms that are *not* part of the flexible portion of the molecule) and then you select Align At this point, all of the other molecules in the list will be aligned with the reference molecule. You can then display as many molecules from the list as you wish. This makes it very easy to see which parts of the molecule were manipulated during the conformer search and which were not. It is also very easy to see whether two conformers are mirror images (a fairly common occurrence from automatic conformer searches on simple molecules), or just differ in small, inconsequential ways. But, first, you have to find someone at CMU with a copy of Spartan. Best wishes, Alan On Tue, Apr 26, 2022 at 8:13 PM Andrew DeYoung andrewdaviddeyoung**gmail.com wrote: > Hi, > > I'm a postdoc and quantum chemistry novice. I've run geometry > optimization ("Opt") using Gaussian to find several molecular geometries > corresponding to local minima on the potential energy surface for a single > molecule. The geometries are similar but not exact. I'd like to overlay > several geometries in order to visualize, qualitatively, how they differ. > In other words I want to overlay multiple conformers. > > Could someone please suggest a relatively simple way to overlay geometries > for visualization? I have access to GaussView, Avogadro, VMD, and any > other freeware applications you can think of. The molecular geometries are > in separate .log files (i.e., output from Gaussian), but of course it is > easy to convert these to almost any other chemical file format, using > Avogadro or the like. > > I realize, though, that "overlaying several conformers" is not a unique > specification; one would need to specify which atom(s) to try to overlap > exactly. Is there an algorithm in a computational chemistry program that > does this? > > Thank you for any guidance you can provide! > > Andrew > > Andrew DeYoung, PhD > Department of Chemistry > Carnegie Mellon University > -- Alan Shusterman Chemistry Department Reed College 3203 SE Woodstock Blvd Portland, OR 97202-8199 http://blogs.reed.edu/alan/ "Patience, persistence, and a sense of humor." Dave Barrett (1956-2017, Reed College '77) --00000000000053262f05dda65673 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable

Hi Andrew,

I know that you&#= 39;re looking for free software, but if someone at your location has a copy= of Spartan, try that. It contains a simple, easy-to-use Align tool that al= lows you to overlay conformers very easily, and also perform other useful t= asks using a built-in spreadsheet.

Briefly, to ove= rlay structures in Spartan...

1. You get all of your structur= es into a single data file (Spartan calls this a "list" model)

2. You select one structure from the list as your reference structu= re and choose the Align tool

3. You select the atoms in the refer= ence structure that you want to use as your points of reference (I usually = choose the atoms that are not part of the flexible portion of the mo= lecule) and then you select Align

At this point, a= ll of the other molecules in the list will be aligned with the reference mo= lecule. You can then display as many molecules from the list as you wish. T= his makes it very easy to see which parts of the molecule were manipulated = during the conformer search and which were not. It is also very easy to see= whether two conformers are mirror images (a fairly common occurrence from = automatic conformer searches on simple molecules), or just differ in small,= inconsequential ways.

But, first, you have to fin= d someone at CMU with a copy of Spartan.

Best wish= es,

Alan

On Tue, Apr 26, 2022 at 8:13 PM Andrew DeYoun= g andrewdaviddeyoung**gmail.com <owner-chemistry%%ccl.net> wrote:=

Hi,

I'm a postdoc and quantum chemistry novice.=C2= =A0 I've run geometry optimization ("Opt") using Gaussian to = find several molecular geometries corresponding to local minima on the pote= ntial energy surface for a single molecule.=C2=A0 The geometries are simila= r but not exact.=C2=A0 I'd like to overlay several geometries in order = to visualize, qualitatively, how they differ.=C2=A0 In other words I want t= o overlay multiple conformers.

Could someone pleas= e suggest a relatively=C2=A0simple way to overlay geometries for visualizat= ion?=C2=A0 I have access to GaussView, Avogadro, VMD, and any other freewar= e applications you can think of.=C2=A0 The molecular geometries are in sepa= rate .log files (i.e., output from Gaussian), but of course it is easy to c= onvert these to almost any other chemical file format, using Avogadro or th= e like.

I realize, though, that "overlaying s= everal conformers" is not a unique specification; one would need to sp= ecify which atom(s) to try to overlap exactly.=C2=A0 Is there an algorithm = in a computational chemistry program that does this?

Thank you for any guidance you can provide!

And= rew

Andrew DeYoung, PhD
Department of Ch= emistry
Carnegie Mellon University

Alan Shusterman
Chemistry Department
Reed College
3203 SE Woodst= ock Blvd
Portland, OR 97202-8199
http://blogs.reed.edu/alan/
"Patience, pe= rsistence, and a sense of humor." Dave Barrett (1956-2017, Reed Colleg= e '77)

--00000000000053262f05dda65673-- From owner-chemistry@ccl.net Wed Apr 27 19:13:00 2022 From: "Hans-Ullrich Siehl ullrich.siehl-*-uni-ulm.de" To: CCL Subject: CCL:G: Overlaying conformers for visualization Message-Id: <-54656-220427150825-30295-nANl1vHuUK5L3Wevg0uu4Q{:}server.ccl.net> X-Original-From: Hans-Ullrich Siehl Content-Language: en-GB Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8; format=flowed Date: Wed, 27 Apr 2022 21:08:16 +0200 MIME-Version: 1.0 Sent to CCL by: Hans-Ullrich Siehl [ullrich.siehl]![uni-ulm.de] Dear Andrew DeYoung There is an program for superposition called ´suppose´: https://structbio.vanderbilt.edu/~jsmith/suppose/suppose.man.html best regards Hans-Ullrich Siehl 27.04.2022 21:07 CET -- ********************************************************************** Prof. Dr. Hans-Ullrich Siehl Universität Ulm e-mail: Hans Ullrich Siehl ********************************************************************** On 26/04/2022 19:14, Andrew DeYoung andrewdaviddeyoung**gmail.com wrote: > Hi, > > I'm a postdoc and quantum chemistry novice. I've run geometry optimization > ("Opt") using Gaussian to find several molecular geometries corresponding > to local minima on the potential energy surface for a single molecule. The > geometries are similar but not exact. I'd like to overlay several > geometries in order to visualize, qualitatively, how they differ. In other > words I want to overlay multiple conformers. > > Could someone please suggest a relatively simple way to overlay geometries > for visualization? I have access to GaussView, Avogadro, VMD, and any > other freeware applications you can think of. The molecular geometries are > in separate .log files (i.e., output from Gaussian), but of course it is > easy to convert these to almost any other chemical file format, using > Avogadro or the like. > > I realize, though, that "overlaying several conformers" is not a unique > specification; one would need to specify which atom(s) to try to overlap > exactly. Is there an algorithm in a computational chemistry program that > does this? > > Thank you for any guidance you can provide! > > Andrew > > Andrew DeYoung, PhD > Department of Chemistry > Carnegie Mellon University >