From owner-chemistry ^at^ 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=

=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

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