CCL:G: Overlaying conformers for visualization
- From: Brian Skinn <brian.skinn%a%gmail.com>
- Subject: CCL:G: Overlaying conformers for visualization
- Date: Wed, 27 Apr 2022 07:30:18 -0400
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 “compare” command. Here is a tutorial on
how to use it.
> This deals with 2 proteins, but it could be applied to any 2 conformations.
>
> 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 <https://go.microsoft.com/fwlink/?LinkId=550986>; for
> Windows
>
>
>
> *From: *Andrew DeYoung andrewdaviddeyoung**gmail.com
> <owner-chemistry+_+ccl.net>
> *Sent: *Tuesday, April 26, 2022 7:45 PM
> *To: *Keller, John W <jwkeller+_+alaska.edu>
> *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 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
>
>
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<div dir="auto">Andrew,<div
dir="auto"><br></div><div
dir="auto">I'm pretty sure RDKit can do what you want, I
was looking into the same sort of tool a while ago.</div><div
dir="auto"><br></div><div dir="auto">A
quick scan of their docs turned up this, which at least seems like it's
in the right ballpark: <a href="https://www.rdkit.org/docs/source/rdkit.Chem.rdMolAlign.html";>https://www.rdkit.org/docs/source/rdkit.Chem.rdMolAlign.html</a></div><div
dir="auto"><br></div><div
dir="auto"><br></div><div
dir="auto">Good luck!</div><div
dir="auto"><br></div><div
dir="auto">-Brian</div><div
dir="auto"><br></div><div
dir="auto"><br></div></div><br><div
class="gmail_quote"><div dir="ltr"
class="gmail_attr">On Wed, Apr 27, 2022, 02:54 John Keller
jwkeller]~[<a href="http://alaska.edu"; target="_blank"
rel="noreferrer">alaska.edu</a> <<a href="mailto:owner-chemistry:ccl.net"; target="_blank"
rel="noreferrer">owner-chemistry:ccl.net</a>>
wrote:<br></div><blockquote class="gmail_quote"
style="margin:0 0 0 .8ex;border-left:1px #ccc
solid;padding-left:1ex">
Sent to CCL by: John Keller [jwkeller,<a href="http://alaska.edu";
rel="noreferrer noreferrer"
target="_blank">alaska.edu</a>]
<div lang="EN-US" link="blue" vlink="#954F72"
style="word-wrap:break-word"><div><p
class="MsoNormal">Andrew,</p><p
class="MsoNormal">Jmol has a useful “compare”
command. Here is a tutorial on how to use it. This deals with 2 proteins, but it
could be applied to any 2 conformations. </p><p
class="MsoNormal"><a href="https://proteopedia.org/wiki/index.php/Jmol/superposition";
rel="noreferrer noreferrer" target="_blank">https://proteopedia.org/wiki/index.php/Jmol/superposition</a></p><p
class="MsoNormal">The online reference for all Jmol commands is
at</p><p class="MsoNormal"><a href="https://chemapps.stolaf.edu/jmol/docs/";
rel="noreferrer noreferrer" target="_blank">https://chemapps.stolaf.edu/jmol/docs/</a></p><p
class="MsoNormal"><u></u> <u></u></p><p
class="MsoNormal">John Keller</p><p
class="MsoNormal">Department of Chemistry and
Biochemistry</p><p class="MsoNormal">University of Alaska
Fairbanks</p><p
class="MsoNormal"><u></u> <u></u></p><p
class="MsoNormal"><u></u> <u></u></p><p
class="MsoNormal">Sent from <a href="https://go.microsoft.com/fwlink/?LinkId=550986"; rel="noreferrer
noreferrer" target="_blank">Mail</a> for
Windows</p><p
class="MsoNormal"><u></u> <u></u></p><div
style="border:none;border-top:solid #e1e1e1 1.0pt;padding:3.0pt 0cm 0cm
0cm"><p class="MsoNormal"
style="border:none;padding:0cm"><b>From: </b><a
href="mailto:owner-chemistry+_+ccl.net"; rel="noreferrer
noreferrer" target="_blank">Andrew DeYoung
andrewdaviddeyoung**gmail.com</a><br><b>Sent:
</b>Tuesday, April 26, 2022 7:45 PM<br><b>To: </b><a
href="mailto:jwkeller+_+alaska.edu"; rel="noreferrer
noreferrer" target="_blank">Keller, John W
</a><br><b>Subject: </b>CCL:G: Overlaying conformers for
visualization</p></div><p
class="MsoNormal"><u></u> <u></u></p><div><p
class="MsoNormal">Hi,</p><div><p
class="MsoNormal"><u></u> <u></u></p></div><div><p
class="MsoNormal">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.</p></div><div><p
class="MsoNormal"><u></u> <u></u></p></div><div><p
class="MsoNormal">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.</p></div><div><p
class="MsoNormal"><u></u> <u></u></p></div><div><p
class="MsoNormal">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?</p></div><div><p
class="MsoNormal"><u></u> <u></u></p></div><div><p
class="MsoNormal">Thank you for any guidance you can
provide!</p></div><div><p
class="MsoNormal"><u></u> <u></u></p></div><div><p
class="MsoNormal">Andrew</p></div><div><p
class="MsoNormal"><u></u> <u></u></p></div><div><p
class="MsoNormal">Andrew DeYoung,
PhD</p></div><div><p
class="MsoNormal">Department of
Chemistry</p></div></div><p
class="MsoNormal">Carnegie Mellon University</p><p
class="MsoNormal"><u></u> <u></u></p></div></div>
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