Re: [Jmol-users] Fw: Getting Jmol to detect cation-pi interactions reliably

[Amr A. <amr...@ho...>]

Hi Eric,

I believe my son would be happy to do it over this summer. I can still help him if he needs.
Would you like to give him a try?

Amr



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From: m0lviz--- via Jmol-users <jmo...@li...>
Sent: Tuesday, June 2, 2026 11:52 AM
To: jmo...@li...
Cc: m0...@ya...; dad...@ca...
Subject: [Jmol-users] Fw: Getting Jmol to detect cation-pi interactions reliably

Hi Jmolers, I'm forwarding this encouragement from Dennis Dougherty at Caltech (leading expert on cation-pi interactions) just to keep everyone in the loop. -Eric

----- Forwarded Message -----
From: Dougherty, Dennis A. <da...@ca...<mailto:da...@ca...>>
To: m0...@ya...<mailto:m0...@ya...> <m0...@ya...<mailto:m0...@ya...>>
Cc: Mark Perri <pe...@so...<mailto:pe...@so...>>; Robert Hanson <ha...@st...<mailto:ha...@st...>>; jmo...@li...<mailto:jmo...@li...> <jmo...@li...<mailto:jmo...@li...>>; Dougherty, Dennis A. <da...@ca...<mailto:da...@ca...>>
Sent: Monday, June 1, 2026 at 12:32:32 PM EDT
Subject: Re: [Jmol-users] Getting Jmol to detect cation-pi interactions reliably

Hi All:

Sorry for the slow response; travel ....

I am very enthusiastic about this effort, and I would be happy to support it in any way I can. I have contacted Justin Gallivan (who wrote CaPTURE) a few times over the years, and unfortunately the media that contains the source code (which was written in C++) is not readable. I will follow up with Justin to be sure.

It might be easier to just write something new from scratch in Python or another more modern coding tool. I’m sure you have considered whether ChatGPT or similar could create such code. I’ve had many requests over the years to provide the code, but Justin and I made the (perhaps poor) decision long ago not to do so. If you want a more thorough description of the model, I can help or provide pages from Justin’s thesis.

Again, I am happy to help in any way I can, and thanks for your efforts on this.

Dennis

Dennis A. Dougherty
George Grant Hoag Professor of Chemistry
Division of Chemistry and Chemical Engineering
California Institute of Technology
1200 E. California Blvd., MC 164-30
Pasadena, CA  91125

Phone: 626-395-6089
Fax:  626-564-9297