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

[Robert H. <ha...@st...>]

Hi Dennis. Been a while. I'm now retired from teaching.

ProLIF is in Python or is it just a C++ wrapper?

https://github.com/chemosim-lab/ProLIF

(Poor choice of name I think. )

Bob

On Mon, Jun 1, 2026, 11:32 AM Dougherty, Dennis A. <da...@ca...>
wrote:

> 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
> <https://www.google.com/maps/search/1200+E.+California+Blvd?entry=gmail&source=g>.,
> MC 164-30
> Pasadena, CA  91125
>
> Phone: 626-395-6089
> Fax:  626-564-9297
>
>
>
>
> On May 30, 2026, at 3:23 PM, m0...@ya... wrote:
>
> Dear Bob and Mark,
>
> I have prepared a document "Cation-Pi in Jmol" detailing desired output.
> Also the CaPTURE server outputs for two examples.
> I was wrong thinking that CaPTURE does not work -- it does not work when
> you specify a PDB ID code.
> It DOES work when you UPLOAD a PDB file.
>
> All files are available here:
>
>
> https://www.dropbox.com/scl/fo/dhqxr2cscwlcuqgzf2lcr/AEfZ_g0nstLAaECau1Ye6KI?rlkey=v84oin9mojxdxurwdu52n7ulv&dl=0
>
>
> I do not see computational methods in the 1999 PNAS paper (also at the
> above link).
> Mark, where did the Python computational procedure come from?
>
> It would be really fabulous if reliable energy-based cation-pi
> determination can be incorporated into Jmol!
>
> -Eric
>
> On Friday, May 29, 2026 at 03:51:09 PM EDT, Robert Hanson <
> ha...@st...> wrote:
>
>
> OK, well, I think it's just this module:
> https://raw.githubusercontent.com/chemosim-lab/ProLIF/refs/heads/master/prolif/fingerprint.py
>
> Eric, what are you looking for here? What are the inputs and outputs?
>
> Bob
>
>
>