Re: [Jmol-users] Natural Bond Orbital Display Issues

[Conor B. <cbr...@ma...>]

Hi Drs. Hanson and Keller,

I was able to replicate Dr. Keller's protocol, so I at least have the
ability to visualize the orbitals as needed -- thank you very much for the
advice! I am still hoping that the workflow that Dr. Hanson recommended
will work within jmol to save a bit of time, so to that end, I've attached
the .log file I'm using below, along with all available xxx.## files from
webMO. I'm wondering if part of the issue is that I'm unsure how to handle
the xxx.32-xxx.41 files (jmol seems to require the .47, but webMO doesn't
appear to generate that file). I tried using the "NBO [orbital number]"
command while the .log file is open in jmol and in the same folder as the
xxx.## files, but it still has the same issue with loading what appear to
be MOs instead.

Best, and thank you for your help!

- Conor
 NBODATA.34
<https://drive.google.com/file/d/1SnFPml5jYKxpcuRK0NHQ72_6L6G6R2y6/view?usp=drive_web>
 NBODATA.36
<https://drive.google.com/file/d/1oA1aBVzrjJ-kwfqa7y66LeA8-20ARymX/view?usp=drive_web>
 NBODATA.84
<https://drive.google.com/file/d/1kTOMEZx3ws_xifdJwJebWCayeqctR9e2/view?usp=drive_web>
 NBODATA.86
<https://drive.google.com/file/d/1A0kmduxvgxn62hVVdWpxjPt7h1UssKWO/view?usp=drive_web>
 NBODATA.92
<https://drive.google.com/file/d/1p8AXPcnQGtsYEjHyDLT1OwghvnJX4ZaE/view?usp=drive_web>
 NBODATA.94
<https://drive.google.com/file/d/1xUlYK149OQSb73kXJ_Kn8kWf3ZqKM6A3/view?usp=drive_web>
 NBODATA.96
<https://drive.google.com/file/d/1fSpeVnZJKmxxgJXRWLCqbZ4AWYYaDufa/view?usp=drive_web>
 chb-COMP-11-DPPE-NDI_dirad_NBO.log
<https://drive.google.com/file/d/1eS833lRX3NpUQXpzv1skSJB45tnp-Vos/view?usp=drive_web>

On Wed, Oct 28, 2020 at 5:27 AM Robert Hanson via Jmol-users <
jmo...@li...> wrote:

> Just pointing out that Jmol can natively read all of the many NBO file
> types. Note the NBO command. There should be no longer any necessity to
> work through WebMO or cube files.
>
> Connor, feel free to send me links to these files so that I can do some
> checks.
> nbo
> *The NBO (Natural Bond Order) command is a variant of the MO
> <https://chemapps.stolaf.edu/jmol/docs/index.htm?ver=14.29#mo> command. The
> two commands are the same, but for a few additional capabilities specific
> to NBO. The NBO command allows a TYPE keyword. Specifying the orbital type
> -- one of AO, PNAO, NAO, PNHO, NHO, PNBO, NBO, PNLMO, NLMO or MO -- results
> in immediate loading of the corresponding ""plot"" file xxx.32-xxx.41 if
> present. This is generally done after a .47 archive file has been loaded,
> but any of the other files loading will trigger the loading of the .47
> file. (In this case in Jmol file extensions are significant and are used.) *
>
> (Actually, it is no longer experimental -- it has been in service for
> several years.)
>
> Bob
>
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