Re: [Jmol-users] Displaying multiple NBOs

[John K. <jwk...@al...>]

Bruce,
That’s a nice page!
Am I correct that your .jvxl surface files were generated beforehand and saved in the same folder as the .html file?
Actually, in this exercise I am trying to avoid that whole process by just loading the NBO plot output file, then using the “nbo n” command to display nbo’s.

Part of the problem seems to be that the mo command, and presumably the nbo command, depends on loading and reading a WebMO “.mo” file, or Spartan’s .spartan file. Recent versions of WebMO do not save surfaces in the .mo format as they once did. Currently only .cub files can be saved in WebMO. Also, many folks do not have access to Spartan, and the /examples-11/mo.htm is focused on this file format.

John Keller

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From: Bruce Tattershall
Sent: Monday, March 11, 2019 11:06 AM
To: jmo...@li...
Subject: Re: [Jmol-users] Displaying multiple NBOs

Further to this:   I generated all eight isosurfaces one at a time, and saved them to disc, so that during this process there was never more than one present at a particular instant.  Once you have the isosurfaces, you can load as many as you wish at once, providing they have different file names and you give them all different isosurface names after reloading .   Putting them into separate frames is a convenient way to switch them on and off at will.  My example gets a bit cluttered if all four are on at once, whether for the orbital surfaces or for the contour plots, but it is very instructive for the user to switch them on or off experimentally, one at a time, until they understand what they are looking  at.

The web page works well in Chrome as the browser.    I think it is OK in Safari as well, if  you are Apple based.

  Bruce

From: Bruce Tattershall [mailto:bru...@ne...] 
Sent: 11 March 2019 17:33
To: jmo...@li...
Subject: Re: [Jmol-users] Displaying multiple NBOs

John

Why not load your different NBOs into separate frames and then superimpose them using ‘frames all’?
I have done this successfully in
https://www.staff.ncl.ac.uk/bruce.tattershall/structs/p5e2x/showjmol.php?use=HTML5&filestem=p5s2cl&lpnow=true

You can see enough of the code for this by View Source

Best wishes
  Bruce

Newcastle University, England


From: John Keller [mailto:jwk...@al...] 
Sent: 10 March 2019 22:01
To: jmo...@li...
Subject: [Jmol-users] Displaying multiple NBOs

Hi All,
Displaying multiple NBOs, where one is an electron pair donor and the other an acceptor, is quite useful in the analysis of various non-covalent complexes. 
I know one can do this in Jmol using .cub files generated by say, WebMO. However, now I am trying to use Jmol to display NBOs directly from Gaussian output. I am using Jmol 14.29.26 for Linux and G09 linked to NBO6. For example, the following input file was used to calculate the NBOs of water, and the resulting h2o.37 file was opened in Jmol. The various NBOs can be displayed using the “NBO n “ command. And an NBO can be modified using cutoff, color, mesh, nofill, resolution, and other modifiers as one would do with the “MO” command.

#N B3LYP/6-31G(d,p) SP GFINPUT POP=(FULL,NBO6Read) 
title 
molecule specification
$NBO file=h2o plot archive $END

However, I am not able to create an NBO isosurface, or display multiple NBOs as isosurfaces, or visualize two NBOs by loading h2o.37 twice, as described for MOs on the  /examples-11/mo/htm page.  Nor can I generate a .jvxl file using a “write” command from a displayed NBO. 

So, is it possible to display multiple NBOs in Jmol starting with the G09/NBO6 output?  

(Also, in Jmol I have not been able to display ANY NBO generated by G09 and the built-in NBO3 function, i.e. the above input file with “NBORead” in place of “NBO6Read”.)

John Keller
University of Alaska Fairbanks
P.S. If you don’t have local access to Gaussian, short jobs can be run on the WebMO working demo site https://www.webmo.net/demoserver/cgi-bin/webmo/login.cgi  (but only NBO3: not NBO6).
P.P.S. To see the Gaussian job referred to above, visit the UAF WebMO site at https://corsair2.cns.uaf.edu/~frank/cgi-bin/webmo/login.cgi .  Log on as guest, pwd webmo. It’s job 13202.



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