Daniel, By “second file” I only meant the file that is not working.
Like Angel, I’m no expert on MO visualization, either. In version 14.3.16 of the Jmol app, the console shows (when reading Gaussian files) which model has the mo’s. For example, the console reads, upon loading a gaussian log file: 24 models 26 molecular orbitals in model 1.2 26 molecular orbitals in model 1.10 26 molecular orbitals in model 1.12 $ model 1.12 $ mo 1 So, you may want to download a more recent version to have a console confirm for you that mo’s exist in your file. Gaussian performs a population analysis before and after geometry optimization, so you get MO’s in model 1.2 and model 1.10. I must confess I do not know what, exactly, is the difference between mo’s in model 1.10 vs model 1.12. They look identical to me. Subsequent models hold the normal mode information.) (File read by Jmol was generated by g09, using a route section of # HF/6-31G opt freq pop=full gfprint) Matt On Sep 8 , 2015, at 8:02 AM, Friese Daniel Henrik <daniel.h.fri...@uit.no<mailto:daniel.h.fri...@uit.no>> wrote: Dear Matthew, Thank you for your reply. I do not use a second file. The command I am typing is $ jmol jmol ecd_camb3lyp_6hel.molden Then I get a jmol window with the structure. For a file for a molecule with similar size but without symmetry I can easily get the mos by typing e.g. $ mo 80 in the jmol console. Then it takes some time to render the orbital. What happens in this case is that the calculation time is way shorter (although the molecule is of the same size) and nothing happens after it is through (indicated by a movement of the mouse indicator in the jmol window). I have also already compared the entries in the molden input files for the different molecules and the only difference I found is that for certain orbitals there is another indicator for the point group. Without point group symmetry the indicator is always A, in my case (C2 symmetry) it is either A or B. Also playing around with the cutoff values does not have any influence. When I open the console the number of orbitals is recognized properly, however I should mention that the order is not in energy order but in in energy order within the irreducible representation. The molden input file has been generated by the Dalton program by the way. I already had a look at the manual page but I did not find any solution for the problem. Do I maybe have to tell jmol that the orbitals contain symmetry? Best regards, Daniel ______________________________________________________________________ Dr. Daniel Friese Centre for Theoretical and Computational Chemistry Universitetet i Tromsø - Norges Arktiske Universitet Norway Best regards also to the secret reader from the National Security Agency ________________________________________ Von: Kubasik, Matthew A. <mkuba...@fairfield.edu<mailto:mkuba...@fairfield.edu>> Gesendet: Dienstag, 8. September 2015 13:22 An: jmol-users@lists.sourceforge.net<mailto:jmol-users@lists.sourceforge.net> Betreff: Re: [Jmol-users] Plotting molecular orbitals with jmol from a molden input file: Problem with symmetry Daniel, Could it be the MO settings in your second file? The MO’s may be there, just hard to see. You may need to adjust the Jmol’s MO parameters in your second model that isn’t showing MO’s. MO documentation is here: http://chemapps.stolaf.edu/jmol/docs/index.htm?command=mo&ver=14.3.16_2015.08.21 Specifically, try the CUTOFF parameter: mo CUTOFF (decimal) Sets the cutoff value for the isosurface that defines the orbital. This number may be dependent upon the computational package used to generate the orbitals. Values in the range 0.005 - 0.05 may need to be experimented with in order to get the best display. Values closer to zero lead to surfaces further from the atoms (larger orbitals). Both positive and negative cutoffs are allowed. A positive number indicates to use both positive and negative cutoffs. Adding an explicit "+" sign before the number indicates that only the positive part of the surface is desired. Matt On Sep 8, 2015, at 5:47 AM, Friese Daniel Henrik <daniel.h.fri...@uit.no<mailto:daniel.h.fri...@uit.no>> wrote: Dear jmol users and developers, Yesterday I was really happy when I found out that I can plot molecular orbitals in JMOL by just loading a molden input file which is generated automatically by the Dalton program. Today I tried this for another molecule and it turned out to be that it did not work. The major difference between the molecules is that the one I tried yesterday had no point group symmetry while the one I tried today has it. If I request plotting for e.g. orbital 80 by typing "mo 80" in the console nothing happens. There is neither an error message nor a result. Do I do anything wrong there or is it a bug? I am using version 13.2.7 Thanks to everybody who takes the time to answer. Best regards, Daniel ______________________________________________________________________ Dr. Daniel Friese Centre for Theoretical and Computational Chemistry Universitetet i Tromsø - Norges Arktiske Universitet Norway Best regards also to the secret reader from the National Security Agency ------------------------------------------------------------------------------ _______________________________________________ Jmol-users mailing list Jmol-users@lists.sourceforge.net<mailto:Jmol-users@lists.sourceforge.net> https://lists.sourceforge.net/lists/listinfo/jmol-users ------------------------------------------------------------------------------ _______________________________________________ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users ------------------------------------------------------------------------------ _______________________________________________ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users ------------------------------------------------------------------------------ _______________________________________________ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
