Re: [Jmol-users] orbitals as cartoons
right, so please brainstorm on some sort of command syntax that you think might work. I'm interested in seeing what people think would be the right way to do this. Say we have a carbon double bond between 3 and 4. Should Jmol be able to handle something like the following to show the antibonding combination? orbital myorb1 (atomno=3) 100 "p" orbital myorb1 (atomno=4) -100 "p" I can imagine it would NOT be trivial to get this right. Bob Hens Borkent wrote: > Bob Hanson wrote: > > >>> >>> >> >>What we can now do is depict isosurfaces for: >> >>(a) CUBE files, >>(b) essentially equivalent but 1/500 the size JVXL files, >>(c) atomic orbitals centered at (0,0,0) and aligned with the molecular >>xyz axis. >> >>The fact that we can do (c) suggests that any reasonable built-in >>function could be mapped. >>The isosurface method is just calling: >> >> value = getPsi2(x,y,z) >> >>so I don't se why we couldn't substitute in a few other functions as >>well -- perhaps a small set of hybrids. >> >>The real question is simply: How does one orient these so that they are >>actually useful in relation to molecules? >> >> > > You mean: like a p orbital at any heavy atom, perpendicular to the plane > of the atom and its neighbours? > And an sp3 type, pointing along the axis defined by the other three > substituents at an atom? > Or a hybrid of the two, defined by the deviation from planarity of the > central atom? > I think that would be great, and cover many text book examples. > > Hens > > > ___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson, [EMAIL PROTECTED], 507-646-3107 Professor of Chemistry, St. Olaf College 1520 St. Olaf Ave., Northfield, MN 55057 mailto:[EMAIL PROTECTED] http://www.stolaf.edu/people/hansonr "Imagination is more important than knowledge." - Albert Einstein ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] orbitals as cartoons
Bob Hanson wrote: >> >> >What we can now do is depict isosurfaces for: > > (a) CUBE files, > (b) essentially equivalent but 1/500 the size JVXL files, > (c) atomic orbitals centered at (0,0,0) and aligned with the molecular >xyz axis. > >The fact that we can do (c) suggests that any reasonable built-in >function could be mapped. >The isosurface method is just calling: > > value = getPsi2(x,y,z) > >so I don't se why we couldn't substitute in a few other functions as >well -- perhaps a small set of hybrids. > >The real question is simply: How does one orient these so that they are >actually useful in relation to molecules? > > You mean: like a p orbital at any heavy atom, perpendicular to the plane of the atom and its neighbours? And an sp3 type, pointing along the axis defined by the other three substituents at an atom? Or a hybrid of the two, defined by the deviation from planarity of the central atom? I think that would be great, and cover many text book examples. Hens ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] orbitals as cartoons
Hens Borkent wrote: >Jonathan Gutow wrote: > > > >>Bob, >> I think I see where you are going, but am a little worried. >>If it is a cartoon, it needs to be clear that it is. >> >> >> >.. > > > >> I think a tool like Jmol should be used to provide as >>accurate a representation of things as we can. Thus in relation to >>orbitals the use of .cube and .jvxl files seems like a good idea. I >>do see how someone might want to think about the orbitals on a >>molecule in terms of the cartoon orbitals, but I still think that >>learning to use the more complete MOs is better. >> >> >> >Yes, I agree with the last statement. >However, I can also imagine applications where a cartoon better explains >what you're trying to tell. >As is done in pictures in text books, showing a cartoon of a pi system >instead of a more complicated MO. >In particular I'm thinking of showing free electron pairs (a subject >which returns regularly in this forum), for instance as a cartoon of an >sp3 (or sp2, or ...) orbital on a nitrogen atom. >Is that an option, Bob? > > What we can now do is depict isosurfaces for: (a) CUBE files, (b) essentially equivalent but 1/500 the size JVXL files, (c) atomic orbitals centered at (0,0,0) and aligned with the molecular xyz axis. The fact that we can do (c) suggests that any reasonable built-in function could be mapped. The isosurface method is just calling: value = getPsi2(x,y,z) so I don't se why we couldn't substitute in a few other functions as well -- perhaps a small set of hybrids. The real question is simply: How does one orient these so that they are actually useful in relation to molecules? I have some ideas on that, but I want to add (d) solvent-accessible surfaces first (which I hope to code this afternoon). . >Often the calculated MO describing this f.e.p. shows many more >contributions that you don't want to show at this point. >[Now we can prepare ourselves for the discussion on how to show the 2 >fep's on a carbonyl oxygen] > > > I think it's important to remember that anyone who wants to use CUBE files can certainly still do so, with or without the JVXL compression. All I'm doing here (I think) is providing alternatives to that. For atomic orbitals, it seems to me, there is absolutely no need for cube files, since Jmol can now create high precision CUBE data on the fly at least as well as any external program. Surely this beats delivering a 3 Mb file for each atomic orbital. Bob ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] orbitals as cartoons
Jonathan Gutow wrote: >Bob, > I think I see where you are going, but am a little worried. >If it is a cartoon, it needs to be clear that it is. > .. > I think a tool like Jmol should be used to provide as >accurate a representation of things as we can. Thus in relation to >orbitals the use of .cube and .jvxl files seems like a good idea. I >do see how someone might want to think about the orbitals on a >molecule in terms of the cartoon orbitals, but I still think that >learning to use the more complete MOs is better. > Yes, I agree with the last statement. However, I can also imagine applications where a cartoon better explains what you're trying to tell. As is done in pictures in text books, showing a cartoon of a pi system instead of a more complicated MO. In particular I'm thinking of showing free electron pairs (a subject which returns regularly in this forum), for instance as a cartoon of an sp3 (or sp2, or ...) orbital on a nitrogen atom. Is that an option, Bob? Often the calculated MO describing this f.e.p. shows many more contributions that you don't want to show at this point. [Now we can prepare ourselves for the discussion on how to show the 2 fep's on a carbonyl oxygen] Hens ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
