10.x.14 OK, getting back to a project I started for John Gelder back in March at the ACS meeting in Atlanta, I've now completed work on dipoles.
http://www.stolaf.edu/people/hansonr/jmol/test/proto/dipole.htm In a nutshell, you can now: -read partial charge and molecular dipole data from Spartan SMOL files. I started with these because they are what John is using, but it obviously could be extended to more file types. Suggestions welcome. -display file-based molecular dipoles as arrows. Either direction (there are two conventions) and with or without the lively 3D cross at the tail end. -display Jmol-calculated semiqualitative bond dipoles. For this I'm just using (distance12) (charge1)(charge2)/2 is that too simplistic? -color these selectively, just like bonds -move them around parallel and perpenticular to their associated bond. (see examples) -change their width (i.e. diameter) and length -scale one or more or all of them together (set dipoleVectorScale x.xxx) -tabulate the data for use in other programs -designer dipoles -- create your own. You can use atom positions (atomno=3) or molecular coordinates {1.0,2.0,3}. You can also mix and match: dipole number1 {0 0 0} (hydrogen and connected(atomno=3)) that sort of thing. Of course, you can use fractional coordinates in unit-cell systems: dipole number1 {0 0.5, -0.5/} {1/2 1/2 1/2} nocross width 0.10 (I can imagine this might be useful to somebody.) -Animate them (selectively move them around based on a script) -For those users who want the occasional simple arrow to point something out, "dipole nocross" should do the job quite nicely. -Extract the dipole data using getProperty shapeinfo I haven't tested these yet on multiple-file or multiple frame model sets, so there might be bugs there. But all the visibility coding is there, building on what I developed earlier for draw objects. So we should be able to have multiple models with different sets of dipoles. One could even think of the different frames as "layers" if one wished and selectively display different sets for the same molecule loaded into different frames. Let me know if you try this and it doesn't work. I haven't implemented "clickability" -- click on a dipole or hover over it to see its data, but that's another thing I built into Jmol when I worked on visibility. So expect to see clickable dipoles that "report" about themselves when you click on them. Other ideas? Comments? Suggestions? On to Slater and Gaussian orbitals for displaying molecular orbitals directly without the need for CUBE files. (Thank you, Won Kyu, for mocube.f. That is just what I needed.) Some say it can't be done in Java.... Bob _______________________________________________ Jmol-developers mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-developers
