Jmol 10.x.25 (SOON to be 11.0 if people would just stop giving me irresistable ideas...) implements a new command, based on an excellent suggestion by Nick Greeves that pointed out how similar molecular orbitals are to frames and vibrations. Basically, you have a file that contains a series of objects. You want to be able to flip through them rapidly and efficiently. In the case of MOs you want to see the energy, symmetry, occupancy displayed, perhaps. MOs are a category of "isosurface" objects, but that command is overkill for what we want to do generally. Thus the command:
MO [index number/NEXT/PREV] MO [cutoff option] MO [resolution option] MO [rendering options] MO [planar slice option] The MO (molecular orbital) command allows you to quickly browse through the molecular orbitals contained in a variety of file formats. One simply loads the file, then selects which orbital to display. NEXT and LAST are provided. (HOMO and LUMO perhaps later, but not implemented yet.) See http://www.stolaf.edu/people/hansonr/jmol/test/proto/new.htm MO 1 MO next MO prev In addition, you can separately specify parameters describing the orbital, including cutoff and resolution (in grid points per Angstrom): MO cutoff 0.01 MO resolution 5 And you can specify how to render the surface: MO mesh MO nofill MO color red green MO color blue MO translucent MO opaque The standard "color" command is a bit more efficient, but it doesn't allow two colors: color mo translucent green color mo red So the MO command is more efficient in that regard. MO is a simple command. You are allowed ONE characteristic per line: MO mesh MO nofill not MO mesh nofill Finally, you can specify a plane that you want to use for a slice through the MO: MO plane "xy" MO plane "xz" MO plane "yz" MO plane {1 1 1 0} The four numbers in braces, {a b c d}, specify the equation for the plane in the form ax + by + cz = d. So, for example, the "xy" plane is where z=0, that is, {0 0 1 0}. The three shortcuts "xy" "xz" "yz" are provided as a convenience. Their equivalents are {0 0 1 0} {0 1 0 0} {1 0 0 0}, respectively. Anything more complicated than this (for example, displaying multiple orbitals at the same time, or a planar slice and standard orbital) requires use of the ISOSURFACE command. Note that the set of MOs for a model are all held with that model in one "frame". Nonetheless, at least for now, there can be only one molecular orbital in the applet, no matter how many models are loaded. This may change if people feel it is too restrictive. Loading multiple models in multiple frames, each with multiple MOs has not been fully tested. Supported file types include: Spartan "archive" files (starting with "Spartan '04 Semi-Empirical Program:...") Spartan SMOL files (starting with INPUT=256~1551~ARCHIVE=2101~105613~PROPARC...") Spartan .spartan binary Compound Document files Gaussian output files Gamess output files WebMO orbital/electron density files Enjoy. I THINK I'm done for what will be added to make 11.0. Bob Hanson Nick Greeves wrote: > Bob, > I've been thinking about the ways to use this new-found ability to > display the MOs from Spartan files. (Still working very well for me) > Obviously we can provide links/buttons to look at HOMO, LUMO etc. but > it might be useful (fun) to allow the user to look at Next Higher and > Next Lower. Just as you have Next Frame and Prev Frame for vibrations. > > For extra credit, a popup menu containing all the MOs and their > energies could be created automatically like you did for vibrations. > http://www.stolaf.edu/people/hansonr/jmol/test/json/vibrate.htm > > OK, OK, I'd settle for next/prev. > > All the best > > Nick > > -- > > WWW Pages: http://www.liv.ac.uk/Chemistrywww/Staff/greeves.html > > Tel: +44 (0)151-794-3506 (3500 secretary) > > > ------------------------------------------------------------------------- Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
