Happy New Year to all Jmol users! Miguel reminds me that it's been almost 5 years since Jmol took over my life. Can it be that long? My how time flies when you are having fun.
I'm working on crystallography this month. So if you have ideas in that regard, do speak up. Jmol 11.9.17 has some pretty remarkable new features, and not just for crystallography. Here's a partial list. Check these out at http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm . Not documented yet. version=11.9.17 # new feature: draw BOUNDBOX (backlit for backside only) # new feature: draw UNITCELL (backlit for backside only) # these both allow for scaling: # draw scale 2.0 UNITCELL MESH NOFILL # draw scale 0.8 BOUNDBOX POINTS NOFILL # new feature: draw INTERSECTION BOUNDBOX HKL {h k l} # new feature: draw INTERSECTION UNITCELL HKL {h k l} # new feature: draw INTERSECTION BOUNDBOX PLANE {a b c d} # new feature: draw INTERSECTION UNITCELL PLANE {a b c d} # new feature: draw SYMOP {atom1} {atom2} # new feature: draw SYMOP n {atom1} {atom2} # extends draw SYMOP n {atom} # extends draw SYMOP n # new feature: show SYMOP {atom1} {atom2} # new feature: show SYMOP n {atom1} {atom2} # new feature: show SYMOP n # new feature: show SYMOP # new feature: spacefill AUTO # new feature: spacefill JMOL # new feature: spacefill BABEL # new feature: spacefill BABEL21 # new feature: spacefill RASMOL # new feature: spacefill 20%JMOL # new feature: spacefill 23%BABEL # etc. # # default atom size changed from 20%Jmol to 23%Auto for C atom size match in small molecules # # new feature: update of Babel VDW forces. We had been using Babel 1.0 numbers # that were changed long ago; # new feature: set defaultVDW BABEL21 -- older 2.1 numbers previously "BABEL" # # bug fix: MAJOR -- proper model-based Van der Waals radii. # this bug has been with Jmol since its inception -- that # the inflated Jmol parameters for H, C, N, and O are not # proper for anything but traditional "no hydrogen" PDB files # That "Jmol" data set should not be used with small molecules, # and it has long been noted that it looks incorrect. While we # have had the (old) Babel data set, one should not have to # know to use that manually. The new feature associated with this # fix is # # set defaultVDW AUTO (default) # # So now Jmol will apply a proper Babel-based VDW set when # the file has hydrogen atoms present. One can always override this # if desired, but I think the only reason to do that is to have # the identical match to an improperly defined VDW size in previous # output. # # Note -- script files already in place will not be affected, # as they explicitly define defaultVDW to be JMOL. # new feature: math function hkl(a,b,c) # new feature: isosurface OFFSET {x, y, z} # new feature: isosurface SCALE3D x.xx Creates a "mountain" plot from a planar map Bob -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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