From: Robert H. <ha...@st...> - 2009-08-01 06:10:54
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The 2009 Gordon Research Conference on Visualization in Science and Education is over. It was unbelievably cool. It's strict policy not to discuss anything that was at that meeting, so please don't ask me to do that. However, some ideas were transmitted to me during the meeting from Jmol users, and I did have a few hours to work on Jmol here and there outside of the actual conference hours, so there are a few new features in Jmol 11.8.RC4 even though I try not to do that with a "release candidate." Three new features and one crazy idea of note: Mouse-movable labels Lone pairs and radicals CIF data in structured form Mouse-movable labels -------------------------------- Using set Picking Label which generally turns labels on and off when an atom is clicked now also allows fast movement of a label using the mouse. Just hold SHIFT down while picking the atom associated with an already-displayed label. Dragging the mouse then drags the ("SHIFTS" the) label position around. Lone pairs and radicals ---------------------------------- Thank Mike Abraham for reminding me that we've wanted lone pairs for SOME TIME (like forever). Now you have them. It occurred to me that really they are cartoonish more than real, and if you think about it, the LcaoCartoon objects are positionable exactly the way we would want to position lone pairs. So now you can position a lone pair any way you would a lobe. Just use LONEPAIR instead of CREATE: select oxygen lcaoCartoon color red lcaoCartoon LONEPAIR "sp2a" lcaoCartoon LONEPAIR "sp2b" The default is 0.5 Angstroms from the associated atom center, which basically places it directly in the center of an LCAO orbital. But you can place the electrons wherever you want: lcaoCartoon scale 1.5 LONEPAIR "sp2b" The actual size of the dots or distance between the dots is not adjustable. (The current setting was chosen by an august consultant panel.) The scale factor just moves them along the axis. While considering that, it seemed simple enough to do single electrons, so we also have: lcaoCartoon RADICAL "pza" which, of course, places a single dot along that axis. CIF data in structured form --------------------------------------- Recently I added a method of getting PDB header data directly into a variable. This is now expanded to CIF files and renamed "fileInfo". It's obtainable via the getProperty() function. Realize that the file is read a second time to do this -- it isn't stored by default -- but once it is read the second time, it is then saved. This could be an issue with very large files. load 1crn.pdb print getProperty("fileInfo","HELIX") H1 ILE A 7 PRO A 19 13/10 CONFORMATION RES 17,19 13 H2 GLU A 23 THR A 30 1DISTORTED 3/10 AT RES 30 8 load 1mng.cif print getProperty("fileInfo","models",0,"_audit_author.name") Lah, M.S. Dixon, M. Pattridge, K.A. Stallings, W.C. Fee, J.A. Ludwig, M.L. Note that for _loop data, the individual "columns" of data become an array: load quartz.cif x = getProperty("fileinfo","models",0,"_atom_site_label") show x x = ["Si", "O"] Thanks go to Brian McMahon for that suggestion. The crazy idea is really crazy. It's to extend Jmol to display N-dimensional data as 3-dimensional projections. This is important in some fields, but not at all trivial. We have the know-how in my collaborator Andy Hanson, of Indiana University. This can be done relatively simply, I think, but we'll see. Mostly it's a matter of porting Andy's C++ code over to Java and then figuring out how to patch that into Jmol. I'll start a new branch for it when we get going on it and see how it goes. All for now, Bob (enroute to Berlin) -- 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 nday, February 5, 1900 |