I kinda agree with Bob. I certainly wouldn't want Jmol to be able to produce something of the quality of the image in that first link Egon quoted :-) But, if Jmol is to be a tool to produce hard-copy images for publications then an argument could be made for a really good-looking ORTEP style image (putting a simple black & white image in a paper is still easier than a colour one).
However, if Jmol is to be used for static images it's atom labeling needs some substantial improvement. Using atom-by-atom tweaking the user can get labels positioned pretty well but Jmol could do a far better job of providing a good starting point. One of the best programs I have seen for this is the old Pluto code. It divides the space around the atom into octants and put the label into the octant which has the fewest overlaps with other atoms or bonds. If Jmol did this then only a few labels might need some manual adjustment prior to writing the static image. Obviously this choice of a labeling scheme shouldn't be the one used when the molecule is being moved. It needs to be a separate instruction once the view is chosen. Rich On Mon, 8 Mar 2010 07:57:48 -0600, Robert Hanson <[email protected]> wrote: > That's ridiculous. > > Sorry, but to try to go retro on this is just too strange. Stay with 3D. > Enjoy the modern world of color (or grey scales) and interactivity. The > Jmol > documentation gives plenty of help with getting the anisotropic ellipsoids > rendered various ways. We have the cutouts and lines if desired. Jmol's > images will match ORTEP's exactly but look WAY better. If desired, bonds > can > be made thin, black, and lifeless. > > Bob > > On Sun, Mar 7, 2010 at 5:46 AM, Egon Willighagen > <[email protected] >> wrote: > >> Hi all, >> >> I saw this interesting question on the CCL mailing list: >> >> On Tue, Mar 2, 2010 at 9:55 PM, Anthony F wrote: >> > My next question is on visualizing my XYZ files. I have used Avogadro, >> VMD, and Gabedit. But I want to make diagrams like these: >> > >> > http://bhgroup.lsa.umich.edu/files/u1/ge-prop-ortep.gif >> > >> > I prefer how the ellipsoids have the 3D effect and that everything is >> > in >> black and white. I don't like how bonds have two different colors in >> Avogadro and VMD. >> >> There is a nice tutorial by the IUCR that shows how ORTEP diagrams can be >> used: >> >> http://journals.iucr.org/services/help/jtkt/7.html >> >> And I know the scripting language can be used to change the colors of >> atoms and bonds... >> >> But that would not cover a border around atoms and bonds, I guess, so >> that we can make them all white-on-white... >> >> Has someone tried to make black-and-white ORTEP diagrams with Jmol? >> >> Kind regards, >> >> Egon >> >> -- >> Post-doc @ Uppsala University >> Proteochemometrics / Bioclipse Group of Prof. Jarl Wikberg >> Homepage: http://egonw.github.com/ >> Blog: http://chem-bla-ics.blogspot.com/ >> PubList: http://www.citeulike.org/user/egonw/tag/papers >> >> >> ------------------------------------------------------------------------------ >> Download Intel® Parallel Studio Eval >> Try the new software tools for yourself. Speed compiling, find bugs >> proactively, and fine-tune applications for parallel performance. >> See why Intel Parallel Studio got high marks during beta. >> http://p.sf.net/sfu/intel-sw-dev >> _______________________________________________ >> Jmol-users mailing list >> [email protected] >> https://lists.sourceforge.net/lists/listinfo/jmol-users >> > > > > -- > 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 ------------------------------------------------------------------------------ Download Intel® Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
