I managed to load TiO.struct and set the vibrations for the Ti, and it is there for all equivalent sites so this works fine. (The button at the top is fine; the right-mouse click does not show vibrations as an option.)
However, I could not find a way to alter the number of unit cells being shown without reloading the structure; is there a way of doing this? The alternative is to use embedded jmol scripting either in an xyz file (to set the cell so, maybe {1 1 1} PACKED or similar will be understood) or in a cif. I'll try this. N.B., does a "jmolscript:" get embedded in a { } (i.e. C)? On 5/21/09, Robert Hanson <hans...@stolaf.edu> wrote: > The Jmol application probably does have some minor issues there. I'm not > sure if you load vibrational data by script, for example, that the vibration > button works. Most of us use the console. But should that be the case, then > a bug report should be filed so I can get to it. > > If you have implemented vibrations in an XYZ file, then that's all you need. > Just write a little Jmol script that > > 1) loads the Wien2k or other file with full symmetry > 2) reads that xyz file into a variable using vibdata = file("yyy.xyz") > 3) changes that to Jmol script format and runs it. > > > I think this is a few lines of Jmol script: > > function applyVibData(filename) > var vibdata = load(filename) > var S = vibdata.split() > var myscript = "" > for (var i = 3; i <= S.size; i=i+1) > var line = S[i] > # change the numbers below to match your file format -- I'm guessing > here > var x = "{" + (S[i])[3][45] + "}" > var v = "{" + (S[i])[48][0] + "}" > myscript = myscript + "x=" + x + ";v=" + v+";{within(-2.5,x)}.vxyz = > v\n" > end for > script inline @myscript > end function > > > > Bob > > > > On Thu, May 21, 2009 at 7:11 AM, Laurence Marks <l-ma...@northwestern.edu> > wrote: > > > > Let me be a bit more specific. I have implemented vibrations using an > > xyz file, but since this does not contain the crystal lattice > > information cell repeats have to be done ahead of time. What I would > > like to do is for a crystal (cif, Wien2k, other) add vibrations > > (probably with a script) and then display these using "standard" tools > > for repeating the unit cell etc, with the vibrations obeying the > > appropriate symmetry and translational operations. > > > > When I attempted to do this it looked like this is not currently > > supported (the vibrations button was inactive) although I might not > > have done it correctly and I don't think I used the console. > > > > N.B., there are some issues with the vibrations having a lower > > symmetry than the unit cell so strictly speaking the cell should have > > P1 symmetry. Walk before run; are vibrations active for crystals. > > > > N.N.B., an alternative would be to be able to add crystalline repeat > > information to an xyz format. > > > > -- > > Laurence Marks > > Department of Materials Science and Engineering > > MSE Rm 2036 Cook Hall > > 2220 N Campus Drive > > Northwestern University > > Evanston, IL 60208, USA > > Tel: (847) 491-3996 Fax: (847) 491-7820 > > email: L-marks at northwestern dot edu > > Web: www.numis.northwestern.edu > > Chair, Commission on Electron Crystallography of IUCR > > www.numis.northwestern.edu/ > > Electron crystallography is the branch of science that uses electron > > scattering to study the structure of matter. > > > > > ------------------------------------------------------------------------------ > > Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT > > is a gathering of tech-side developers & brand creativity professionals. > Meet > > the minds behind Google Creative Lab, Visual Complexity, Processing, & > > iPhoneDevCamp asthey present alongside digital heavyweights like Barbarian > > Group, R/GA, & Big Spaceship. http://www.creativitycat.com > > _______________________________________________ > > Jmol-users mailing list > > Jmol-users@lists.sourceforge.net > > 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 > > ------------------------------------------------------------------------------ > Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT > is a gathering of tech-side developers & brand creativity professionals. > Meet > the minds behind Google Creative Lab, Visual Complexity, Processing, & > iPhoneDevCamp asthey present alongside digital heavyweights like Barbarian > Group, R/GA, & Big Spaceship. http://www.creativitycat.com > _______________________________________________ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users > > -- Laurence Marks Department of Materials Science and Engineering MSE Rm 2036 Cook Hall 2220 N Campus Drive Northwestern University Evanston, IL 60208, USA Tel: (847) 491-3996 Fax: (847) 491-7820 email: L-marks at northwestern dot edu Web: www.numis.northwestern.edu Chair, Commission on Electron Crystallography of IUCR www.numis.northwestern.edu/ Electron crystallography is the branch of science that uses electron scattering to study the structure of matter. ------------------------------------------------------------------------------ Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT is a gathering of tech-side developers & brand creativity professionals. Meet the minds behind Google Creative Lab, Visual Complexity, Processing, & iPhoneDevCamp asthey present alongside digital heavyweights like Barbarian Group, R/GA, & Big Spaceship. http://www.creativitycat.com _______________________________________________ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users