On Thu, May 21, 2009 at 8:59 AM, Laurence Marks <l-ma...@northwestern.edu>wrote:
> 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? > No. These are determined in the loading code and no where else. What people do sometimes is load more than you need, then only DISPLAY the ones you want. > > 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. > Embedded scripts are run after loading, not before. It's an interesting idea to provide some sort of load functionality within the file, but to date we don't have that. > > N.B., does a "jmolscript:" get embedded in a { } (i.e. C)? > There's Jmol script, Jmol math, and Jmol selection syntax. Generally @{ } sets off math. { } sets off either coordinates or selection, depending upon the context. What is "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 > -- 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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