Alright. Time to test. See http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm http://chemapps.stolaf.edu/jmol/docs/examples-11/ellipsoids.jpg http://chemapps.stolaf.edu/jmol/docs/examples-11/Jmol-11_5.zip
Bob Bob Hanson wrote: >Alan, Thomas, Brian, Rich, others, > >OK, progress. I have just uploaded code introducing the ELLIPSOID >command. All it does at this point is draw the axes. But that's enough >to convince me I do have the Uij --> ellipsoid axes conversion correct, >and that is no small achievement! The ellipsoid axes are determined by >first transforming the Uij to Bij, then expressing the B matrix in terms >of cartesian coordinates. Then solving the eigenvector problem to find >the rotation that sets all nondiagonal elements 0 so that the >characteristic equation is of the form > > a11 x^2 + a22 y^2 + a33 z^2 = constant > >For the record, this required adding a small eigenvector/eigenvalue >solver class (public domain, NIST - JAMA; org/jmol/symmetry/Eigen.java). > >Still to do are (a) symmetry considerations and (b) footballs. > >I hope to look at this later today. Symmetry should be no problem. I'm >pretty sure just have to make sure I'm multiplying matrices properly. >Some nice examples with different symmetries and poor data (lots of >anisotropy) would be helpful. Alan, do you have any BAD data??? (Feel >free to send it to me off line if you would prefer.) Once we have >symmetry, we will at least have visualizations to check. Footballs can >come later. > >At some point we need to confirm that the axes are the correct absolute >length. I think I can do footballs without isosurfaces. Tricky, though. >We need to find out how to draw ellipsoids in POV-Ray. We might even get >the POV-Ray output going first if that turns out to be a relatively easy >operation. > >Colors -- for now let's just stick with what Jmol can do with colors >already. This includes temperature, which I believe can be calculated >from Uij using: > >bFactor = (U11 + U22 + U33)/3 > >but I'm not 100% sure that is correct. > >Bob > > > > > >Thomas Stout wrote: > > > >>Yes, Bob - I believe that is correct! >>-Tom >> >>On Tue, Apr 15, 2008 at 1:47 PM, Bob Hanson <[EMAIL PROTECTED] >><mailto:[EMAIL PROTECTED]>> wrote: >> >> Thank you, Thomas. That's very interesting information. I hope >> that Jmol >> can be at the forefront of visualizing whatever is needed in that >> area. >> >> Am I correct that the PDB ANISOU records are coefficients for the >> equation >> >> U11 x^2 + U22 y^2 + U33 z^2 + U12 xy + U13 xz + U23 yz - c = 0 >> >> where x, y, and z are not Cartesian coordinates but, rather, >> coordinates >> in the reciprocal lattice space: >> >> x a* + y b* + z c* >> >> ? This means also that the space group must be read properly so >> that the >> unit cell parameters and reciprocal axes can be determined. Correct? >> >> Bob >> >> >> Thomas Stout wrote: >> >> > >> > I too am very supportive of adding this functionality! For >> > macromolecules however, I would like to comment though that the >> number >> > of "ultra-high-resolution" (sub 1.0-1.4Angstrom) structures is >> > continuing to increase rapidly. This is due to both better crystals >> > and much more powerful synchrotron X-ray sources (amongst other >> > factors). Therefore, the number of macromolecular structures with >> > anisotropic thermal parameters is also greatly on the rise. One >> > caveat however is that the entire issue of the aniso-Bs (or Us) is >> > currently under debate in the macromolecular field. The recent rise >> > of TLS refinement (essentially, anisotropic motion of domains) is >> > proving a distinct advantage in the refinement of moderate (and >> lower) >> > resolution structures. There is not yet a consensus on how those >> > modified Bs (or Us) should be properly represented within the PDB >> > format, and as a result there is considerable "variety" amongst >> > structures in the PDB with ANISO records. (Some are the "raw" >> (whole) >> > nine components of the atomic thermal parameter, others are the >> > directional modifications to the isotropic thermal parameter). >> > However, the format is fixed so I would still encourage the >> inclusion >> > of PDB structures in the anisotropic thermal ellipsoid >> representations >> > (and leave it up to the macromolecular crystallographers to sort out >> > what those fields actually mean). >> > >> > This would be a very useful addition! >> > Cheers, >> > Tom >> > >> > On Tue, Apr 15, 2008 at 7:06 AM, Alan Hewat <[EMAIL PROTECTED] >> <mailto:[EMAIL PROTECTED]> >> > <mailto:[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>>> wrote: >> > >> > I strongly support Brian's request for drawing anisotropic >> temperature >> > ellipsoids, and agree with Rich that the full ellipsoid surface >> > should be >> > drawn, with an option for showing axial lengths. Actually, near >> > the end of >> > last year we discussed standards for output of anisotropic >> temperature >> > factors from the Inorganic Crystal Structure Database ICSD, >> and at >> > that >> > time Brian pointed out the IUCr CIF recommendations, which >> are for >> > Uij: >> > >> > On Fri, Nov 16, 2007 at 6:32 PM, Brian McMahon <[EMAIL PROTECTED] >> <mailto:[EMAIL PROTECTED]> >> > <mailto:[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>>> wrote: >> > > For structural papers (e.g. Acta C and E) there is a list of >> > > required items >> > (http://journals.iucr.org/services/cif/reqditems.html) >> > > which stipulates _atom_site_U_iso_or_equiv. Does this answer >> > > your question? I think the biological crystallography >> journals >> > > accept Bij values in line with that community's normal >> practice. >> > >> > Bob, you may obtain CIFs containing Uij anisotropic temperature >> > factors >> > from the ICSD on http://icsd.ill.fr/ The IUCr published CIFs >> are also >> > freely available to download, and definitions of Uij are >> contained >> > on the >> > IUCr website. Let me know if you have any specific questions. >> > Anisotropic >> > temperature factors would be really great for inorganic and >> small >> > organic >> > structures. They are perhaps less useful for large organic >> > molecules where >> > PDB format usually applies. >> > >> > Alan. >> > ______________________________________________ >> > Dr Alan Hewat, NeutronOptics, Grenoble, FRANCE >> > <[EMAIL PROTECTED]> +33.476.98.41.68 >> > http://www.NeutronOptics.com/hewat >> > ______________________________________________ >> > >> > >> > >> ------------------------------------------------------------------------- >> > This SF.net email is sponsored by the 2008 JavaOne(SM) >> Conference >> > Don't miss this year's exciting event. There's still time to >> save >> > $100. >> > Use priority code J8TL2D2. >> > >> >> http://ad.doubleclick.net/clk;198757673;13503038;p?http://java.sun.com/javaone >> > _______________________________________________ >> > Jmol-users mailing list >> > [email protected] >> <mailto:[email protected]> >> > <mailto:[email protected] >> <mailto:[email protected]>> >> > https://lists.sourceforge.net/lists/listinfo/jmol-users >> > >> > >> >------------------------------------------------------------------------ >> > >> >------------------------------------------------------------------------- >> >This SF.net email is sponsored by the 2008 JavaOne(SM) Conference >> >Don't miss this year's exciting event. There's still time to save >> $100. >> >Use priority code J8TL2D2. >> >> >http://ad.doubleclick.net/clk;198757673;13503038;p?http://java.sun.com/javaone >> > >> >------------------------------------------------------------------------ >> > >> >_______________________________________________ >> >Jmol-users mailing list >> >[email protected] >> <mailto:[email protected]> >> >https://lists.sourceforge.net/lists/listinfo/jmol-users >> > >> > >> >> >> -- >> Robert M. Hanson >> Professor of Chemistry >> St. Olaf College >> Northfield, MN >> http://www.stolaf.edu/people/hansonr >> >> >> 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 >> >> >> >> ------------------------------------------------------------------------- >> This SF.net email is sponsored by the 2008 JavaOne(SM) Conference >> Don't miss this year's exciting event. There's still time to save >> $100. >> Use priority code J8TL2D2. >> >> http://ad.doubleclick.net/clk;198757673;13503038;p?http://java.sun.com/javaone >> _______________________________________________ >> Jmol-users mailing list >> [email protected] >> <mailto:[email protected]> >> https://lists.sourceforge.net/lists/listinfo/jmol-users >> >> >>------------------------------------------------------------------------ >> >>------------------------------------------------------------------------- >>This SF.net email is sponsored by the 2008 JavaOne(SM) Conference >>Don't miss this year's exciting event. There's still time to save $100. >>Use priority code J8TL2D2. >>http://ad.doubleclick.net/clk;198757673;13503038;p?http://java.sun.com/javaone >> >>------------------------------------------------------------------------ >> >>_______________________________________________ >>Jmol-users mailing list >>[email protected] >>https://lists.sourceforge.net/lists/listinfo/jmol-users >> >> >> >> > > > > -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr 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 ------------------------------------------------------------------------- This SF.net email is sponsored by the 2008 JavaOne(SM) Conference Don't miss this year's exciting event. There's still time to save $100. 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