For anyone interested in modulated structures and especially Jmol's visulaization - see http://publcif.iucr.org/cifmoldb/mscif/
Not a fully 'public' page yet - will probably add some of Bob's links... Quoting Robert Hanson <[email protected]>: > [Sorry for the blog-like nature of this message. I'm not ready to blog yet > -- maybe Henry Rzepa can take this on :) ] > > I have just come back from the IUCr World Congress meeting in Montreal > conference: http://www.iucr2014.org > presentation: http://stolaf.edu/depts/chemistry/bh/iucr2014 > > and the SMARTER 4 conference in Durham UK > conference: http://www.ccpnc.ac.uk/smarter4 > presentation: http://stolaf.edu/depts/chemistry/bh/durham2014 > > [Note that That is not meant to be self-explanatory, but the pictures are > pretty!] > > Now back to normal life after 15 months of sabbatical during which the main > foci ended up being > (a) database integration with Jmol and > (b) crystallography, > I thought I would give a bit of update on (b). I won't cover everything > here. Just get a discussion going. > > XRD and XRPD > > Jmol is thriving like never before. It has been embraced in all areas of > chemistry, in materials science, in computational physics, and in > crystallography (both single-crystal [XRD] and powder diffraction [XRPD]). > We are really having a very broad impact on science! > > XRPD, in particular, has made many advances recently, and is now providing > full structure models, just like XRD. Estimates I heard were in the range > of roughly 100 new XRPD structures per year, and growing. > > Jmol is the preferred viewer in this area because it can handle all aspects > of CIF file structure definition. > > 3D EDT > > If you do not know about the emergent field of Precession 3D Electron > Diffraction Tomography <http://www.edt3d.com/> [3D EDT], you might want to > do some Googling. See, for example, > > http://www.microscopy-analysis.com/magazine/issues/structure-determination-nanocrystals-precession-3d-electron-diffraction-tomography > > Expect one or more Nobel prizes in this area. It is set to totally > revolutionize crystallography. > > The basic idea is that it is now possible to take a nanocrystal, place it > in the vacuum of a *standard *scanning electron microsope, and record the > diffraction of electrons from it at various beam angles. The phrase "anyone > can do it" is not far off. The results can be integrated to get unit cell > measurements in minutes and atomic resolution crystal structures after > further analysis. Software is still under development, but it is likely > that Jmol will be a significant part of that. > > [3+n]D > > Jmol is one of just a few software packages that can be used to > visualize *incommensurately > modulated* crystal structures, which can be understood using higher > dimensional space groups (4D, 5D, thus [3+n]D where n=1 or n=2). see > http://infoscience.epfl.ch/record/183336/files/aperiodic_structures_infoscience.pdf > > These are crystal structures that have unit cells, but each one is slightly > different. It's really not so difficult to understand why that might be. A > classic case is a "misfit layer" compound. See, for example, < > http://www.mdpi.com/1996-1944/3/4/2606>. > > These crystalline compounds have two or more semi-independent unit cells. > Each unit cell is "incommensurate" with the other -- one or more of its > dimensions is not a multiple or rational fraction of the other -- so they > never line up, and since they are in the same physical crystal, the > presence of one "modulates" the structure of the other. > > There aren't a lot of these structures around, but their numbers are > growing as crystallographers become more familiar with the new techniques > and software tools that are being developed that can be used for structure > solving and visualization. > > The images you can create of these systems using Jmol are stunning and > informative. I'm pretty sure there is absolutely nothing else like Jmol out > there that can do this sort of thing. Expect Jmol integration into > "standard" processing programs used in this area (such as Jana2006) soon. > > I had better stop there for now.... > > Bob > > - > > Robert M. Hanson > Larson-Anderson Professor of Chemistry > Chair, Department 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 > ------------------------------------------------------------------------------ Want excitement? Manually upgrade your production database. When you want reliability, choose Perforce Perforce version control. Predictably reliable. http://pubads.g.doubleclick.net/gampad/clk?id=157508191&iu=/4140/ostg.clktrk _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
