The diffraction pattern we see results from the convolution of the crystal lattice with the fourier transform of the electron density, as I understand it. I guess I am interested in seeing the unconvoluted transform of the electron density, just to get a feeling for what the characteristics of those transforms are. As I put it in a previous message, I am curious what the diffraction would look like from a theoretical radiation-damage-impervious single molecule of either protein or nucleic acid. I suspect that for nucleic acids one would see the stacked bases a la Rosalind Franklin's fiber diffraction images, and perhaps other interesting features. Maybe there would be a powder-diffraction-like ring for CC and CN bond lengths? Anyway, I guess the goal would be to see whether one could find any other relationships like phase triplets etc.
Jacob On Tue, Jan 10, 2012 at 2:21 AM, Tim Gruene <t...@shelx.uni-ac.gwdg.de> wrote: > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > Dear Jacob, > > what do you mean by 'molecular transform'? Would you like to visualise > the summed structure factors from the atoms inside the unit cell? > - - What pattern are you talking about/ what pattern do you expect? > - - What benefit do you expect from seeing the phases? What you can > physically observe on the detector are the intensities - the concept of > 'phases' is just a mathematical notion to explain the intensities in > terms of interference from single waves and an atomistic model inside > the crystal. > - - What makes you think the pattern from a larger molecule would have a > more complex pattern? > > Cheers, > Tim > > On 01/10/2012 12:13 AM, Jacob Keller wrote: >> I like that animation a lot, as it shows the gradual nature of the >> lattice effect, but it is not exactly what I am looking for. I am >> actually just curious what the pattern behind the spots looks like for >> various molecules, and would like to see an image of that in various >> orientations. I guess one way to put it is that I would like to see >> what the 1.5-2 Ang diffraction pattern would be for a single, >> radiation-damage-impervious protein or RNA/DNA molecule given enough >> x-rays and time. >> >> Would the intensities-based transform image be much less complicated >> than the phases-based one? >> >> Would larger molecules have more complex patterns, corresponding to >> the amount of information in their structures? >> >> JPK >> >> >> >> On Fri, Jan 6, 2012 at 6:23 PM, James M Holton <jmhol...@lbl.gov> wrote: >>> You mean something like the animation at the top of this web page? >>> >>> http://bl831.als.lbl.gov/~jamesh/fastBragg/ >>> >>> This program is a relative of nearBragg, which Dale already mentioned. >>> >>> -James Holton >>> MAD Scientist >>> >>> On Jan 6, 2012, at 5:44 PM, Jacob Keller <j-kell...@fsm.northwestern.edu> >>> wrote: >>> >>>> Actually, as a way to make this type of figure, I think there are >>>> programs which output simulated diffraction images, so perhaps I could >>>> just input a .pdb file with some really huge (fake) cell parameters >>>> (10,000 Ang?), and then the resulting spots would be really close >>>> together and approximate the continuous molecular transform. I think >>>> this would amount to the same thing as the molecular transform of the >>>> model itself--am I right? >>>> >>>> Does anyone know which software outputs simulated diffraction images? >>>> >>>> Jacob >>>> >>>> On Fri, Jan 6, 2012 at 10:25 AM, Jacob Keller >>>> <j-kell...@fsm.northwestern.edu> wrote: >>>>> Dear Crystallographers, >>>>> >>>>> has anyone come across a figure showing a normal diffraction image, >>>>> and then next to it the equivalent molecular transform, perhaps with >>>>> one image as phases and one as amplitudes? Seems like it would be a >>>>> very instructional slide to have to explain how crystallography works >>>>> (I know about Kevin Cowtan's ducks and cats--I was looking for >>>>> approximately the same but from protein or NA molecules.) I don't >>>>> think I have ever seen an actual molecular transform of a protein or >>>>> NA molecule. >>>>> >>>>> All the best, >>>>> >>>>> Jacob >>>>> >>>>> -- >>>>> ******************************************* >>>>> Jacob Pearson Keller >>>>> Northwestern University >>>>> Medical Scientist Training Program >>>>> email: j-kell...@northwestern.edu >>>>> ******************************************* >>>> >>>> >>>> >>>> -- >>>> ******************************************* >>>> Jacob Pearson Keller >>>> Northwestern University >>>> Medical Scientist Training Program >>>> email: j-kell...@northwestern.edu >>>> ******************************************* >> >> >> > > - -- > - -- > Dr Tim Gruene > Institut fuer anorganische Chemie > Tammannstr. 4 > D-37077 Goettingen > > GPG Key ID = A46BEE1A > > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v1.4.10 (GNU/Linux) > Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ > > iD8DBQFPC/T1UxlJ7aRr7hoRAr81AJwLxccoF8rs/MawKVq1hmAQ/Na0kgCfSPsN > xrIfcX훘㑆곇뱀缄㼌= > =eybj > -----END PGP SIGNATURE----- -- ******************************************* Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu *******************************************
