-----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 <[email protected]> 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 <[email protected]> >> 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 >>> <[email protected]> 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: [email protected] >>>> ******************************************* >>> >>> >>> >>> -- >>> ******************************************* >>> Jacob Pearson Keller >>> Northwestern University >>> Medical Scientist Training Program >>> email: [email protected] >>> ******************************************* > > > - -- - -- 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 xrIfcX+1tg0RqzHvEB/BD8M= =eybj -----END PGP SIGNATURE-----
