It is better to spent time learning how to collect without ice… :-) FF Dr Felix Frolow Professor of Structural Biology and Biotechnology Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel
Acta Crystallographica F, co-editor e-mail: [email protected] Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Jun 27, 2012, at 21:00 , JORGE IULEK wrote: > I thank for the references and the comprehensive discussion from Dr. > Holton. Also, for the reference indicated by Dr. Berry. I think I will get > what I am looking for, now I need to "process" all this information. > Partially answering Dr. Holton, my aim is to have a side guide for > improving parameters to process images with ice diffraction rings. In > general, the idea is to exclude the minimum area from the detector, but large > enough to avoid bad regions. In this, ice ring widths have a role, so, > besides the amount of ice, exposure time and beam intensity, relative > diffraction intensities contribute, and this way one could decide better what > the "best" width might be for each individual ring. Sure, looking at the > images are the base here, but it is interesting to be seconded by the ring > expected positions and "relative intensities". > Yours, > > Jorge > > > On Tuesday 26 June 2012 09:16 PM, James Holton wrote: >> I think an appropriate reference is Bragg (1921) >> http://dx.doi.org/10.1088/1478-7814/34/1/322 who compared various >> possible crystal structures to the relative "strength" of the >> reflections from "ice powder" measured by Dennison (1921) >> http://dx.doi.org/10.1103/PhysRev.17.20. >> >> However, as Bragg noted Dennison's intensities don't agree all that >> well with those you would expect from what we now know is the >> structure of hexagonal ice (Ih). It is possible that Dennison's >> preparation (plunge-cooling pure water in a capillary) actually >> created some cubic ice (ice Ic) along with his hexagonal ice (ice Ih). >> The high intensity he saw for the "middle" line of the triplet we >> normally see for true hexagonal ice is consistent with this. Cubic >> ice is actually more commonly seen in MX diffraction patterns than >> hexagonal ice (in my experience). >> >> However, you do have to be very careful about what you mean by >> "intensity". Are you talking about photons/pixel? Photons/spot? >> Photons integrated over a powder_ring? All these will be different >> relative numbers. I'm not sure if they knew about Lorentz factors yet >> in 1921 There is no mention of correcting for them in either paper. >> Anyway, if you are after the "true" hexagonal ice ring intensities, I >> would advise taking the following PDB file: >> >> CRYST1 4.511 4.511 7.346 90.00 90.00 120.00 P 63/m m c >> SCALE1 0.221680 0.127987 -0.000000 -0.00000 >> SCALE2 -0.000000 0.255974 -0.000000 0.00000 >> SCALE3 0.000000 -0.000000 0.136129 -0.00000 >> ATOM 1 O WAT A 1 0.000 2.604 0.457 1.00 0.00 >> O >> ANISOU 1 O WAT A 1 603 630 172 302 0 0 >> O >> ATOM 2 H WAT A 1 0.000 2.604 1.308 0.50 0.00 >> H >> ANISOU 2 H WAT A 1 510 510 56 255 0 0 >> H >> ATOM 3 H WAT A 1 0.000 3.432 0.148 0.50 0.00 >> H >> ANISOU 3 H WAT A 1 487 361 163 185 199 95 >> H >> >> Calculate structure factors from it, add up F2 of same-resolution >> indicies and plot them out that way. remember, the square of a >> structure factor is proportional to the integrated intensity of a >> single-crystal spot, which is not the same thing as a powder ring >> intensity. The relationship was described most recently by Norby >> (1997) http://dx.doi.org/10.1107/S0021889896009995 >> Which I paraphrase as: >> for a flat detector, the average intensity of a pixel in a powder ring >> is given by: >> >> Ipix = k*p*sum(F2)*omega/sin(theta)/sin(2*theta) >> >> where Ipix is the recorded value of one pixel, 'k" is a >> resolution-independent scale factor, "p" is the polarization factor >> (see Holton& Frankel 2010), "F" is the structure factor of an hkl >> index that falls on the ring (there can be more than one, hence the >> "sum"), "omega" is the solid angle subtended by the pixel and "theta" >> is the Bragg angle. >> >> For the above PDB, I get: >> d sum(F2) >> 3.907 121 >> 3.673 156 >> 3.449 111 >> 2.676 88.5 >> 2.255 111 >> 2.075 153 >> 1.953 62.9 >> 1.922 84.2 >> 1.888 62.5 >> 1.836 4.33 >> 1.725 47.8 >> 1.662 1.84 >> 1.527 96.7 >> 1.477 42.8 >> 1.448 39.5 >> 1.375 78.9 >> 1.370 34.6 >> >> HTH, >> >> -James Holton >> MAD Scientist >> >> >> On Tue, Jun 26, 2012 at 2:34 PM, Edward A. Berry<[email protected]> wrote: >>> Maybe figure 4 in >>> Viatcheslav Berejnov et al. Vitrification of aqueous solutions >>> J. Appl. Cryst. (2006). 39, 244–251 ? >>> >>> >>> JORGE IULEK wrote: >>>> Hi, all, >>>> >>>> I thought I could easily find a reference to comment upon the >>>> relative >>>> intensity of >>>> rings in an image due to diffraction by polycrystal ice, but no luck >>>> googling for that. A >>>> reference that would contain a picture (with visual relative intensities) >>>> would be even >>>> better. Of course absolute intensity depends on the amount of ice, but a >>>> relative "scale" >>>> is what I am looking for now. >>>> Yours, >>>> >>>> Jorge >>>> >
